Infrared Spectroscopy of RNA Nucleosides in a Wide Range of Temperatures

The RNA world hypothesis suggests that early cellular ancestors relied solely on RNA molecules for both genetic information storage and cellular functions. RNA, composed of four nucleosides-adenosine, guanosine, cytidine, and uridine-forms the basis of this theory. These nucleosides consist of purine nucleobases, adenine and guanine, and pyrimidine nucleobases, cytosine and uracil, bonded to ribose sugar. Notably, carbonaceous chondrite meteorites have revealed the presence of these bases and sugar, hinting at the potential existence of nucleosides in space. This study aims to present the infrared spectra of four RNA nucleosides commonly found in terrestrial biochemistry, facilitating their detection in space, especially in astrobiological and astrochemical contexts. Laboratory measurements involved obtaining mid- and far-IR spectra at three temperatures (-180 °C, room temperature, and +180 °C), followed by calculating molar extinction coefficients (ε) and integrated molar absorptivities (ψ) for corresponding bands. These spectral data, along with ε and ψ values, serve to provide quantitative insights into the presence and relative abundance of nucleosides in space and aid in their detection.

The Landscape of US and Global Rare Tumor Research Programs: A Systematic Review

Rare cancers and other rare nonmalignant tumors comprise 25% of all cancer diagnoses and account for 25% of all cancer deaths. They are difficult to study due to many factors, including infrequent occurrence, lack of a universal infrastructure for data and/or tissue collection, and a paucity of disease models to test potential treatments. For each individual rare cancer, the limited number of diagnosed cases makes it difficult to recruit sufficient patients for clinical studies, and rare cancer research studies are often siloed. As a result, progress has been slow for many of these cancers. While rare cancer research efforts have increased over time, the breadth of the research landscape is not known. A recent literature search revealed a sharp increase in rare tumor, and rare cancer publications began in the early 2000s. To identify rare cancer research efforts being conducted in the US and globally, we conducted an online search of rare tumor/rare cancer research programs and identified 76 programs. To gain a deeper understanding of these programs, we composed and conducted a survey to ask programs for details about their research efforts. Of the 42 programs contacted to complete the survey, 23 programs responded. Survey results show most programs are collecting clinical data, molecular data, and biospecimens, and many are conducting molecular analyses. This landscape analysis demonstrates that multiple rare cancer research efforts are ongoing, and the rare cancer community may benefit from collaboration among stakeholders to accelerate research and improve patient outcomes.

GradWise: A Novel Application of a Rank-Based Weighted Hybrid Filter and Embedded Feature Selection Method for Glioma Grading with Clinical and Molecular Characteristics

Glioma grading plays a pivotal role in guiding treatment decisions, predicting patient outcomes, facilitating clinical trial participation and research, and tailoring treatment strategies. Current glioma grading in the clinic is based on tissue acquired at the time of resection, with tumor aggressiveness assessed from tumor morphology and molecular features. The increased emphasis on molecular characteristics as a guide for management and prognosis estimation underscores is driven by the need for accurate and standardized grading systems that integrate molecular and clinical information in the grading process and carry the expectation of the exposure of molecular markers that go beyond prognosis to increase understanding of tumor biology as a means of identifying druggable targets. In this study, we introduce a novel application (GradWise) that combines rank-based weighted hybrid filter (i.e., mRMR) and embedded (i.e., LASSO) feature selection methods to enhance the performance of feature selection and machine learning models for glioma grading using both clinical and molecular predictors. We utilized publicly available TCGA from the UCI ML Repository and CGGA datasets to identify the most effective scheme that allows for the selection of the minimum number of features with their names. Two popular feature selection methods with a rank-based weighting procedure were employed to conduct comprehensive experiments with the five supervised models. The computational results demonstrate that our proposed method achieves an accuracy rate of 87.007% with 13 features and an accuracy rate of 80.412% with five features on the TCGA and CGGA datasets, respectively. We also obtained four shared biomarkers for the glioma grading that emerged in both datasets and can be employed with transferable value to other datasets and data-based outcome analyses. These findings are a significant step toward highlighting the effectiveness of our approach by offering pioneering results with novel markers with prospects for understanding and targeting the biologic mechanisms of glioma progression to improve patient outcomes.

Short stories from Sphagnum of rare species, taxonomy, and speciation

Conserving species and their genetic variation are a global priority to safeguard evolutionary potential in a rapidly changing world. Species are fundamental units in research and nature management, but taxonomic work is increasingly undermined. Increasing knowledge on the species genetic diversity would aid in prioritizing conservation efforts. Sphagnum is a diverse, well-known bryophyte genus, which makes the genus suited to study speciation and cryptic variation. The species share specific characteristics and can be difficult to separate in the field. By combining molecular data with thorough morphological examination, new species have recently been discovered. Still, there are taxonomic uncertainties, even for species assessed on the IUCN Red List of threatened species. Here, we use molecular data to examine three rare species within the subgenus Acutifolia described based on morphological characters. All species have narrow distributions and limited dispersability. First, we confirm the genetic origin of S. skyense. Second, we show that S. venustum is a haploid species genetically distinct from morphologically similar species. Lastly, S. nitidulum was found to have a distinct haplotype, but cannot be genetically separated from other red Acutifolia species. We also found high genetic variation within red Acutifolia specimens, indicating the need of further morphological examination and possibly taxonomic revision. Until then, our results have shown that genetic data can aid in prioritizing targets of conservation efforts when taxonomy is unresolved. All three taxa should be further searched for by field biologists to increase knowledge about their distribution ranges.

Evidence using morphology, molecules, and biogeography clarifies the taxonomic status of mole crabs of the genus Emerita Scopoli, 1777 (Anomura, Hippidae) and reveals a new species from the western Atlantic

Uncertainties regarding the taxonomic status and biogeographical distribution of some species of the genus Emerita from the western Atlantic led to thorough examination of the subtle morphological differences between two coexistent species (E.brasiliensis Schmitt, 1935 and E.portoricensis Schmitt, 1935) along the Brazilian coast and compare them using two genetic markers. The molecular phylogenetic analysis based on sequences of the 16S rRNA and COI genes showed that individuals identified as E.portoricensis were clustered into two clades: one containing representatives from the Brazilian coast and another containing specimens distributed in Central America. Our molecular-based phylogeny, combined with a detailed morphological analysis, revealed the Brazilian population as a new species, which is described here as Emeritaalmeidai Mantelatto & Balbino, sp. nov. The number of species in the genus Emerita is now raised to 12, with five of them occurring in the western Atlantic, five in the Indo-Pacific, and two in the eastern Pacific.

