Capturing the generation and structural transformations of molecular ions.

Molecular ions are ubiquitous and play pivotal roles1-3 in many reactions, particularly in the context of atmospheric and interstellar chemistry4-6. However, their structures and conformational transitions7,8, particularly in the gas phase, are less explored than those of neutral molecules owing to experimental difficulties. A case in point is the halonium ions9-11, whose highly reactive nature and ring strain make them short-lived intermediates that are readily attacked even by weak nucleophiles and thus challenging to isolate or capture before they undergo further reaction. Here we show that mega-electronvolt ultrafast electron diffraction (MeV-UED)12-14, used in conjunction with resonance-enhanced multiphoton ionization, can monitor the formation of 1,3-dibromopropane (DBP) cations and their subsequent structural dynamics forming a halonium ion. We find that the DBP+ cation remains for a substantial duration of 3.6 ps in aptly named 'dark states' that are structurally indistinguishable from the DBP electronic ground state. The structural data, supported by surface-hopping simulations15 and ab initio calculations16, reveal that the cation subsequently decays to iso-DBP+, an unusual intermediate with a four-membered ring containing a loosely bound17,18 bromine atom, and eventually loses the bromine atom and forms a bromonium ion with a three-membered-ring structure19. We anticipate that the approach used here can also be applied to examine the structural dynamics of other molecular ions and thereby deepen our understanding of ion chemistry.

Direct observation of ultrafast hydrogen bond strengthening in liquid water.

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network1, including unusually efficient vibrational energy redistribution and relaxation2. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments2-7. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here, we measure the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of approximately 1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on femtosecond timescales. Our experiment and simulations unveil the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

Photo-induced structural dynamics of o-nitrophenol by ultrafast electron diffraction.

The photo-induced dynamics of o-nitrophenol, particularly its photolysis, has garnered significant scientific interest as a potential source of nitrous acid in the atmosphere. Although the photolysis products and preceding photo-induced electronic structure dynamics have been investigated extensively, the nuclear dynamics accompanying the non-radiative relaxation of o-nitrophenol on the ultrafast timescale, which include an intramolecular proton transfer step, have not been experimentally resolved. Herein, we present a direct observation of the ultrafast nuclear motions mediating photo-relaxation using ultrafast electron diffraction. This work spatiotemporally resolves the loss of planarity which enables access to a conical intersection between the first excited state and the ground state after the proton transfer step, on the femtosecond timescale and with sub-Angstrom resolution. Our observations, supported by ab initio multiple spawning simulations, provide new insights into the proton transfer mediated relaxation mechanism in o-nitrophenol.

Femtosecond Electronic and Hydrogen Structural Dynamics in Ammonia Imaged with Ultrafast Electron Diffraction.

Directly imaging structural dynamics involving hydrogen atoms by ultrafast diffraction methods is complicated by their low scattering cross sections. Here we demonstrate that megaelectronvolt ultrafast electron diffraction is sufficiently sensitive to follow hydrogen dynamics in isolated molecules. In a study of the photodissociation of gas phase ammonia, we simultaneously observe signatures of the nuclear and corresponding electronic structure changes resulting from the dissociation dynamics in the time-dependent diffraction. Both assignments are confirmed by ab initio simulations of the photochemical dynamics and the resulting diffraction observable. While the temporal resolution of the experiment is insufficient to resolve the dissociation in time, our results represent an important step towards the observation of proton dynamics in real space and time.

Room temperature mid-infrared fiber lasing beyond 5 µm in chalcogenide glass small-core step index fiber.

This Letter, to the best of our knowledge, reports mid-infrared fiber lasing beyond 5 µm at room temperature for the first time, Ce3+-doped, chalcogenide glass, step index fiber employed in-band pumping with a 4.15 µm quantum cascade laser. The lasing fiber is was 64 mm long, with a calculated numerical aperture of 0.48 at the lasing wavelengths. The core glass was Ge15As21Ga1Se63 atomic % (at. %), doped with 500 parts-per-million-by-weight Ce, with a 9 µm core diameter. The cladding glass was Ge21Sb10Se69 at. % with a 190 µm outer diameter. As pump power increases continuous wave lasing corresponding to the 2F7/2→2F5/2, transition in the Ce3+ ion occurs at 5.14 µm, 5.17 µm, and 5.28 µm.

