Optical characterization of inhomogeneity of polymer-like thin films arising in the initial phase of plasma-enhanced chemical vapor deposition.

In this study, an optical investigation in a wide spectral range of polymer-like (SiOxCyHz) thin films deposited by plasma-enhanced chemical vapor deposition (PECVD) is presented. The primary focus is on assessing the homogeneity of the grown films. Within the PECVD, it is possible to alter the properties of the deposited material by continually adjusting deposition process parameters and hence allow for the growth of inhomogeneous layers. However, as shown in this study, the growth of homogeneous layers could be similarly challenging. This challenge is especially pronounced at the beginning of the deposition process, where it is necessary to consider the influence of the substrate among other factors, as even slight variations in the deposition conditions can lead to the formation of inhomogeneous layers. Several series of polymer-like thin films were deposited onto silicon substrates with the goal of producing homogeneous layers, i.e. all deposition parameters were held constant. These samples were optically characterized with a special interest in homogeneity, especially at the beginning of the growth. It was found that initial inhomogeneous growth is always present. The thickness of the initial inhomogeneous part was found to be surprisingly large.

Solving Vibronic Dynamics in Electron Continuum.

We present a general two-dimensional model of conical intersection between metastable states that are vibronically coupled not only directly but also indirectly through a virtual electron in the autodetachment continuum. This model is used as a test ground for the design and comparison of iterative solvers for resonance dynamics in low-energy electron-molecule collisions. Two Krylov-subspace methods with various preconditioning schemes are compared. To demonstrate the applicability of the proposed methods on even larger models, we also test the performance of one of the methods on a recent model of vibrational excitation of CO2 by electron impact based on three vibronically coupled discrete states in continuum (Renner-Teller doublet of shape resonances coupled to a sigma virtual state) including four vibrational degrees of freedom. Two-dimensional electron energy-loss spectra resulting from electron-molecule scattering within the models are briefly discussed.

Uncovering the essential roles of glutamate carboxypeptidase 2 orthologs in Caenorhabditis elegans.

Human glutamate carboxypeptidase 2 (GCP2) from the M28B metalloprotease group is an important target for therapy in neurological disorders and an established tumor marker. However, its physiological functions remain unclear. To better understand general roles, we used the model organism Caenorhabditis elegans to genetically manipulate its three existing orthologous genes and evaluate the impact on worm physiology. The results of gene knockout studies showed that C. elegans GCP2 orthologs affect the pharyngeal physiology, reproduction, and structural integrity of the organism. Promoter-driven GFP expression revealed distinct localization for each of the three gene paralogs, with gcp-2.1 being most abundant in muscles, intestine, and pharyngeal interneurons, gcp-2.2 restricted to the phasmid neurons, and gcp-2.3 located in the excretory cell. The present study provides new insight into the unique phenotypic effects of GCP2 gene knockouts in C. elegans, and the specific tissue localizations. We believe that elucidation of particular roles in a non-mammalian organism can help to explain important questions linked to physiology of this protease group and in extension to human GCP2 involvement in pathophysiological processes.

Divide, conquer and reconstruct: How to solve the 3D structure of recalcitrant Micro-Exon Gene (MEG) protein from Schistosoma mansoni.

Micro-Exon Genes are a widespread class of genes known for their high variability, widespread in the genome of parasitic trematodes such as Schistosoma mansoni. In this study, we present a strategy that allowed us to solve the structures of three alternatively spliced isoforms from the Schistoma mansoni MEG 2.1 family for the first time. All isoforms are hydrophobic, intrinsically disordered, and recalcitrant to be expressed in high yield in heterologous hosts. We resorted to the chemical synthesis of shorter pieces, before reconstructing the entire sequence. Here, we show that isoform 1 partially folds in a-helix in the presence of trifluoroethanol while isoform 2 features two rigid elbows, that maintain the peptide as disordered, preventing any structuring. Finally, isoform 3 is dominated by the signal peptide, which folds into a-helix. We demonstrated that combining biophysical techniques, like circular dichroism and nuclear magnetic resonance at natural abundance, with in silico molecular dynamics simulation for isoform 1 only, was the key to solve the structure of MEG 2.1. Our results provide a crucial piece to the puzzle of this elusive and highly variable class of proteins.

Current-induced bond rupture in single-molecule junctions: Effects of multiple electronic states and vibrational modes.