A global survey of tapeworms (Cestoda: Proteocephalidae) of 'true' frogs (Amphibia: Ranidae), including a tabulated list of all proteocephalids parasitising amphibians

Proteocephalid tapeworms of frogs of the family Ranidae ('true' frogs) are reviewed with emphasis on their species diversity, host specificity and geographical distribution. New molecular data (nuclear lsrDNA and mitochondrial COI sequences) are presented for tapeworms of four species of ranid frogs in North America, including the poorly known Ophiotaenia saphena Osler, 1931 of Rana clamitans Latreille and R. catesbeiana (Shaw), which is redescribed using new material from Arkansas, USA. Tapeworms of R. sphenocephala (Cope) and R. pipiens Schreber, the latter previously identified as O. saphena, represent another, putative new species, but are not formally described due to insufficient available material. Proteocephalus papuensis Bursey, Goldberg et Kraus, 2008 from Sylvirana supragrisea (Menzies) is transferred to Ophiotaenia La Rue, 1911 as a new combination. After a critical review of the literature, only nine nominal species of Ophiotaenia are recognised as valid, which is in contrast to the large number of ranid frogs (> 440 spp.). The reasons for this striking disparity are briefly discussed, and a key based on morphology is presented for the identification of all species of Ophiotaenia from the Ranidae. Molecular data are available for only two taxa from North America that form a monophyletic group. The relationships among tapeworms of ranid frogs occurring in other zoogeographical regions are not yet known. The taxonomic status of Batrachotaenia Rudin, 1917, which was erected to accommodate proteocephalids from amphibians, is also discussed. To facilitate future studies, a tabulated summary of all 32 species of proteocephalids belonging to three genera reported from amphibians (frogs and salamanders) is presented, with information on their hosts, distribution, and taxonomically important characters, including key measurements.

Fish parasites (special issue)

Fish (Elasmobranchia and Actinopterygii) inhabit the majority of aquatic habitats globally. They are crucial for human nutrition but they may be negatively affected by parasitic protists and metazoan parasites. Fish parasites are also an extraordinary group of animals because of their ecological and evolutionary importance and unique adaptations to parasitism. They also play a key role in ecosystem functioning. In the present special issue, 13 review and research articles on major groups of fish parasites are provided to document the current advancement in our understanding of different aspects of their biology, ecology and associations with their fish hosts. The existing gaps in our knowledge of these peculiar animals are mapped and future trends in their research outlined.

Hierarchical Voting-Based Feature Selection and Ensemble Learning Model Scheme for Glioma Grading with Clinical and Molecular Characteristics

Determining the aggressiveness of gliomas, termed grading, is a critical step toward treatment optimization to increase the survival rate and decrease treatment toxicity for patients. Streamlined grading using molecular information has the potential to facilitate decision making in the clinic and aid in treatment planning. In recent years, molecular markers have increasingly gained importance in the classification of tumors. In this study, we propose a novel hierarchical voting-based methodology for improving the performance results of the feature selection stage and machine learning models for glioma grading with clinical and molecular predictors. To identify the best scheme for the given soft-voting-based ensemble learning model selections, we utilized publicly available TCGA and CGGA datasets and employed four dimensionality reduction methods to carry out a voting-based ensemble feature selection and five supervised models, with a total of sixteen combination sets. We also compared our proposed feature selection method with the LASSO feature selection method in isolation. The computational results indicate that the proposed method achieves 87.606% and 79.668% accuracy rates on TCGA and CGGA datasets, respectively, outperforming the LASSO feature selection method.

The impact of molecular data on the phylogenetic position of the putative oldest crown crocodilian and the age of the clade

The use of molecular data for living groups is vital for interpreting fossils, especially when morphology-only analyses retrieve problematic phylogenies for living forms. These topological discrepancies impact on the inferred phylogenetic position of many fossil taxa. In Crocodylia, morphology-based phylogenetic inferences differ fundamentally in placing Gavialis basal to all other living forms, whereas molecular data consistently unite it with crocodylids. The Cenomanian Portugalosuchus azenhae was recently described as the oldest crown crocodilian, with affinities to Gavialis, based on morphology-only analyses, thus representing a potentially important new molecular clock calibration. Here, we performed analyses incorporating DNA data into these morphological datasets, using scaffold and supermatrix (total evidence) approaches, in order to evaluate the position of basal crocodylians, including Portugalosuchus. Our analyses incorporating DNA data robustly recovered Portugalosuchus outside Crocodylia (as well as thoracosaurs, planocraniids and Borealosuchus spp.), questioning the status of Portugalosuchus as crown crocodilian and any future use as a node calibration in molecular clock studies. Finally, we discuss the impact of ambiguous fossil calibration and how, with the increasing size of phylogenomic datasets, the molecular scaffold might be an efficient (though imperfect) approximation of more rigorous but demanding supermatrix analyses.

Supplementary studies on Myxobolus talievi Dogiel, 1957 (Cnidaria, Myxozoa) from the skeletal muscle of the cottoid fish Cyphocottus eurystomus in Lake Baikal: Morphological, histological and molecular characterisations

Myxobolus talievi Dogiel, 1957 was originally described from the eyes, skeletal muscles and body cavity of endemic cottoid fish from Lake Baikal. In the present study, we supply new information on the myxospore morphology and histopathology of M. talievi; furthermore, we complete the original species description by Dogiel and Bogolepova (1957) with 18S ribosomal DNA (rDNA) sequence data. Histopathological analysis showed that the plasmodium was encapsulated by a thin layer of connective tissue and located in the intermuscular connective tissue among muscle cells. No inflammation was observed. Phylogenetic analysis revealed that M. talievi clustered with Myxobolus sp. 2 (NCBI Acc. No. U13830), an unidentified Myxobolus species from cottoid fish studied by Smothers et al. (1994), and located in the sister clade of Myxobolus spp. developing spores in the nerves of salmonids.

ExTaxsI: an exploration tool of biodiversity molecular data

BACKGROUND

The increasing availability of multi-omics data is leading to regularly revised estimates of existing biodiversity data. In particular, the molecular data enable novel species to be characterized and the information linked to those already observed to be increased with new genomics data. For this reason, the management and visualization of existing molecular data, and their related metadata, through the implementation of easy-to-use IT tools have become a key point to design future research. The more users are able to access biodiversity-related information, the greater the ability of the scientific community to expand its knowledge in this area.

RESULTS

In this article we focus on the development of ExTaxsI (Exploring Taxonomy Information), an IT tool that can retrieve biodiversity data stored in NCBI databases and provide a simple and explorable visualization. We use 3 case studies to show how an efficient organization of the available data can lead to obtaining new information that is fundamental as a starting point for new research. Using this approach highlights the limits in the distribution of data availability, a key factor to consider in the experimental design phase of broad-spectrum studies such as metagenomics.

CONCLUSIONS

ExTaxsI can easily retrieve molecular data and its metadata with an explorable visualization, with the aim of helping researchers to improve experimental designs and highlight the main gaps in the coverage of available data.

Next-generation sequencing yields the complete mitochondrial genome of Pterygoplichthys pardalis (Loricariidae; Siluriformes)

In this study, we report the complete mitochondrial genome of Pterygoplichthys pardalis has derived by next-generation sequencing. The complete mitochondrial genome of P. pardalis contains 16,425 bp encompassing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). The base composition is A 31.79%, C 26.89%, G 14.63%, and T 26.69%, and its gene arrangement is consistent with mitochondrial genomes derived from other representatives of Loricariidae. A phylogenetic tree of 24 Loricariidae species constructed based on the 13 coding genes shows that P. pardalis is clustered with other Pterygoplichthys genus. It suggests that the molecular classification results confirm its external morphological characteristics. These results have reference value for the further study of phylogenetic relationship, taxonomic classification, and phylogeography of Loricariidae.