Strong-field induced fragmentation and isomerization of toluene probed by ultrafast femtosecond electron diffraction and mass spectrometry.

We investigate the fragmentation and isomerization of toluene molecules induced by strong-field ionization with a femtosecond near-infrared laser pulse. Momentum-resolved coincidence time-of-flight ion mass spectrometry is used to determine the relative yield of different ionic products and fragmentation channels as a function of laser intensity. Ultrafast electron diffraction is used to capture the structure of the ions formed on a picosecond time scale by comparing the diffraction signal with theoretical predictions. Through the combination of the two measurements and theory, we are able to determine the main fragmentation channels and to distinguish between ions with identical mass but different structures. In addition, our diffraction measurements show that the independent atom model, which is widely used to analyze electron diffraction patterns, is not a good approximation for diffraction from ions. We show that the diffraction data is in very good agreement with ab initio scattering calculations.

Structure retrieval in liquid-phase electron scattering.

Electron scattering on liquid samples has been enabled recently by the development of ultrathin liquid sheet technologies. The data treatment of liquid-phase electron scattering has been mostly reliant on methodologies developed for gas electron diffraction, in which theoretical inputs and empirical fittings are often needed to account for the atomic form factor and remove the inelastic scattering background. In this work, we present an alternative data treatment method that is able to retrieve the radial distribution of all the charged particle pairs without the need of either theoretical inputs or empirical fittings. The merits of this new method are illustrated through the retrieval of real-space molecular structure from experimental electron scattering patterns of liquid water, carbon tetrachloride, chloroform, and dichloromethane.

Checklist of nematodes parasitizing fish in the Brazilian Amazon.

This study presents a list of parasitic fish nematodes from the Brazilian Amazon based on the previous Brazilian list including scientific assessments carried out between 2010 and 2021. A total of 16 families, 48 species and 28 undetermined species of nematodes associated with fish are included in the checklist, in addition to 93 host species and 15 geographical records.

The effect of denudation and injection timing in the reproductive outcomes of ICSI cycles: new insights into the risk of in vitro oocyte ageing.