Current-induced bond rupture is a fundamental process in nanoelectronic architectures, such as molecular junctions, and scanning tunneling microscopy measurements of molecules at surfaces. The understanding of the underlying mechanisms is important for the design of molecular junctions that are stable at higher bias voltages and is a prerequisite for further developments in the field of current-induced chemistry. In this work, we analyze the mechanisms of current-induced bond rupture employing a recently developed method, which combines the hierarchical equations of motion approach in twin space with the matrix product state formalism and allows accurate, fully quantum mechanical simulations of the complex bond rupture dynamics. Extending previous work [Ke et al. J. Chem. Phys. 154, 234702 (2021)], we consider specifically the effect of multiple electronic states and multiple vibrational modes. The results obtained for a series of models of increasing complexity show the importance of vibronic coupling between different electronic states of the charged molecule, which can enhance the dissociation rate at low bias voltages profoundly.

Proteases and their inhibitors involved in Schistosoma mansoni egg-host interaction revealed by comparative transcriptomics with Fasciola hepatica eggs.

Schistosoma mansoni eggs are the main causative agents of the pathological manifestations of schistosomiasis. The eggs are laid in the host bloodstream, then they migrate through the intestinal wall into the lumen. However, a significant proportion of the eggs become lodged in the liver, where they cause inflammation and fibrosis. In this study, we focus on a specific group of proteins expressed by the egg, namely proteases and their inhibitors. These molecules are often involved in schistosome-host interactions, but are still unexplored in the egg stage. Using RNA-seq and comparative transcriptomics of immature and mature S. mansoni eggs, we mapped the portfolio of proteases and their inhibitors, and determined their gene expression levels. In addition, we compared these data with gene expression of proteases and their inhibitors in Fasciola hepatica eggs. Fasciola hepatica eggs served as a useful comparative model, as they do not migrate through tissues and inflict pathology. We detected transcription of 135 and 117 proteases in S. mansoni and F. hepatica eggs, respectively, with 87 identified as orthologous between the two species. In contrast, we observed only four orthologous inhibitors out of 21 and 16 identified in S. mansoni and F. hepatica eggs, respectively. Among others, we measured high and developmentally regulated levels of expression of metalloproteases in S. mansoni eggs, specifically aminopeptidase N1, endothelin-converting enzyme 1, and several leishmanolysin-like peptidases. We identified highly transcribed protease inhibitors serpin and alpha-2-macroglobulin that are unique to S. mansoni eggs, and antistasin-like inhibitor in F. hepatica eggs. This study provides new insights into the portfolio of proteases and inhibitors expressed by S. mansoni with potential roles in egg tissue migration, stimulation of angiogenesis, and interaction with host blood and immunity.

A literature review of schistosomiasis in Ghana: a reference for bridging the research and control gap.

Schistosomiasis is endemic in most sub-Saharan African countries, including Ghana, where the need for effective control involving preventive chemotherapy was indicated by the WHO. Mass drug administration commenced in 2008 and has continued since then in Ghana, but the country remains highly endemic. Here, we review the literature on schistosomiasis to identify research and knowledge gaps potentially affecting disease control. A total of 100 Ghana-related schistosomiasis literature sources were reviewed, showing that most studies were conducted on epidemiology, control of transmission and diagnosis. By contrast, many aspects of this disease remain neglected, including livestock schistosomiasis and its zoonotic potential, recent distribution of disease vectors or widely overlooked genital schistosomiasis. Stratified by region, the highest number of studies focus on Greater Accra, while studies are limited or absent for several other regions. Although this review shows apparent progress in terms of schistosomiasis research and control, a considerable amount of work remains to achieve at least a reduction in the prevalence of the disease, which affects a significant proportion of the population. National epidemiological data based on a nationwide survey, integrated control and improved monitoring and evaluation must be ensured.

Effect of pelvic floor status on the outcome of pelvic organ prolapse surgery.

Pelvic organ prolapse (POP) is a common diagnosis with an incidence in the population of up to 50%. POP causes restrictions in everyday life and reduces patients' quality of life. Therapy is either conservative in the form of physiotherapy or the use of different types of pessaries, possibly. in case of inappropriateness or failure of conservative treatment, an operative solution is chosen. Avulsion injury of the levator ani muscle (MLA) is a strong factor in the development of POP. Some patients undergo repeated surgeries for POP, negatively impacting their quality of life. Studies show that the stage of POP and avulsion injury is associated with an increased risk of recurrence after index prolapse surgery. Ultrasound diagnosis of MLA injuries might help in predicting the risk of recurrence. Assessment of pelvic floor function is crucial for the success of surgical management of POP.

Characterization of glutamate carboxypeptidase 2 orthologs in trematodes.