Full spectroscopic model and trihybrid experimental-perturbative-variational line list for CN

Accurate line lists are important for the description of the spectroscopic nature of small molecules. While a line list for CN (an important molecule for chemistry and astrophysics) exists, no underlying energy spectroscopic model has been published, which is required to consider the sensitivity of transitions to a variation of the proton-to-electron mass ratio. Here we have developed a Duo energy spectroscopic model as well as a novel hybrid style line list for CN and its isotopologues, combining energy levels that are derived experimentally (Marvel), using the traditional/perturbative approach (Mollist), and the variational approach (from a Duo spectroscopic model using standard ExoMol methodology). The final Trihybrid ExoMol-style line list for ¹²C¹⁴N consists of 28 004 energy levels (6864 experimental, 1574 perturbative, the rest variational) and 2285 103 transitions up to 60 000 cm^-1 between the three lowest electronic states (X ²Σ⁺, A ²Π, and B ²Σ⁺). The spectroscopic model created is used to evaluate CN as a molecular probe to constrain the variation of the proton-to-electron mass ratio; no overly promising sensitive transitions for extragalactic study were identified.

Laboratory Detection of Cyanoacetic Acid: A Jet-Cooled Rotational Study

Herein we present a laboratory rotational study of cyanoacetic acid (CH2(CN)C(O)OH), an organic acid as well as a -CN bearing molecule, that is a candidate molecular system to be detected in the interstellar medium (ISM). Our investigation aims to provide direct experimental frequencies of cyanoacetic acid to guide its eventual astronomical search in low-frequency surveys. Using different jet-cooled rotational spectroscopic techniques in the time domain, we have determined a precise set of the relevant rotational spectroscopic constants, including the 14N nuclear quadrupole coupling constants for the two distinct structures, cis- and gauche- cyanoacetic acid. We believe this work will potentially allow the detection of cyanoacetic acid in the interstellar medium, whose rotational features have remained unknown until now.

Cumulene carbenes in TMC-1: Astronomical discovery of l-H2C5 ★

We report the first detection in space of the cumulene carbon chain l-H2C5. A total of eleven rotational transitions, with Jup = 7-10 and Ka = 0 and 1, were detected in TMC-1 in the 31.0-50.4 GHz range using the Yebes 40m radio telescope. We derive a column density of (1.8±0.5)×1010 cm-2. In addition, we report observations of other cumulene carbenes detected previously in TMC-1, to compare their abundances with the newly detected cumulene carbene chain. We find that l-H2C5 is ~4.0 times less abundant than the larger cumulene carbene l-H2C6, while it is ~300 and ~500 times less abundant than the shorter chains l-H2C3 and l-H2C4. We discuss the most likely gas-phase chemical routes to these cumulenes in TMC-1 and stress that chemical kinetics studies able to distinguish between different isomers are needed to shed light on the chemistry of C n H2 isomers with n > 3.

Graph Neural Networks with Multiple Feature Extraction Paths for Chemical Property Estimation

Feature extraction is essential for chemical property estimation of molecules using machine learning. Recently, graph neural networks have attracted attention for feature extraction from molecules. However, existing methods focus only on specific structural information, such as node relationship. In this paper, we propose a novel graph convolutional neural network that performs feature extraction with simultaneously considering multiple structures. Specifically, we propose feature extraction paths specialized in node, edge, and three-dimensional structures. Moreover, we propose an attention mechanism to aggregate the features extracted by the paths. The attention aggregation enables us to select useful features dynamically. The experimental results showed that the proposed method outperformed previous methods.

TMC-1, the starless core sulfur factory: Discovery of NCS, HCCS, H2CCS, H2CCCS, and C4S and detection of C5S

We report the detection of the sulfur-bearing species NCS, HCCS, H2CCS, H2CCCS, and C4S for the first time in space. These molecules were found towards TMC-1 through the observation of several lines for each species. We also report the detection of C5S for the first time in a cold cloud through the observation of five lines in the 31-50 GHz range. The derived column densities are N(NCS) = (7.8±0.6)×1011 cm-2, N(HCCS) = (6.8±0.6)×1011 cm-2, N(H2CCS) = (7.8±0.8)×1011 cm-2, N(H2CCCS) = (3.7±0.4)×1011 cm-2, N(C4S) = (3.8±0.4)×1010 cm-2, and N(C5S) = (5.0±1.0)×1010 cm-2. The observed abundance ratio between C3S and C4S is 340, that is to say a factor of approximately one hundred larger than the corresponding value for CCS and C3S. The observational results are compared with a state-of-the-art chemical model, which is only partially successful in reproducing the observed abundances. These detections underline the need to improve chemical networks dealing with S-bearing species.

Discovery of CH2CHCCH and detection of HCCN, HC4N, CH3CH2CN, and, tentatively, CH3CH2CCH in TMC-1

We present the discovery in TMC-1 of vinyl acetylene, CH2CHCCH, and the detection, for the first time in a cold dark cloud, of HCCN, HC4N, and CH3CH2CN. A tentative detection of CH3CH2CCH is also reported. The column density of vinyl acetylene is (1.2±0.2)×1013 cm-2, which makes it one of the most abundant closed-shell hydrocarbons detected in TMC-1. Its abundance is only three times lower than that of propylene, CH3CHCH2. The column densities derived for HCCN and HC4N are (4.4±0.4)×1011 cm-2 and (3.7±0.4)×1011 cm-2, respectively. Hence, the HCCN/HC4N abundance ratio is 1.2±0.3. For ethyl cyanide we derive a column density of (1.1 ±0.3)×1011 cm-2. These results are compared with a state-of-the-art chemical model of TMC-1, which is able to account for the observed abundances of these molecules through gas-phase chemical routes.

Discovery of allenyl acetylene, H2CCCHCCH, in TMC-1. A study of the isomers of C5H4

We present the discovery in TMC-1 of allenyl acetylene, H2CCCHCCH, through the observation of nineteen lines with a signal-to-noise ratio ~4-15. For this species, we derived a rotational temperature of 7±1K and a column density of 1.2±0.2×1013 cm-2. The other well known isomer of this molecule, methyl diacetylene (CH3C4H), has also been observed and we derived a similar rotational temperature, Tr=7.0±0.3 K, and a column density for its two states (A and E) of 6.5±0.3×1012 cm-2. Hence, allenyl acetylene and methyl diacetylene have a similar abundance. Remarkably, their abundances are close to that of vinyl acetylene (CH2CHCCH). We also searched for the other isomer of C5H4, HCCCH2CCH (1.4-Pentadiyne), but only a3σ upper limit of 2.5×1012 cm-2 to the column density can be established. These results have been compared to state-of-the-art chemical models for TMC-1, indicating the important role of these hydrocarbons in its chemistry. The rotational parameters of allenyl acetylene have been improved by fitting the existing laboratory data together with the frequencies of the transitions observed in TMC-1.

Discovery of the acetyl cation, CH3CO+, in space and in the laboratory

Using the Yebes 40m and IRAM 30m radiotelescopes, we detected two series of harmonically related lines in space that can be fitted to a symmetric rotor. The lines have been seen towards the cold dense cores TMC-1, L483, L1527, and L1544. High level of theory ab initio calculations indicate that the best possible candidate is the acetyl cation, CH3CO+, which is the most stable product resulting from the protonation of ketene. We have produced this species in the laboratory and observed its rotational transitions Ju = 10 up to Ju = 27. Hence, we report the discovery of CH3CO+ in space based on our observations, theoretical calculations, and laboratory experiments. The derived rotational and distortion constants allow us to predict the spectrum of CH3CO+ with high accuracy up to 500 GHz. We derive an abundance ratio N(H2CCO)/N(CH3CO+)~44. The high abundance of the protonated form of H2CCO is due to the high proton affinity of the neutral species. The other isomer, H2CCOH+, is found to be 178.9 kJ mol-1 above CH3CO+. The observed intensity ratio between the K=0 and K=1 lines, ~2.2, strongly suggests that the A and E symmetry states have suffered interconversion processes due to collisions with H and/or H2, or during their formation through the reaction of H 3 + with H2CCO.

