Accurate and interpretable gene expression imputation on scRNA-seq data using IGSimpute.

Single-cell ribonucleic acid sequencing (scRNA-seq) enables the quantification of gene expression at the transcriptomic level with single-cell resolution, enhancing our understanding of cellular heterogeneity. However, the excessive missing values present in scRNA-seq data hinder downstream analysis. While numerous imputation methods have been proposed to recover scRNA-seq data, high imputation performance often comes with low or no interpretability. Here, we present IGSimpute, an accurate and interpretable imputation method for recovering missing values in scRNA-seq data with an interpretable instance-wise gene selection layer (GSL). IGSimpute outperforms 12 other state-of-the-art imputation methods on 13 out of 17 datasets from different scRNA-seq technologies with the lowest mean squared error as the chosen benchmark metric. We demonstrate that IGSimpute can give unbiased estimates of the missing values compared to other methods, regardless of whether the average gene expression values are small or large. Clustering results of imputed profiles show that IGSimpute offers statistically significant improvement over other imputation methods. By taking the heart-and-aorta and the limb muscle tissues as examples, we show that IGSimpute can also denoise gene expression profiles by removing outlier entries with unexpectedly high expression values via the instance-wise GSL. We also show that genes selected by the instance-wise GSL could indicate the age of B cells from bladder fat tissue of the Tabula Muris Senis atlas. IGSimpute can impute one million cells using 64 min, and thus applicable to large datasets.

Female terminalia morphology and cladistic relations among Tok-Tok beetles (Tenebrionidae: Sepidiini).

Tok-tokkies are one of the most iconic lineages within Tenebrionidae. In addition to containing some of the largest darkling beetles, this tribe is recognized for its remarkable form of sexual communication known as substrate tapping. Nevertheless, the phylogenetic relationships within the group remain poorly understood. This study investigates the usefulness of female terminalia morphology for delimiting Sepidiini and reconstructing relationships among it. Data on the structure of the ovipositors, genital tubes and spicula ventrali have been generated for >200 species representing 28 Pimeliinae tribes. This dataset was used in a comparative analysis at the subfamilial level, which resulted in recognition of several unique features of tok-tokkie terminalia. Additionally, new features linking phenotypically challenging tribes also were recovered (Cryptochilini + Idisiini + Pimeliini). Secondly, 23 characters linked to the structure of female terminalia were defined for tok-tok beetles. Cladistic analysis demonstrates the nonmonophyletic nature of most of the recognized subtribes. The morphological dataset was analysed separately and in combination with available molecular data (CAD, Wg, cox1, cox2, 28S). All obtained topologies were largely congruent, supporting the following changes: Palpomodina Kaminski & Gearner subtr.n. is erected to accommodate the genera Namibomodes and Palpomodes; Argenticrinis and Bombocnodulus are transferred from Hypomelina to Molurina; 153 species and subspecies previously classified within Psammodes are distributed over three separate genera (Mariazofia Kaminski nom.n., Piesomera stat.r., Psammodes sens.n.). Psammodes sklodowskae Kaminski & Gearner sp.n. is described. Preliminary investigation of the ovipositor of Mariazofia basuto (Koch) comb.n. was carried out with the application of microcomputed tomography, illuminating the muscular system as a reliable reference point for recognizing homologous elements in highly modified ovipositors.

[From external assessment of pain to automated multimodal measurement of pain intensity : Narrative review of state of research and clinical perspectives]. / Von der Fremdbeurteilung des Schmerzes zur automatisierten multimodalen Messung der Schmerzintensität : Narrativer Review zum Stand der Forschung und zur klinischen Perspektive.

BACKGROUND: In patients with limited communication skills, the use of conventional scales or external assessment is only possible to a limited extent or not at all. Multimodal pain recognition based on artificial intelligence (AI) algorithms could be a solution. OBJECTIVE: Overview of the methods of automated multimodal pain measurement and their recognition rates that were calculated with AI algorithms. METHODS: In April 2018, 101 studies on automated pain recognition were found in the Web of Science database to illustrate the current state of research. A selective literature review with special consideration of recognition rates of automated multimodal pain measurement yielded 14 studies, which are the focus of this review. RESULTS: The variance in recognition rates was 52.9-55.0% (pain threshold) and 66.8-85.7%; in nine studies the recognition rate was ≥80% (pain tolerance), while one study reported recognition rates of 79.3% (pain threshold) and 90.9% (pain tolerance). CONCLUSION: Pain is generally recorded multimodally, based on external observation scales. With regard to automated pain recognition and on the basis of the 14 selected studies, there is to date no conclusive evidence that multimodal automated pain recognition is superior to unimodal pain recognition. In the clinical context, multimodal pain recognition could be advantageous, because this approach is more flexible. In the case of one modality not being available, e.g., electrodermal activity in hand burns, the algorithm could use other modalities (video) and thus compensate for missing information.