BACKGROUND: Glutamate carboxypeptidase 2 (GCP2) belongs to the M28B metalloprotease subfamily encompassing a variety of zinc-dependent exopeptidases that can be found in many eukaryotes, including unicellular organisms. Limited information exists on the physiological functions of GCP2 orthologs in mammalian tissues outside of the brain and intestine, and such data are completely absent for non-mammalian species. Here, we investigate GCP2 orthologs found in trematodes, not only as putative instrumental molecules for defining their basal function(s) but also as drug targets. METHODS: Identified genes encoding M28B proteases Schistosoma mansoni and Fasciola hepatica genomes were analyzed and annotated. Homology modeling was used to create three-dimensional models of SmM28B and FhM28B proteins using published X-ray structures as the template. For S. mansoni, RT-qPCR was used to evaluate gene expression profiles, and, by RNAi, we exploited the possible impact of knockdown on the viability of worms. Enzymes from both parasite species were cloned for recombinant expression. Polyclonal antibodies raised against purified recombinant enzymes and RNA probes were used for localization studies in both parasite species. RESULTS: Single genes encoding M28B metalloproteases were identified in the genomes of S. mansoni and F. hepatica. Homology models revealed the conserved three-dimensional fold as well as the organization of the di-zinc active site. Putative peptidase activities of purified recombinant proteins were assayed using peptidic libraries, yet no specific substrate was identified, pointing towards the likely stringent substrate specificity of the enzymes. The orthologs were found to be localized in reproductive, digestive, nervous, and sensory organs as well as parenchymal cells. Knockdown of gene expression by RNAi silencing revealed that the genes studied were non-essential for trematode survival under laboratory conditions, reflecting similar findings for GCP2 KO mice. CONCLUSIONS: Our study offers the first insight to our knowledge into M28B protease orthologs found in trematodes. Conservation of their three-dimensional structure, as well as tissue expression pattern, suggests that trematode GCP2 orthologs may have functions similar to their mammalian counterparts and can thus serve as valuable models for future studies aimed at clarifying the physiological role(s) of GCP2 and related subfamily proteases.

Optical characterization of inhomogeneous thin films with randomly rough boundaries exhibiting wide intervals of spatial frequencies.

Results concerning the optical characterization of two inhomogeneous polymer-like thin films deposited by the plasma enhanced chemical vapor deposition onto silicon single crystal substrates are presented. One of these films is deposited onto a smooth silicon surface while the latter film is deposited on a randomly rough silicon surface with a wide interval of spatial frequencies. A combination of variable-angle spectroscopic ellipsometry and spectroscopic reflectometry applied at near-normal incidence are utilized for characterizing both the films. An inhomogeneity of the films is described by the method based on multiple-beam interference of light and method replacing inhomogeneous thin films by multilayer systems. Homogeneous transition layers between the films and substrates are considered. The Campi-Coriasso dispersion model is used to express spectral dependencies of the optical constants of the polymer-like films and transition layers. A combination of the scalar diffraction theory and Rayleigh-Rice theory is used to include boundary roughness into formulae for the optical quantities of the rough polymer-like film. Within the optical characterization, the spectral dependencies of the optical constants at the upper and lower boundaries of both the polymer-like films are determined together with their thickness values and profiles of the optical constants. Roughness parameters are determined for the rough film. The values of the roughness parameters are confirmed by atomic force microscopy. Moreover, the optical constants and thicknesses of both the transition layers are determined. A discussion of the achieved results for both the polymer-like films and transition layers is performed.

When to assess residual anal sphincter defect after OASI by ultrasound.

OBJECTIVES: Obstetrical anal sphincter injuries (OASIS) are complications of vaginal delivery. Unrepaired anal sphincter after delivery increases the risk of anal incontinence. The aim of our study is to search for residual defect after OASI repair by 4D introital ultrasound (US). We hypothesised that imaging prior to hospital discharge would show the same number of defects as assessment at 3 months. STUDY DESIGN: This is a retrospective analysis of 138 patients with immediate repair after OASIS. Since 2009, we have been routinely inviting all our patients with OASIS to the perineal clinic for postoperative follow-up. We scheduled the first visit before discharge from hospital and followed up with a second visit after three months. During both visits, patients underwent transperineal 4D ultrasound examination. We provided examination while at rest and during contraction; volumes were saved for further evaluation. RESULTS: Eighty-one patients (58.7%) completed both exams and were included in the analysis. Residual external anal sphincter defect was found in 17.3% at the first visit versus 13.6% at the second (delayed) visit. We were not able to assess the sphincter in 9.9% at early versus none in the delayed examination. In 9.9%, the residual defect was not confirmed by the second examination, and in 4.9% the residual defect was missed by the first examination. CONCLUSIONS: In conclusion, we have found that a 3 month scan yields a smaller number of defects than a scan before discharge.