Combining Nuclear and Mitochondrial Loci Provides Phylogenetic Information in the Philopterus Complex of Lice (Psocodea: Ischnocera: Philopteridae)

The Philopterus Complex includes several lineages of lice that occur on birds. The complex includes the genera Philopterus (Nitzsch, 1818; Psocodea: Philopteridae), Philopteroides (Mey, 2004; Psocodea: Philopteridae), and many other lineages that have sometimes been regarded as separate genera. Only a few studies have investigated the phylogeny of this complex, all of which are based on morphological data. Here we evaluate the utility of nuclear and mitochondrial loci for recovering the phylogeny within this group. We obtained phylogenetic trees from 39 samples of the Philopterus Complex (Psocodea: Philopteridae), using sequences of two nuclear (hyp and TMEDE6) and one mitochondrial (COI) marker. We evaluated trees derived from these genes individually as well as from concatenated sequences. All trees show 20 clearly demarcated taxa (i.e., putative species) divided into five well-supported clades. Percent sequence divergence between putative species (~5-30%) for the COI gene tended to be much higher than those for the nuclear genes (~1-15%), as expected. In cases where species are described, the lineages identified based on molecular divergence correspond to morphologically defined species. In some cases, species that are host generalists exhibit additional underlying genetic variation and such cases need to be explored by further future taxonomic revisions of the Philopterus Complex.

Formation of interstellar cyanoacetamide: a rotational and computational study

CONTEXT

Cyanoacetamide is a -CN bearing molecule that is also an amide derivative target molecule in the interstellar medium.

AIMS

The aim of our investigation is to analyze the feasibility of a plausible formation process of protonated cyanoacetamide under interstellar conditions and to provide direct experimental frequencies of the ground vibrational state of the neutral form in the microwave region in order to enable its eventual identification in the interstellar medium.

METHODS

We used high-level theoretical computations to study the formation process of protonated cyanoacetamide. Furthermore, we employed a high-resolution laser-ablation molecular beam Fourier transform spectroscopic technique to measure the frequencies of the neutral form.

RESULTS

We report the first rotational characterization of cyanoacetamide, and a precise set of the relevant rotational spectroscopic constants have been determined as a first step to identifying the molecule in the interstellar medium. We fully explored the potential energy surface to study a gas-phase reaction on the formation process of protonated cyanoacetamide. We found that an exothermic process with no net activation barrier is initiated by the high-energy isomer of protonated hydroxylamine, which leads to protonated cyanoacetamide.

Tentative detection of HC5NH+ in TMC-1

Using the Yebes 40m radio telescope, we report the detection of a series of seven lines harmonically related with a rotational constant B 0=1295.81581 ± 0.00026 MHz and a distortion constant D 0 = 27.3 ± 0.5 Hz towards the cold dense cloud TMC-1. Ab initio calculations indicate that the best possible candidates are the cations HC5NH+ and NC4NH+. From a comparison between calculated and observed rotational constants and other arguments based on proton affinities and dipole moments, we conclude that the best candidate for a carrier of the observed lines is the protonated cyanodiacetylene cation, HC5NH+. The HC5N/HC5NH+ ratio derived in TMC-1 is 240, which is very similar to the HC3N/HC3NH+ ratio. Results are discussed in the framework of a chemical model for protonated molecules in cold dense clouds.

Experimental energy levels of 12C14N through marvel analysis

The cyano radical (CN) is a key molecule across many different factions of astronomy and chemistry. Accurate, empirical rovibronic energy levels with uncertainties are determined for eight doublet states of CN using the marvel (Measured Active Rotational-Vibrational Energy Levels) algorithm. 40 333 transitions were validated from 22 different published sources to generate 8083 spin-rovibronic energy levels. The empirical energy levels obtained from the marvel analysis are compared to current energy levels from the mollist line list. The mollist transition frequencies are updated with marvel energy level data which brings the frequencies obtained through experimental data up to 77.3 per cent from the original 11.3 per cent, with 92.6 per cent of the transitions with intensities over 10-23 cm molecule-1 at 1000 K now known from experimental data. At 2000 K, 100.0 per cent of the partition function is recovered using only marvel energy levels, while 98.2 per cent is still recovered at 5000 K.

Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data

Least absolute shrinkage and selection operator (LASSO) regression is often applied to select the most promising set of single nucleotide polymorphisms (SNPs) associated with a molecular phenotype of interest. While the penalization parameter λ restricts the number of selected SNPs and the potential model overfitting, the least-squares loss function of standard LASSO regression translates into a strong dependence of statistical results on a small number of individuals with phenotypes or genotypes divergent from the majority of the study population—typically comprised of outliers and high-leverage observations.

Robust methods have been developed to constrain the influence of divergent observations and generate statistical results that apply to the bulk of study data, but they have rarely been applied to genetic association studies. In this article, we review, for newcomers to the field of robust statistics, a novel version of standard LASSO that utilizes the Huber loss function. We conduct comprehensive simulations and analyze real protein, metabolite, mRNA expression and genotype data to compare the stability of penalization, the cross-iteration concordance of the model, the false-positive and true-positive rates and the prediction accuracy of standard and robust Huber-LASSO.

Although the two methods showed controlled false-positive rates ≤2.1% and similar true-positive rates, robust Huber-LASSO outperformed standard LASSO in the accuracy of predicted protein, metabolite and gene expression levels using individual SNP data. The conducted simulations and real-data analyses show that robust Huber-LASSO represents a valuable alternative to standard LASSO in genetic studies of molecular phenotypes.

Discovery of HC4NC in TMC-1: A study of the isomers of HC3N, HC5N, and HC7N

We present a study of the isocyano isomers of the cyanopolyynes HC₃N, HC₅N, and HC₇N in TMC-1 and IRC+10216 carried out with the Yebes 40m radio telescope. This study has enabled us to report the detection, for the first time in space, of HCCCCNC in TMC-1 and to give upper limits for HC₆NC in the same source. In addition, the deuterated isotopologues of HCCNC and HNCCC were detected, along with all ¹³C substitutions of HCCNC, also for the first time in space. The abundance ratios of HC₃N and HC₅N, with their isomers, are very different in TMC-1 and IRC+10216, namely, N(HC₅N)/N(HC₄NC) is ~300 and ≥2100, respectively. We discuss the chemistry of the metastable isomers of cyanopolyynes in terms of the most likely formation pathways and by comparing observational abundance ratios between different sources.

Discovery of HC3O+ in space: The chemistry of O-bearing species in TMC-1

Using the Yebes 40m and IRAM 30m radio telescopes, we detected a series of harmonically related lines with a rotational constant B 0=4460.590±0.001 MHz and a distortion constant D 0=0.511 ±0.005 kHz towards the cold dense core TMC-1. High-level-of-theory ab initio calculations indicate that the best possible candidate is protonated tricarbon monoxide, HC3O+. We have succeeded in producing this species in the laboratory and observed its J u -J l = 2-1 and 3-2 rotational transitions. Hence, we report the discovery of HC3O+ in space based on our observations, theoretical calculations, and laboratory experiments. We derive an abundance ratio N(C3O)/N(HC3O+)~7. The high abundance of the protonated form of C3O is due to the high proton affinity of the neutral species. The chemistry of O-bearing species is modelled, and predictions are compared to the derived abundances from our data for the most prominent O-bearing species in TMC-1.