STUDY QUESTION: Does the time elapsed between oocyte pick-up (OPU) and denudation or injection affect the probability of achieving a live birth (LB) in ICSI cycles? SUMMARY ANSWER: Prolonged oocyte culture before denudation (>4 h) was associated with an increase in clinical pregnancy (CP), LB and cumulative LB (CLB) rates when compared with earlier denudation timings. WHAT IS KNOWN ALREADY: Oocyte maturation is a complex and dynamic process involving structural and biochemical modifications in the cell necessary to support fertilization and early embryo development. While meiotic competence is easily identifiable by the presence of an extruded first polar body, cytoplasmic maturation cannot be assessed microscopically. Culturing oocytes with their surrounding cumulus cells (CCs) prior to ICSI can enhance the completion of in vitro cytoplasmic maturation; conversely, prolonged culture may induce cell degeneration. The optimal culture intervals prior to oocyte denudation and/or injection have not yet been established and may prove relevant for the improvement of ICSI reproductive outcomes. STUDY DESIGN, SIZE, DURATION: This is a single-centre retrospective cohort analysis of 1378 ICSI cycles performed between January 2005 and October 2018. Data were categorized according to: (i) the time interval between OPU and denudation (<3 h, 3-4 h and ≥4 h), (ii) the time interval between denudation and ICSI (<1.5 h, 1.5-2 h, ≥2 h) and (iii) the time interval between OPU and ICSI (<5 h, 5-6 h and ≥6 h). The effect of these timings on fertilization, CP, LB and CLB rates were compared. The culture intervals between different procedures were dependent exclusively on laboratory workload. PARTICIPANTS/MATERIALS, SETTING, METHODS: ICSI cycles performed in women younger than 40 years old using autologous gametes with at least one metaphase II injected oocyte were included. The effect of oocyte culture duration prior to denudation and injection of the oocytes was compared using multivariable regression accounting for potential confounding variables. MAIN RESULTS AND THE ROLE OF CHANCE: Fertilization and oocyte damage rate after ICSI was found to be independent of the time interval to denudation (<3 h, 3-4 h and ≥4 h) and/or injection (<5 h, 5-6 h and ≥6 h). Extending oocyte culture before denudation significantly improved CP (29.5%, 42.7% and 50.6%, respectively), LB (25.1%, 34.4% and 40.7%, respectively) and CLB rates (26.0%, 36.1% and 42.2%, respectively), particularly if the time interval was at least 4 h. Additionally, LB (31.7%, 35.8% and 27.4%, respectively) and CLB rates (34.2%, 36.6% and 27.7%, respectively) were also dependent on the time from OPU to injection. LIMITATIONS, REASONS FOR CAUTION: This study is limited by its retrospective nature and potential unmeasured confounding cannot be excluded. Furthermore, the effect of even shorter or longer periods of culture before denudation and/or injection were not evaluated and should not be extrapolated from these results. WIDER IMPLICATIONS OF THE FINDINGS: Our findings propose new evidence of a previously unrecognized protective effect of the CCs-oocyte interactions in human ART, raising the question of a possible downstream effect in embryogenesis which significantly affects LB rates. Additionally, this is the first study to suggest a negative effect of further extending culture before ICSI on LB and CLB rates, thus potentially allowing for the narrowing of an optimal ICSI time interval. Simple strategies such as the establishment of more effective time frames to perform these procedures and adjusting laboratory practice may prove beneficial, ultimately improving ICSI reproductive outcomes. STUDY FUNDING/COMPETING INTEREST(S): None. TRIAL REGISTRATION NUMBER: N/A.

Genome-wide association study reveals genes associated with the absence of intermuscular bones in tambaqui (Colossoma macropomum).

The presence of intermuscular bones in fisheries products limits the consumption and commercialization potential of many fish species, including tambaqui (Colossoma macropomum). These bones have caused medical emergencies and are an undesirable characteristic for fish farming because their removal is labor-intensive during fish processing. Despite the difficulty in identifying genes related to the lack of intermuscular bone in diverse species of fish, the discovery of individuals lacking intermuscular bones in a Neotropical freshwater characiform fish has provided a unique opportunity to delve into the genetic mechanisms underlying the pathways of intermuscular bone formation. In this study, we carried out a GWAS among boneless and wt tambaqui populations to identify markers associated with a lack of intermuscular bone. After analyzing 11 416 SNPs in 360 individuals (12 boneless and 348 bony), we report 675 significant (Padj  < 0.003) associations for this trait. Of those, 13 associations were located near candidate genes related to the reduction of bone mass, promotion of bone formation, inhibition of bone resorption, central control of bone remodeling, bone mineralization and other related functions. To the best of our knowledge, for the first time, we have successfully identified genes related to a lack of intermuscular bones using GWAS in a non-model species.

Oral potentially malignant disorders: clinical-pathological study of 684 cases diagnosed in a Brazilian population.