[Multimodal recognition of pain intensity and pain modality with machine learning]. / Multimodale Erkennung von Schmerzintensität und -modalität mit maschinellen Lernverfahren.

BACKGROUND: The objective recording of subjectively experienced pain is a problem that has not been sufficiently solved to date. In recent years, data sets have been created to train artificial intelligence algorithms to recognize patterns of pain intensity. The multimodal recognition of pain with machine learning could provide a way to reduce an over- or undersupply of analgesics, explicitly in patients with limited communication skills. OBJECTIVES: This study investigated the methodology of automated multimodal recognition of pain intensity and modality using machine-learning techniques of artificial intelligence. Multimodal recognition rates of experimentally induced phasic electrical and heat pain stimuli were compared with uni- and bimodal recognition rates. MATERIAL AND METHODS: On the basis of the X­ITE Pain Database, healthy subjects were stimulated with phasic electro-induced pain and heat pain, and their corresponding pain responses were recorded with multimodal sensors (acoustic, video-based, physiological). After complex signal processing, machine-learning methods were used to calculate recognition rates with respect to pain intensity (baseline vs. pain threshold, pain tolerance, mean value of pain threshold and tolerance) and pain modality (electrical vs. heat). Finally, a statistical comparison of uni- vs. multimodal and bi- vs. multimodal detection rates was performed. RESULTS: With few exceptions, multimodal recognition of pain intensity rates was statistically superior to unimodal recognition rates, regardless of the pain modality. Multimodal pain recognition distinguished significantly better between heat and electro-induced pain. Further, multimodal recognition rates were predominantly superior to bimodal recognition rates. CONCLUSION: Priority should be given to the multimodal approach to the recognition of pain intensity and modality compared with unimodality. Further clinical studies should clarify whether multimodal automated recognition of pain intensity and modality is in fact superior to bimodal recognition.

Erratum: Ultrafast Doublon Dynamics in Photoexcited 1T-TaS_{2} [Phys. Rev. Lett. 120, 166401 (2018)].

This corrects the article DOI: 10.1103/PhysRevLett.120.166401.

Ultrafast Doublon Dynamics in Photoexcited 1T-TaS_{2}.

Strongly correlated materials exhibit intriguing properties caused by intertwined microscopic interactions that are hard to disentangle in equilibrium. Employing nonequilibrium time-resolved photoemission spectroscopy on the quasi-two-dimensional transition-metal dichalcogenide 1T-TaS_{2}, we identify a spectroscopic signature of doubly occupied sites (doublons) that reflects fundamental Mott physics. Doublon-hole recombination is estimated to occur on timescales of electronic hopping ℏ/J≈14 fs. Despite strong electron-phonon coupling, the dynamics can be explained by purely electronic effects captured by the single-band Hubbard model under the assumption of weak hole doping, in agreement with our static sample characterization. This sensitive interplay of static doping and vicinity to the metal-insulator transition suggests a way to modify doublon relaxation on the few-femtosecond timescale.

Comparison of volumetric and functional parameters in simultaneous cardiac PET/MR: feasibility of volumetric assessment with residual activity from prior PET/CT.