Interstellar nitrile anions: Detection of C3N- and C5N- in TMC-1. Astron Astrophys 2020;641:L9. [PMID: 33173234 PMCID: PMC7116340 DOI: 10.1051/0004-6361/202039231]

We report on the first detection of C3N- and C5N- towards the cold dark core TMC-1 in the Taurus region, using the Yebes 40 m telescope. The observed C3N/C3N- and C5N/C5N- abundance ratios are ~140 and ~2, respectively; that is similar to those found in the circumstellar envelope of the carbon-rich star IRC +10216. Although the formation mechanisms for the neutrals are different in interstellar (ion-neutral reactions) and circumstellar clouds (photodissociation and radical-neutral reactions), the similarity of the C3N/C3N- and C5N/C5N- abundance ratios strongly suggests a common chemical path for the formation of these anions in interstellar and circumstellar clouds. We discuss the role of radiative electronic attachment, reactions between N atoms and carbon chain anions C n -, and that of H- reactions with HC3N and HC5N as possible routes to form C n N-. The detection of C5N- in TMC-1 gives strong support for assigning to this anion the lines found in IRC +10216, as it excludes the possibility of a metal-bearing species, or a vibrationally excited state. New sets of rotational parameters have been derived from the observed frequencies in TMC-1 and IRC +10216 for C5N- and the neutral radical C5N.

A new species of Nephus (Nephus) (Coleoptera, Coccinellidae) described from Reunion Island

We report here a new species belonging to Nephus (Nephus) Mulsant. Nephus (Nephus) apoloniasp. nov. was collected in the Reunion Island (Mascarene Archipelago, Indian Ocean). We describe this new species and redescribe and illustrate three other Nephus species already known from Reunion: Nephus (Nephus) oblongosignatus Mulsant, 1850, Nephus (Geminosipho) reunioni (Fürsch, 1974) and Nephus (Nephus) voeltzkowi Weise, 1910. Furthermore, we present a phylogenetic tree for these four species and calculate the genetic distances between them, using high-throughput DNA sequencing of the mitochondrial genome. The similar external morphology of N. apolonia sp. nov. and N. voeltzkowi very probably explains why individuals from the first species have been mistakenly identified as the latter and were not recognized as different until now. Other than external and genitalia traits, the present study provides molecular evidence confirming these are indeed two different species.

The millimeter-wave spectrum and astronomical search for ethyl methyl sulfide

CONTEXT

Sulfur-containing molecules constitute only 8% of the molecules observed in the interstellar medium (ISM), in spite of the fact that sulfur has been shown to be an abundant element in the ISM. In order to understand the chemical behavior of the ISM and specific cases like the missing sulfur reservoir, a detailed chemical molecular composition in the ISM must be mapped out.

AIMS

Our goal is to investigate the rotational spectrum of ethyl methyl sulfide, CH₃CH₂SCH₃, which ms to be a potential candidate for observation in the ISM since the simpler analogs, CH₃SH and CH₃CH₂SH, have already been detected. Rotational spectrum of ethyl methyl sulfide has been observed before, but its experimental rotational parameters are not precise enough to allow its detection in the ISM.

METHODS

The rotational spectrum of ethyl methyl sulfide in the frequency range 72-116.5 GHz was measured using a broadband millimeter-wave spectrometer based on radio astronomy receivers with fast Fourier transform backends. The spectral searches and identification of the vibrational excited states of ethyl methyl sulfide was supported by high-level ab initio calculations on the harmonic and anharmonic force fields.

RESULTS

The rotational spectra for the trans and gauche conformers of ethyl methyl sulfide was analyzed, and a total of 172 and 259 rotational transitions were observed for each one, respectively. The observation of A - E internal rotation splittings allowed the experimental determination of the V ₃ hindered internal rotation barrier height for both trans and gauche species. In addition, the vibrational excited states, resulting from the lowest frequency vibrational mode ν ₃₀ were identified for both conformers. The new experimental rotational parameters were employed to search for ethyl methyl sulfide in the warm and cold molecular clouds Orion KL, Sgr B2(N), B1-b and TMC-1, using the spectral surveys captured by IRAM 30 m at 3 mm and 2 mm.

New species of Parasaccocoelium (Haploporidae) and new genus Pseudohaplosplanchnus (Haplosplanchnidae) from mullet fish in the Far East of Russia and Vietnam: morphological and molecular data

A description and the molecular characterization of two new species in the Haploporidae and Haplosplanchnidae families are provided herein. Parasaccocoelium armatum n. sp. was collected from the intestine of a Mugil cephalus Linnaeus, 1758 from the Primorsky region, Russia, and Pseudohaplosplanchnus catbaensis n. g. n. sp. was collected from Moolgarda seheli (Forsskål, 1775) in the coastal waters of Cat Ba Island, Vietnam. The morphological features of P. armatum n. sp. closely resemble those of Parasaccocoelium polyovum, but these species differ from one another by hermaphroditic sac and vitellaria area length and by maximal egg size. The main difference between P. armatum n. sp. and P. polyovum is the presence of an armed hermaphroditic duct in the new species. Molecular data support the case for inclusion of the studied trematodes in P. armatum n. sp. Worms P. catbaensis n. g. n. sp. from the mullet from Vietnam are morphologically close to Haplosplanchnus (Haplosplosplanchninae). The only difference between P. catbaensis n. g. n. sp. and species of Haplosplanchnus is the presence of few (1-7) large eggs, measuring 135-142 × 92-104 μm, versus numerous small eggs with a maximal size of 75 × 50 μm. Phylogenetic analysis showed that there is a contradiction between the morphological similarity of the worms and their position in the Haplosplanchnidae system, based on the genetic data. Results of this study indicate that P. catbaensis n. g. n. sp. is genetically distant from other representatives of Haplosplanchnus, despite their morphological similarity. According to the molecular data, P. catbaensis n. g. n. sp. is close to Hymenocotta mulli Manter, 1961 (Hymenocottinae). However, these species are considerably different to each other morphologically. Molecular data argue for the possibility of establishing a new subfamily for P. catbaensis n. g. n. sp. However, considering earlier studies of Haplosplanchnidae, we support the view that creating new subfamilies within this family is unreasonable because of the lack of molecular data for most haplosplanchnid species, which are necessary to resolve the problematic systematics and phylogeny of this family.