Vibronic Coupling through the Continuum in the e+CO_{2} System.

We report two-dimensional electron energy-loss spectra of CO_{2}. The high-resolution experiment reveals a counterintuitive fine structure at energy losses where CO_{2} states form a vibrational pseudocontinuum. Guided by the symmetry of the system, we constructed a four-dimensional nonlocal model for the vibronic dynamics involving two shape resonances (forming a Renner-Teller Π_{u} doublet at the equilibrium geometry) coupled to a virtual Σ_{g}^{+} state. The model elucidates the extremely non-Born-Oppenheimer dynamics of the coupled nuclear motion and explains the origin of the observed structures. It is a prototype of the vibronic coupling of metastable states in continuum.

Chronic kidney disease and pregnancy outcomes.

Pregnancy complicated by CKD is currently not fully understood topic. Outcome of pregnancy in patients with CKD is related to impaired glomerular filtration rate and the degree of proteinuria. In our study we evaluated the association of serum creatinine level and proteinuria with both maternal and fetal outcomes in the cohort of 84 pregnant patients with CKD. In CKD group we confirmed negative correlation of highest serum creatinine level in pregnancy to fetal weight (p value < 0.001) and gestation period (p value < 0.001). Likewise, negative correlation of preconception serum creatinine to fetal weight (p value < 0.001) and gestation period (p value 0.002). Negative correlation of proteinuria to gestation period (p value < 0.001) and fetal weight (p value < 0.001) was also demonstrated. CKD is serious risk factor for pregnancy outcome. Proteinuria and serum creatinine level should be examined before pregnancy and regularly monitored during pregnancy. Higher serum creatinine levels and higher proteinuria predispose to shorter gestation period and lower birth weight of the neonate.

Aegilops tauschii genome assembly Aet v5.0 features greater sequence contiguity and improved annotation.

Aegilops tauschii is the donor of the D subgenome of hexaploid wheat and an important genetic resource. The reference-quality genome sequence Aet v4.0 for Ae. tauschii acc. AL8/78 was therefore an important milestone for wheat biology and breeding. Further advances in sequencing acc. AL8/78 and release of the Aet v5.0 sequence assembly are reported here. Two new optical maps were constructed and used in the revision of pseudomolecules. Gaps were closed with Pacific Biosciences long-read contigs, decreasing the gap number by 38,899. Transposable elements and protein-coding genes were reannotated. The number of annotated high-confidence genes was reduced from 39,635 in Aet v4.0 to 32,885 in Aet v5.0. A total of 2245 biologically important genes, including those affecting plant phenology, grain quality, and tolerance of abiotic stresses in wheat, was manually annotated and disease-resistance genes were annotated by a dedicated pipeline. Disease-resistance genes encoding nucleotide-binding site domains, receptor-like protein kinases, and receptor-like proteins were preferentially located in distal chromosome regions, whereas those encoding transmembrane coiled-coil proteins were dispersed more evenly along the chromosomes. Discovery, annotation, and expression analyses of microRNA (miRNA) precursors, mature miRNAs, and phasiRNAs are reported, including miRNA target genes. Other small RNAs, such as hc-siRNAs and tRFs, were characterized. These advances enhance the utility of the Ae. tauschii genome sequence for wheat genetics, biotechnology, and breeding.

Obstetric anal sphincter injury and anal incontinence.

OBJECTIVE: The aim of our study is to clarify the problems of OASI (obstetric anal sphincter injuries) and anal incontinence and prevention of this injury. METHODS: Review of articles in peer reviewed journals with the usage of Google Scholar function and PubMed. CONCLUSION: OASI is a severe injury which is more commonly associated with assisted vaginal delivery. This injury cannot be fully prevented, but its incidence can be averted by the usage of selective mediolateral episiotomy, or by other precautionary moves in high risk patients. The treatment of anal incontinence after OASI requires a complex approach and thorough examination. At first delivery, OASI is not a stern indication for caesarean section in accordance with current state of knowledge.

Spatial expression pattern of serine proteases in the blood fluke Schistosoma mansoni determined by fluorescence RNA in situ hybridization.