OBJECTIVE: To compare cardiac left ventricular (LV) parameters in simultaneously acquired hybrid fluorine-18-fluorodeoxyglucose ([18F] FDG) positron emission tomography/magnetic resonance imaging (PET/MRI) in patients with residual tracer activity of upstream PET/CT. METHODS: Twenty-nine patients (23 men, age 58±17 years) underwent cardiac PET/MRI either directly after a non-cardiac PET/CT with homogenous cardiac [18F] FDG uptake (n=20) or for viability assessment (n=9). Gated cardiac [18F] FDG PET and cine MR sequences were acquired simultaneously and evaluated blinded to the cross-imaging results. Image quality (IQ), end-diastolic (LVEDV), end-systolic volume (LVESV), ejection fraction (LVEF) and myocardial mass (LVMM) were measured. Pearson correlation and intraclass correlation coefficient (ICC), regression and a Bland-Altman analysis were assessed. RESULTS: Except LVMM, volumetric and functional LV parameters demonstrated high correlations (LVESV: r=0.97, LVEDV: r=0.95, LVEF: r=0.91, LVMM: r=0.87, each p<0.05), but wide limits of agreement (LOA) for LVEDV (-25.3-82.5ml); LVESV (-33.1-72.7ml); LVEF (-18.9-14.8%) and LVMM (-78.2-43.2g). Intra- and interobserver reliability were very high (ICC≥0.95) for all parameters, except for MR-LVEF (ICC=0.87). PET-IQ (0-3) was high (mean: 2.2±0.9) with significant influence on LVMM calculations only. CONCLUSION: In simultaneously acquired cardiac PET/MRI data, LVEDV, LVESV and LVEF show good agreement. However, the agreement seems to be limited if cardiac PET/MRI follows PET/CT and only the residual activity is used. KEY POINTS: • [ 18 F] FDG PET-MRI is feasible with residual [ 18 F] FDG activity in patients with homogenous cardiac uptake. • Cardiac volumes and function assessed by PET/MRI show good agreement. • LVEDV and LVESV are underestimated; PET overestimates LVMM and LVEF. • Cardiac PET and MRI data correlate better when acquired simultaneously than sequentially. • PET and MRI should not assess LV parameters interchangeably.

[Mimic activity of differentiated pain intensities : Correlation of characteristics of Facial Action Coding System and electromyography]. / Mimische Aktivität differenzierter Schmerzintensitäten : Korrelation der Merkmale von Facial Action Coding System und Elektromyographie.

BACKGROUND: The monitoring of facial expressions to assess pain intensity provides a way to determine the need for pain medication in patients who are not able to do so verbally. OBJECTIVES: In this study two methods for facial expression analysis - Facial Action Coding System (FACS) and electromyography (EMG) of the zygomaticus muscle and corrugator supercilii - were compared to verify the possibility of using EMG for pain monitoring. MATERIAL AND METHODS: Eighty-seven subjects received painful heat stimuli via a thermode on the right forearm in two identical experimental sequences - with and without EMG recording. RESULTS: With FACS, pain threshold and pain tolerance could be distinguished reliably. Multiple regression analyses indicated that some facial expressions had a predictive value. Correlations between FACS and pain intensity and EMG and pain intensity were high, indicating a closer relationship for EMG and increasing pain intensity. For EMG and FACS, a low correlation was observed, whereas EMG correlates much better with pain intensity. CONCLUSIONS: Results show that the facial expression analysis based on FACS represents a credible method to detect pain. Because of the expenditure of time and personal costs, FACS cannot be used properly until automatic systems work accurately. The use of EMG seems to be helpful in the meantime to enable continuous pain monitoring for patients with acute post-operative pain.

Current status and future role of brain PET/MRI in clinical and research settings.

Hybrid PET/MRI systematically offers a complementary combination of two modalities that has often proven itself superior to the single modality approach in the diagnostic work-up of many neurological and psychiatric diseases. Emerging PET tracers, technical advances in multiparametric MRI and obvious workflow advantages may lead to a significant improvement in the diagnosis of dementia disorders, neurooncological diseases, epilepsy and neurovascular diseases using PET/MRI. Moreover, simultaneous PET/MRI is well suited to complex studies of brain function in which fast fluctuations of brain signals (e.g. related to task processing or in response to pharmacological interventions) need to be monitored on multiple levels. Initial simultaneous studies have already demonstrated that these complementary measures of brain function can provide new insights into the functional and structural organization of the brain.

Dung beetle fauna from Mount Mabu, Mozambique. Part 3: A new species of Proagoderus van Lansberge, 1883 with an annotated checklist of the Proagoderus dives (Harold, 1877) species-group (Coleoptera: Scarabaeidae: Scarabaeinae).