Chemical equilibrium in AGB atmospheres: Successes, failures, and prospects for small molecules, clusters, and condensates

Chemical equilibrium has proven extremely useful for predicting the chemical composition of AGB atmospheres. Here we use a recently developed code and an updated thermochemical database that includes gaseous and condensed species involving 34 elements to compute the chemical equilibrium composition of AGB atmospheres of M-, S-, and C-type stars. We include for the first time Ti x C y clusters, with x = 1-4 and y = 1-4, and selected larger clusters ranging up to Ti13C22, for which thermochemical data are obtained from quantum-chemical calculations. Our main aims are to systematically survey the main reservoirs of each element in AGB atmospheres, review the successes and failures of chemical equilibrium by comparing it with the latest observational data, identify potentially detectable molecules that have not yet been observed, and diagnose the most likely gas-phase precursors of dust and determine which clusters might act as building blocks of dust grains. We find that in general, chemical equilibrium reproduces the observed abundances of parent molecules in circumstellar envelopes of AGB stars well. There are, however, severe discrepancies of several orders of magnitude for some parent molecules that are observed to be anomalously overabundant with respect to the predictions of chemical equilibrium. These are HCN, CS, NH3, and SO2 in M-type stars, H2O and NH3 in S-type stars, and the hydrides H2O, NH3, SiH4, and PH3 in C-type stars. Several molecules have not yet been observed in AGB atmospheres but are predicted with non-negligible abundances and are good candidates for detection with observatories such as ALMA. The most interesting ones are SiC5, SiNH, SiCl, PS, HBO, and the metal-containing molecules MgS, CaS, CaOH, CaCl, CaF, ScO, ZrO, VO, FeS, CoH, and NiS. In agreement with previous studies, the first condensates predicted to appear in C-rich atmospheres are found to be carbon, TiC, and SiC, while Al2O3 is the first major condensate expected in O-rich outflows. According to our chemical equilibrium calculations, the gas-phase precursors of carbon dust are probably acetylene, atomic carbon, and/or C3, while for silicon carbide dust, the most likely precursors are the molecules SiC2 and Si2C. In the case of titanium carbide dust, atomic Ti is the major reservoir of this element in the inner regions of AGB atmospheres, and therefore it is probably the main supplier of titanium during the formation of TiC dust. However, chemical equilibrium predicts that large titanium-carbon clusters such as Ti8C12 and Ti13C22 become the major reservoirs of titanium at the expense of atomic Ti in the region where condensation of TiC is expected to occur. This suggests that the assembly of large Ti x C y clusters might be related to the formation of the first condensation nuclei of TiC. In the case of Al2O3 dust, chemical equilibrium indicates that atomic Al and the carriers of Al-O bonds AlOH, AlO, and Al2O are the most likely gas-phase precursors.

Testing Densities and Refractive Indices of Extraterrestrial Ice Components Using Molecular Structures - Organic Compounds and Molar Refractions

The use of infrared spectra to determine molecular abundances of icy astronomical objects and to study their chemistry requires laboratory measurements of reference spectra and related quantities, such as the index of refraction (n) and density (ρ) of candidate ices. Here we present new n and ρ measurements on ices involving over thirty C-, H-, and O-containing compounds, both acyclic and cyclic, representing seven chemical families. We examine the results in a way that is rare in the astrochemical literature, namely one in which data from an ice formed from molecules of a particular chemical family are compared to measurements on another member of the same family, such as of a homologous series or a pair of isomers. Apart from the intrinsic usefulness of the n and ρ data, a structure-based comparison can help establish trends and identify possibly spurious results. As liquid-phase data sometimes are used in low-temperature astrochemical work in the absence of solid-phase measurements, we compare our new ice results to those for the corresponding room-temperature liquids. We emphasize the use of our n and ρ data to compute the molar refraction (R _M ) for each of our ices, and how the resulting R _M values compare to those expected from molecular structures. The use of calculated RM values and measured n values to calculate ice densities, in the absence of direct measurements, also is addressed.

Discovery of two new magnesium-bearing species in IRC+10216: MgC3N and MgC4H

We report on the detection of two series of harmonically related doublets in IRC +10216. From the observed frequencies, the rotational constant of the first series is B = 1380.888 MHz and that of the second series is B = 1381.512 MHz. The two series correspond to two species with a 2Σ electronic ground state. After considering all possible candidates, and based on quantum chemical calculations, the first series is assigned to MgC3N and the second to MgC4H. For the latter species, optical spectroscopy measurements support its identification. Unlike diatomic metal-containing molecules, the line profiles of the two new molecules indicate that they are formed in the outer layers of the envelope, as occurs for MgNC and other polyatomic metal-cyanides. We also confirm the detection of MgCCH that was previously reported from the observation of two doublets. The relative abundance of MgC3N with respect to MgNC is close to one while that of MgC4H relative to MgCCH is about ten. The synthesis of these magnesium cyanides and acetylides in IRC +10216 can be explained in terms of a two-step process initiated by the radiative association of Mg+ with large cyanopolyynes and polyynes followed by the dissociative recombination of the ionic complexes.

The millimeter-wave spectrum and astronomical search of succinonitrile and its vibrational excited states ★

CONTEXT

Dinitriles with a saturated hydrocarbon skeleton and a -C≡N group at each end can have large electric dipole moments. Their formation can be related to highly reactive radicals such as CH2CN, C2N or CN. Thus, these saturated dinitriles are potential candidates to be observed in the ISM.

AIMS

Our goal is the investigation of the rotational spectrum of one of the simplest dinitriles N≡C-CH2-CH2-C≡N, succinonitrile, whose actual rotational parameters are not precise enough to allow its detection in the ISM. In addition, the rotational spectra for its vibrational exicted states will be analyzed.

METHODS

The rotational spectra of succinonitrile was measured in the frequency range 72-116.5 GHz using a new broadband millimeter-wave spectrometer based on radio astronomy receivers with Fast Fourier Transform backends. The identification of the vibrational excited states of succinonitrile was supported by high-level ab initio calculations on the harmonic and anharmonic force fields.

RESULTS

A total of 459 rotational transitions with maximum values of J and Ka quantum numbers 70 and 14, respectively, were measured for the ground vibrational state of succinonitrile. The analysis allowed us to accurately determine the rotational, quartic and sextic centrifugal distortion constants. Up to eleven vibrational excited states, resulting from the four lowest frequency vibrational modes ν 13, ν 12, ν 24 and ν 23 were identified. In addition to the four fundamental modes, we observed overtones together with some combination states. The rotational parameters for the ground state were employed to unsuccessfully search for succinonitrile in the cold and warm molecular clouds Orion KL, Sgr B2(N), B1-b and TMC-1, using the spectral surveys captured by IRAM 30m at 3mm and the Yebes 40m at 1.3cm and 7mm.

CONCLUSIONS

Discovery of the first Ca-bearing molecule in space: CaNC

We report on the detection of calcium isocyanide, CaNC, in the carbon-rich evolved star IRC+10216. We derived a column density for this species of (2±0.5)×1011 cm-2. Based on the observed line profiles and the modelling of its emission through the envelope, the molecule has to be produced in the intermediate and outer layers of the circumstellar envelope where other metal-isocyanides have previously been found in this source. The abundance ratio of CaNC relative to MgNC and FeCN is ≃1/60 and ≃1, respectively. We searched for the species CaF, CaCl, CaC, CaCCH, and CaCH3 for which accurate frequency predictions are available. Only upper limits have been obtained for these molecules.

Broad band high resolution rotational spectroscopy for Laboratory Astrophysics

We present a new experimental setup devoted to the study of gas phase molecules and processes using broad band high spectral resolution rotational spectroscopy. A reactor chamber has been equipped with radio receivers similar to those used by radio astronomers to search for molecular emission in space. The whole Q (31.5-50 GHz) and W bands (72-116.5 GHz) are available for rotational spectroscopy observations. The receivers are equipped with 16×2.5 GHz Fast Fourier Transform spectrometers with a spectral resolution of 38.14 kHz allowing the simultaneous observation of the complete Q band and one third of the W band. The whole W band can be observed in three settings in which the Q band is always observed. Species such as CH3CN, OCS, and SO2 are detected, together with many of their isotopologues and vibrationally excited states, in very short observing times. The system permits automatic overnight observations and integration times as long as 2.4×105 seconds have been reached. The chamber is equipped with a radiofrequency source to produce cold plasmas and with four ultraviolet lamps to study photochemical processes. Plasmas of CH4, N2, CH3CN, NH3, O2, and H2, among other species, have been generated and the molecular products easily identified by their rotational spectrum, and mass spectrometry and optical spectroscopy. Finally, the rotational spectrum of the lowest energy conformer of CH3CH2NHCHO (N-Ethylformamide), a molecule previously characterized in microwave rotational spectroscopy, has been measured up to 116.5 GHz allowing the accurate determination of its rotational and distortion constants and its search in space.