BACKGROUND: The blood flukes of genus Schistosoma are the causative agent of schistosomiasis, a parasitic disease that infects more than 200 million people worldwide. Proteases of schistosomes are involved in critical steps of host-parasite interactions and are promising therapeutic targets. We recently identified and characterized a group of S1 family Schistosoma mansoni serine proteases, including SmSP1 to SmSP5. Expression levels of some SmSPs in S. mansoni are low, and by standard genome sequencing technologies they are marginally detectable at the method threshold levels. Here, we report their spatial gene expression patterns in adult S. mansoni by the high-sensitivity localization assay. METHODOLOGY: Highly sensitive fluorescence in situ RNA hybridization (FISH) was modified and used for the localization of mRNAs encoding individual SmSP proteases (including low-expressed SmSPs) in tissues of adult worms. High sensitivity was obtained due to specifically prepared tissue and probes in combination with the employment of a signal amplification approach. The assay method was validated by detecting the expression patterns of a set of relevant reference genes including SmCB1, SmPOP, SmTSP-2, and Sm29 with localization formerly determined by other techniques. RESULTS: FISH analysis revealed interesting expression patterns of SmSPs distributed in multiple tissues of S. mansoni adults. The expression patterns of individual SmSPs were distinct but in part overlapping and were consistent with existing transcriptome sequencing data. The exception were genes with significantly low expression, which were also localized in tissues where they had not previously been detected by RNA sequencing methods. In general, SmSPs were found in various tissues including reproductive organs, parenchymal cells, esophagus, and the tegumental surface. CONCLUSIONS: The FISH-based assay provided spatial information about the expression of five SmSPs in adult S. mansoni females and males. This highly sensitive method allowed visualization of low-abundantly expressed genes that are below the detection limits of standard in situ hybridization or by RNA sequencing. Thus, this technical approach turned out to be suitable for sensitive localization studies and may also be applicable for other trematodes. The results suggest that SmSPs may play roles in diverse processes of the parasite. Certain SmSPs expressed at the surface may be involved in host-parasite interactions.

Co-located quantitative trait loci mediate resistance to Agrobacterium tumefaciens, Phytophthora cinnamomi, and P. pini in Juglans microcarpa × J. regia hybrids.

Soil-borne plant pathogens represent a serious threat that undermines commercial walnut (Juglans regia) production worldwide. Crown gall, caused by Agrobacterium tumefaciens, and Phytophthora root and crown rots, caused by various Phytophthora spp., are among the most devastating walnut soil-borne diseases. A recognized strategy to combat soil-borne diseases is adoption of resistant rootstocks. Here, resistance to A. tumefaciens, P. cinnamomi, and P. pini is mapped in the genome of Juglans microcarpa, a North American wild relative of cultivated walnut. Half-sib J. microcarpa mother trees DJUG 31.01 and DJUG 31.09 were crossed with J. regia cv. Serr, producing 353 and 400 hybrids, respectively. Clonally propagated hybrids were genotyped by sequencing to construct genetic maps for the two populations and challenged with the three pathogens. Resistance to each of the three pathogens was mapped as a major QTL on the long arm of J. microcarpa chromosome 4D and was associated with the same haplotype, designated as haplotype b, raising the possibility that the two mother trees were heterozygous for a single Mendelian gene conferring resistance to all three pathogens. The deployment of this haplotype in rootstock breeding will facilitate breeding of a walnut rootstock resistant to both crown gall and Phytophthora root and crown rots.

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly.

Until recently, achieving a reference-quality genome sequence for bread wheat was long thought beyond the limits of genome sequencing and assembly technology, primarily due to the large genome size and > 80% repetitive sequence content. The release of the chromosome scale 14.5-Gb IWGSC RefSeq v1.0 genome sequence of bread wheat cv. Chinese Spring (CS) was, therefore, a milestone. Here, we used a direct label and stain (DLS) optical map of the CS genome together with a prior nick, label, repair and stain (NLRS) optical map, and sequence contigs assembled with Pacific Biosciences long reads, to refine the v1.0 assembly. Inconsistencies between the sequence and maps were reconciled and gaps were closed. Gap filling and anchoring of 279 unplaced scaffolds increased the total length of pseudomolecules by 168 Mb (excluding Ns). Positions and orientations were corrected for 233 and 354 scaffolds, respectively, representing 10% of the genome sequence. The accuracy of the remaining 90% of the assembly was validated. As a result of the increased contiguity, the numbers of transposable elements (TEs) and intact TEs have increased in IWGSC RefSeq v2.1 compared with v1.0. In total, 98% of the gene models identified in v1.0 were mapped onto this new assembly through development of a dedicated approach implemented in the MAGAAT pipeline. The numbers of high-confidence genes on pseudomolecules have increased from 105 319 to 105 534. The reconciled assembly enhances the utility of the sequence for genetic mapping, comparative genomics, gene annotation and isolation, and more general studies on the biology of wheat.