A new species of dung beetle, Proagoderus mabuensis Daniel, Josso, Nganhane & Strmpher, new species from Mount Mabu, northern Mozambique, is described, diagnosed, and illustrated. We provide a morphological comparison between the new species and a similar species from Mount Namuli, Mozambique, Proagoderus camiadei Josso, 2014. Both species belong to the Proagoderus dives (Harold, 1877) species-group. Furthermore, we provide an updated checklist of all known members of the dives species-group.

Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection.

Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.

Long-range Coulomb interactions in surface systems: a first-principles description within self-consistently combined GW and dynamical mean-field theory.

Systems of adatoms on semiconductor surfaces display competing ground states and exotic spectral properties typical of two-dimensional correlated electron materials which are dominated by a complex interplay of spin and charge degrees of freedom. We report a fully ab initio derivation of low-energy Hamiltonians for the adatom systems Si(111):X, with X=Sn, Si, C, Pb, that we solve within self-consistently combined GW and dynamical mean-field theory. Calculated photoemission spectra are in agreement with available experimental data. We rationalize experimentally observed trends from Mott physics toward charge ordering along the series as resulting from substantial long-range interactions.

Large temperature dependence of the number of carriers in co-doped BaFe(2)As(2).

Using angle-resolved photoemission spectroscopy, we study the evolution of the number of carriers in Ba(Fe(1-x)Co(x))(2)As(2) as a function of Co content and temperature. We show that there is a k-dependent energy shift compared to density functional calculations, which is large below 100 K at low Co contents and reduces the volume of hole and electron pockets by a factor 2. This k shift becomes negligible at high Co content and could be due to interband charge or spin fluctuations. We further reveal that the bands shift with temperature, changing significantly the number of carriers they contain (up to 50%). We explain this evolution by thermal excitations of carriers among the narrow bands, possibly combined with a temperature evolution of the k-dependent fluctuations.

The complete family of genes encoding G proteins of Caenorhabditis elegans.

Caenorhabditis elegans is the first animal whose genomic sequence has been determined. One of the new possibilities in post-sequence genetics is the analysis of complete gene families at once. We studied the family of heterotrimeric G proteins. C. elegans has 20 Galpha, 2 Gbeta and 2 Ggamma genes. There is 1 homologue of each of the 4 mammalian classes of Galpha genes, G(i)/G(o)alpha, G(s)alpha , G(q)alpha and G12alpha, and there are 16 new alpha genes. Although the conserved Galpha subunits are expressed in many neurons and muscle cells, GFP fusions indicate that 14 new Galpha genes are expressed almost exclusively in a small subset of the chemosensory neurons of C. elegans. We generated loss-of-function alleles using target-selected gene inactivation. None of the amphid-expressed genes are essential for viability, and only four show any detectable phenotype (chemotaxis defects), suggesting extensive functional redundancy. On the basis of functional analysis, the 20 genes encoding Galpha proteins can be divided into two groups: those that encode subunits affecting muscle activity (homologues of G(i)/G(o)alpha, G(s)alpha and G(q)), and those (14 new genes) that encode proteins most likely involved in perception.

A new flightless species of Phoberus Macleay, 1819 (Coleoptera: Trogidae) from the Eastern Cape Province in South Africa.

The loss of flight is common in the keratin beetle genus Phoberus Macleay, 1819 (Coleoptera: Trogidae)-20 out of the 49 species in this genus exhibit metathoracic-wing reduction in various degrees rendering them flightless. In this paper another flightless species, Phoberus villeti Strümpher, new species, is described and illustrated from the Amathole mountains in the Eastern Cape Province of South Africa. The new species is micropterous having tightly fused elytra (only wing rudiments visible), rounded humeral angles and a characteristic rounded body shape. However, it is most notable for its large size (~12 mm) and the distinctive tufts of yellow setae present on the elytra.

Omorgus (Omorgus) khandesh (Coleoptera: Scarabaeoidea: Trogidae), a new species from India, along with an annotated catalogue of the Oriental and Palearctic species of the subgenus Omorgus Erichson, 1847.