Data ambiguity and clinical decision making: A qualitative case study of the use of predictive information technologies in a personalized cancer clinical trial

Personalized medicine aims to tailor the treatment to the specific characteristics of the individual patient. In the process, physicians engage with multiple sources of data and information to decide on a personalized treatment. This article draws on a qualitative case study of a clinical trial testing a method for matching treatments for advanced cancer patients. Specialists in the trial used data and information processed by a specifically developed drug-efficacy predictive algorithm and other information artifacts to make personalized clinical decisions. While using high-resolution data in the trial was expected to provide a more accurate basis for action, sociomaterial engagements of oncologists with data and its representation by artifacts paradoxically hindered personalized clinical decisions. I contend that the engagement between human discretion, ambiguous data, and malleable artifacts in this non-standardized trial produced moments of contradiction within entanglement. Sociomaterial approaches should acknowledge such conflicts in further analyses of medical practice transitions.

PAH Clusters as Interstellar Very Small Grains

PAH clusters are one candidate species for the interstellar "very small grains" or "VSGs", i.e., dust grains small enough to be stochastically heated and contribute to the aromatic infrared emission bands (AIBs). This possibility motivated laboratory experiments on the infrared spectroscopy of PAH clusters using matrix isolation spectroscopy. The spectral shifts due to PAH clustering in argon matrices provide clues for the AIB contribution from PAH clusters in the interstellar medium. Here we review results from a number of small PAH species, extrapolation to the much larger PAHs believed to be present in the interstellar medium, and the implications for a PAH cluster contribution to the VSG population.

Accurate Rotational Rest Frequencies for Ammonium Ion Isotopologues

We report rest frequencies for rotational transitions of the deuterated ammonium isotopologues NH3D+,NH 2 D 2 + and NHD D 3 + , measured in a cryogenic ion trap machine. For the symmetric tops NH3D+ andNHD 3 + one and three transitions are detected, respectively, and five transitions are detected for the asymmetric topNH 2 D 2 + . While the lowest frequency transition of NH3D+ was already known in the laboratory and space, this work enables the future radio astronomical detection of the two other isotopologues.

IRC +10216 as a spectroscopic laboratory: improved rotational constants for SiC2, its isotopologues, and Si2C

This work presents a detailed analysis of the laboratory and astrophysical spectral data available for 28SiC2, 29SiC2,30SiC2, Si13CC, and Si2C. New data on the rotational lines of these species between 70 and 350 GHz have been obtained with high spectral resolution (195 kHz) with the IRAM 30m telescope in the direction of the circumstellar envelope IRC +10216. Frequency measurements can reach an accuracy of 50 kHz for features observed with a good signal to noise ratio. From the observed astrophysical lines and the available laboratory data new rotational and centrifugal distortion constants have been derived for all the isotopologues of SiC2, allowing to predict their spectrum with high accuracy in the millimeter and submillimeter domains. Improved rotational and centrifugal distortion constants have also been obtained for disilicon carbide, Si2C. This work shows that observations of IRC +10216 taken with the IRAM 30m telescope, with a spectral resolution of 195 kHz, can be used for any molecular species detected in this source to derive, or improve, its rotational constants. Hence, IRC +10216 in addition to be one the richest sources in molecular species in the sky, can also be used as a state-of-the-art spectroscopy laboratory in the millimeter and submillimeter domains.

POLYCYCLIC AROMATIC HYDROCARBONS WITH STRAIGHT EDGES AND THE 7.6/6.2 AND 8.6/6.2 INTENSITY RATIOS IN REFLECTION NEBULAE

We have investigated the mid-infrared spectral characteristics of a series of polycyclic aromatic hydrocarbons (PAHs) with straight edges and containing an even or odd number of carbons using density functional theory (DFT). For several even and odd-carbon PAHs, the 8.6/6.2 and 7.6/6.2 intensity ratios computed in emission after the absorption of a 8 eV photon match the observed ratios obtained for three reflection nebulae (RNe), namely NGC 1333, NGC 7023, and NGC 2023. Odd-carbon PAHs are favored, particularly for NGC 1333. Both cations and anions are present with the cations being predominant. Relevant PAHs span sizes ranging from 46 to 103-113 carbons for NGC 7023 and NGC 2023 and from 38 to 127 carbons for NGC 1333 and have symmetries ranging from D2h to C s . Our work suggests that even and odd-carbon PAHs with straight edges are viable candidates for the PAH emission seen towards irradiated Photo-Dissociation Regions (PDRs).

Discovery of the Ubiquitous Cation NS+ in Space Confirmed by Laboratory Spectroscopy

We report the detection in space of a new molecular species which has been characterized spectroscopically and fully identified from astrophysical data. The observations were carried out with the 30m IRAM telescopea. The molecule is ubiquitous as its J=2→1 transition has been found in cold molecular clouds, prestellar cores, and shocks. However, it is not found in the hot cores of Orion-KL and in the carbon-rich evolved star IRC+10216. Three rotational transitions in perfect harmonic relation J' = 2/3/5 have been identified in the prestellar core B1b. The molecule has a 1Σ electronic ground state and its J=2→1 transition presents the hyperfine structure characteristic of a molecule containing a nucleus with spin 1. A careful analysis of possible carriers shows that the best candidate is NS+. The derived rotational constant agrees within 0.3-0.7% with ab initio calculations. NS+ was also produced in the laboratory to unambiguously validate the astrophysical assignment. The observed rotational frequencies and determined molecular constants confirm the discovery of the nitrogen sulfide cation in space. The chemistry of NS+ and related nitrogen-bearing species has been analyzed by means of a time-dependent gas phase model. The model reproduces well the observed NS/NS+ abundance ratio, in the range 30-50, and indicates that NS+ is formed by reactions of the neutral atoms N and S with the cations SH+ and NH+, respectively.

Zeeman effect in sulfur monoxide: A tool to probe magnetic fields in star forming regions

CONTEXT

Magnetic fields play a fundamental role in star formation processes and the best method to evaluate their intensity is to measure the Zeeman effect of atomic and molecular lines. However, a direct measurement of the Zeeman spectral pattern from interstellar molecular species is challenging due to the high sensitivity and high spectral resolution required. So far, the Zeeman effect has been detected unambiguously in star forming regions for very few non-masing species, such as OH and CN.

AIMS

We decided to investigate the suitability of sulfur monoxide (SO), which is one of the most abundant species in star forming regions, for probing the intensity of magnetic fields via the Zeeman effect.

METHODS

We investigated the Zeeman effect for several rotational transitions of SO in the (sub-)mm spectral regions by using a frequency-modulated, computer-controlled spectrometer, and by applying a magnetic field parallel to the radiation propagation (i.e., perpendicular to the oscillating magnetic field of the radiation). To support the experimental determination of the g factors of SO, a systematic quantum-chemical investigation of these parameters for both SO and O2 has been carried out.