A new species of keratin beetle from Western India, Omorgus (Omorgus) khandesh Strümpher & Kalawate, new species, is described and illustrated. The new species is morphologically most similar to O. (O.) rimulosus (Haaf, 1957). The latter is redescribed and illustrated to enable accurate recognition of both species. Based on this work the following taxonomic changes are proposed: Three species are transferred from the subgenus Afromorgus Scholtz, 1986 to the nominotypical subgenus: O. (O.) inclusus (Walker 1858), O. (O.) maissouri (Haaf, 1945a) and O. (O.) rimulosus (Haaf, 1957). Lastly, we include an annotated catalogue of the species of the nominotypical subgenus Omorgus known from the Oriental and Palaearctic regions.

Dung beetle fauna from Mount Mabu, Mozambique. Part 1: A new species of Onthophagus Latreille, 1802, and a checklist of species belonging to group 3 (d'Orbigny 1913) (Coleoptera: Scarabaeidae: Scarabaeinae).

Onthophagus mabuensis Daniel, Strümpher & Josso, new species, is diagnosed, described and illustrated from Mount Mabu, which is situated in north-central Mozambique. Morphological comparison is made between this new forest species and similar species from Malawi and Zambia in group 3 of Onthophagus Latreille, 1802, as classified by d'Orbigny (1913). In addition, we provide a checklist of all known group 3 species.

Dung beetle fauna from Mount Mabu. Part 2: Pedaria ricardogutai (Coleoptera: Scarabaeidae), a new species, with an annotated checklist of species of Pedaria Laporte, 1832 from Mozambique.

Mabu Forest in northern-central Mozambique harbours the largest continuous block of rainforest remaining in southern Africa. Also, the region is known for its exceptional levels of biodiversity, including a high level of endemism. Several new taxa of plants and animals have been discovered from previous biological expeditions. Last year, we conducted the first dung beetle exploration in the regionwhere almost half of the dung beetle species collected are new to science. In this paper, we describe, diagnose and illustrate Pedaria ricardogutai Daniel, Strmpher & Josso, new species. We compared the new species to the most morphologically similar species, Pedaria sudrei Josso & Prvost, 2003. We also provide an annotated checklist of 17 species of Pedaria Laporte, 1832, recorded from Mozambique, including type localities and distribution records.

New mode of vapor-liquid-solid nanowire growth.

We report on the new mode of the vapor-liquid-solid nanowire growth with a droplet wetting the sidewalls and surrounding the nanowire rather than resting on its top. It is shown theoretically that such an unusual configuration happens when the growth is catalyzed by a lower surface energy metal. A model of a nonspherical elongated droplet shape in the wetting case is developed. Theoretical predictions are compared to the experimental data on the Ga-catalyzed growth of GaAs nanowires by molecular beam epitaxy. In particular, it is demonstrated that the experimentally observed droplet shape is indeed nonspherical. The new VLS mode has a major impact on the crystal structure of GaAs nanowires, helping to avoid the uncontrolled zinc blende-wurtzite polytylism under optimized growth conditions. Since the triple phase line nucleation is suppressed on surface energetic grounds, all nanowires acquire pure zinc blende phase along the entire length, as demonstrated by the structural studies of our GaAs nanowires.

TB preventive treatment among pregnant women with HIV.

BACKGROUND: The WHO recommends TB preventive treatment (TPT) for people living with HIV, including pregnant women. Uptake of this policy recommendation in this subpopulation and country alignment with WHO guidance is unclear.METHODS: We conducted a policy review in 38 WHO high TB and TB-HIV burden countries to assess if the uptake of TPT policy among pregnant women living with HIV was in line with the WHO´s 2018 Updated and Consolidated Guidelines for Programmatic Management for LTBI. Data sources included TB national guidelines and HIV/AIDS/ART national guidelines, complemented by results from a previous survey on policy uptake held at the WHO.RESULTS: Uptake of WHO policy to provide TB preventive treatment among women with HIV accessing antenatal care was moderate: 64% (23 of 36 countries) explicitly recommended at least one clinical guideline or policy recommendation on screening, testing or treatment of LTBI among pregnant women living with HIV. There was considerable variation between countries on the stages in pregnancy that TPT should be provided. Two countries (5%) provided clinical monitoring recommendations for pregnant women.CONCLUSIONS: There is moderate uptake of TPT policy for pregnant women with HIV. Failure to provide TPT as part of antenatal or prevention of mother-to-child services is a missed opportunity for TB control.