RESULTS

An effective experimental-computational strategy for providing accurate g factors as well as for identifying the rotational transitions showing the strongest Zeeman effect has been presented. Revised g factors have been obtained from a large number of SO rotational transitions between 86 and 389 GHz. In particular, the rotational transitions showing the largest Zeeman shifts are: N, J = 2, 2 ← 1, 1 (86.1 GHz), N, J = 4, 3 ← 3, 2 (159.0 GHz), N, J = 1, 1 ← 0, 1 (286.3 GHz), N, J = 2, 2 ← 1, 2 (309.5 GHz), and N, J = 2, 1 ← 1, 0 (329.4 GHz). Our investigation supports SO as a good candidate for probing magnetic fields in high-density star forming regions.

A hybrid line list for CH4 and hot methane continuum

AIMS

Molecular line lists (a catalogue of transition frequencies and line strengths) are important for modelling absorption and emission processes in atmospheres of different astronomical objects, such as cool stars and exoplanets. In order to be applicable for high temperatures, line lists for molecules like methane must contain billions of transitions, which makes their direct (line-by-line usage) application in radiative transfer calculations impracticable. Here we suggest a new, hybrid line list format to mitigate this problem, based on the idea of temperature-dependent absorption continuum.

METHODS

The line list is partitioned into a large set of relatively weak lines and a small set of important, stronger lines. The weaker lines are then used either to construct a temperature-dependent (but pressure-independent) set of intensity cross sections or are blended into a greatly reduced set of 'super-lines'. The strong lines are kept in the form of temperature-independent Einstein A coefficients.

RESULTS

A line list for methane (CH₄) is constructed as a combination of 17 million strong absorption lines relative to the reference absorption spectra and a background methane continuum in two temperature-dependent forms of cross sections and super-lines. This approach significantly eases the use of large high temperature line lists as the computationally expensive calculation of pressure- dependent profiles (e.g. Voigt) only need to be performed for a relatively small number of lines. Both the line list and cross sections were generated using a new 34 billion methane line list (known as 34to10), which extends the 10to10 line list to higher temperatures (up to 2000 K). The new hybrid scheme can be applied to any large line lists containing billions of transitions. We recommend using super-lines generated on a high resolution grid based on a resolving power of R = 1,000,000 to model the molecular continuum as a more flexible alternative to the temperature-dependent cross sections.

State-to-state chemistry and rotational excitation of CH+ in photon-dominated regions

We present a detailed theoretical study of the rotational excitation of CH+ due to reactive and nonreactive collisions involving C+(2P), H2, CH+, H and free electrons. Specifically, the formation of CH+ proceeds through the reaction between C+(2P) and H2(νH2 = 1, 2), while the collisional (de)excitation and destruction of CH+ is due to collisions with hydrogen atoms and free electrons. State-to-state and initial-state-specific rate coefficients are computed in the kinetic temperature range 10-3000 K for the inelastic, exchange, abstraction and dissociative recombination processes using accurate potential energy surfaces and the best scattering methods. Good agreement, within a factor of 2, is found between the experimental and theoretical thermal rate coefficients, except for the reaction of CH+ with H atoms at kinetic temperatures below 50 K. The full set of collisional and chemical data are then implemented in a radiative transfer model. Our Non-LTE calculations confirm that the formation pumping due to vibrationally excited H2 has a substantial effect on the excitation of CH+ in photon-dominated regions. In addition, we are able to reproduce, within error bars, the far-infrared observations of CH+ toward the Orion Bar and the planetary nebula NGC 7027. Our results further suggest that the population of νH2 = 2 might be significant in the photon-dominated region of NGC 7027.

Accurate Frequency Determination of Vibration-Rotation and Rotational Transitions of SiH. Astrophys J 2017;849:60. [PMID: 29142330 PMCID: PMC5683345 DOI: 10.3847/1538-4357/aa8fca]

The fundamental 28SiH+ ion has been characterized in a collaborative work, utilizing a hollow-cathode-discharge laser-spectrometer and a cryogenic ion trap spectrometer. Twenty-three vibration-rotation transitions around 4.75 μm have been detected with high accuracy. This has facilitated the first direct measurement of the pure rotational transition J = 1 ← 0 at 453056.3632(4) MHz in the trap spectrometer. The measured and accurately predicted transitions enable the search for this ion in space with IR and sub-mm telescopes.

The High Resolution Infrared Spectrum of HCl. Astrophys J Lett 2016;833:L32. [PMID: 28261442 PMCID: PMC5331965 DOI: 10.3847/2041-8213/833/2/l32]

The chloroniumyl cation, HCl⁺, has been recently identified in space from Herschel's spectra. A joint analysis of extensive vis-UV spectroscopy emission data together with a few high-resolution and high-accuracy millimiter-wave data provided the necessary rest frequencies to support the astronomical identification. Nevertheless, the analysis did not include any infrared (IR) vibration-rotation data. Furthermore, with the end of the Herschel mission, infrared observations from the ground may be one of the few available means to further study this ion in space. In this work, we provide a set of accurate rovibrational transition wavenumbers as well as a new and improved global fit of vis-UV, IR and millimiter-wave spectroscopy laboratory data, that will aid in future studies of this molecule.

Millimeter wave spectra of carbonyl cyanide

CONTEXT

More than 30 cyanide derivatives of simple organic molecules have been detected in the interstellar medium, but only one dicarbonitrile has been found and that very recently. There is still a lack of high-resolution spectroscopic data particularly for dinitriles derivatives. The carbonyl cyanide molecule is a new and interesting candidate for astrophysical detection. It could be formed by the reaction of CO and CN radicals, or by substitution of the hydrogen atom by a cyano group in cyanoformaldehyde, HC(=O)CN, that has already been detected in the interstellar medium.

AIMS

The available data on the rotational spectrum of carbonyl cyanide is limited in terms of quantum number values and frequency range, and does not allow accurate extrapolation of the spectrum into the millimeter-wave range. To provide a firm basis for astrophysical detection of carbonyl cyanide we studied its millimeter-wave spectrum.

METHODS

The rotational spectrum of carbonyl cyanide was measured in the frequency range 152 - 308 GHz and analyzed using Watson's A- and S-reduction Hamiltonians.

RESULTS

The ground and first excited state of v5 vibrational mode were assigned and analyzed. More than 1100 distinct frequency lines of the ground state were fitted to produce an accurate set of rotational and centrifugal distortion constants up to the eighth order. The frequency predictions based on these constants should be accurate enough for astrophysical searches in the frequency range up to 500 GHz and for transition involving energy levels with J ≤ 100 and Ka ≤ 42. Based on the results we searched for interstellar carbonyl cyanide in available observational data without success. Thus, we derived upper limits to its column density in different sources.

High-Resolution Rotational Spectrum, Dunham Coefficients, and Potential Energy Function of NaCl

We report laboratory spectroscopy for the first time of the J = 1-0 and J = 2-1 lines of Na35Cl and Na37Cl in several vibrational states. The hyperfine structure has been resolved in both transitions for all vibrational levels, which permit us to predict with high accuracy the hyperfine splitting of the rotational transitions of the two isotopologues at higher frequencies. The new data have been merged with all previous works at microwave, millimeter, and infrared wavelengths and fitted to a series of mass-independent Dunham parameters and to a potential energy function. The obtained parameters have been used to compute a new dipole moment function, from which the dipole moment for infrared transitions up to Δv = 8 has been derived. Frequency and intensity predictions are provided for all rovibrational transitions up to J = 150 and v = 8, from which the ALMA data of evolved stars can be modeled and interpreted.