BACKGROUND: The frequency and distribution of oral potentially malignant disorders (OPMD) may vary among different populations. The aim of the present study was to evaluate the clinical-pathological characteristics of OPMD diagnosed in a Brazilian oral pathology laboratory over a period of 11 years. MATERIAL AND METHODS: All cases diagnosed as leukoplakia, speckled leukoplakia, erythroplakia, and actinic cheilitis from 2005 to 2015 were analyzed. Clinical information was obtained from laboratory forms and histological information was obtained from histological slides stained with hematoxylin and eosin. RESULTS: the final sample was comprised of 684 cases, of which 292 were males and 392 were females. The mean age was 58 years. The anatomical site most often involved was the lateral border of the tongue (23%), followed by the lower lip (20%), and by the buccal mucosa/vestibule (18%). Leukoplakia accounted for 82% of the sample (564 cases). The mean size of the leukoplakia and speckled leukoplakia lesions was 13 mm (ranging from 1 to 100 mm) and 15 mm (ranging from 5 to 30 mm), respectively (p=0.460). Males reported smoking and drinking alcohol more frequently than females (p=0.001 and p<0.0001, respectively). In half of the cases, dysplasia was not histologically detected, while slight dysplasia was detected in 28% of the cases. The lesions from patients aged from 41 to 80 years presented moderate and severe dysplasia more often than lesions from patients in other age groups. CONCLUSIONS: OPMD were more common in females in their sixties. Females were more frequently affected in all anatomical sites, except for the lips. Leukoplakia lesions were the most common OPMD, followed by actinic cheilitis. The lateral border of the tongue was the most affected anatomical site. OPMD located in the floor of the mouth/sublingual mucosa and lesions from older patients presented severe epithelial dysplasia with greater frequency.

Different outcomes of a cardiac rehabilitation programme in functional parameters among myocardial infarction survivors according to ejection fraction.

INTRODUCTION: Exercise-based cardiac rehabilitation (EBCR) is part of the management of patients who have suffered an acute myocardial infarction (AMI). Patients with a reduced ejection fraction (EF) comprise a higher-risk subgroup and are referred less often for these programmes. This study aimed at assessing the impact of the baseline EF on the functional benefits, as assessed by peak oxygen uptake (pVO2) and exercise duration, of an EBCR programme in AMI survivors. METHODS: Observational, retrospective cohort study including all patients admitted to a tertiary centre due to an AMI who completed a phase II EBCR programme after discharge, between November 2012 and April 2017. Functional parameters were assessed by a symptom-limited cardiopulmonary exercise test. RESULTS: A total of 379 patients were included [40.9% with reduced EF (<50%) at discharge]. After the programme, pVO2 and exercise duration increased significantly (p < 0.001). Patients with a reduced EF had a lower pVO2 and completed a shorter duration of exercise at the beginning and end of the programme. This group presented a higher increase in pVO2 (p = 0.001) and exercise duration (p = 0.007). This was maintained after adjusting for age, gender, history of coronary artery disease, number of sessions, Killip classification, arterial hypertension, dyslipidaemia, diabetes mellitus, smoking status and baseline pVO2. CONCLUSION: A phase II EBCR programme was associated with significant improvements in pVO2 and exercise duration among AMI survivors, irrespective of baseline EF classification. Those with a reduced baseline EF derived an even greater improvement, highlighting the importance of EBCR in this subgroup of patients.

Surgery in ovarian cancer - Brazilian Society of Surgical Oncology consensus.

Surgical management in epithelial ovarian cancer (EOC) has a significant impact in overall survival and progression-free survival. The Brazilian Society of Surgical Oncology (BSSO) supported a taskforce of experts to reach a consensus: experienced and specialised trained surgeons, in cancer centres, provide the best EOC surgery. Laparoscopic and/or radiological staging prognosticates the possibility of complete cytoreduction (CC0) and helps to reduce unnecessary laparotomies. Surgical techniques were reviewed. Multidisciplinary input is essential for treatment planning. Quality assurance criteria are proposed and require national consensus. Genetic testing is mandatory. This consensus states the final recommendations from BSSO for management of EOC. TWEETABLE ABSTRACT: Brazilian Society of Surgical Oncology consensus for surgery in epithelial ovarian cancer patients.

Predicting the effectiveness of different mulching techniques in reducing post-fire runoff and erosion at plot scale with the RUSLE, MMF and PESERA models.

Wildfires have become a recurrent threat for many Mediterranean forest ecosystems. The characteristics of the Mediterranean climate, with its warm and dry summers and mild and wet winters, make this a region prone to wildfire occurrence as well as to post-fire soil erosion. This threat is expected to be aggravated in the future due to climate change and land management practices and planning. The wide recognition of wildfires as a driver for runoff and erosion in burnt forest areas has created a strong demand for model-based tools for predicting the post-fire hydrological and erosion response and, in particular, for predicting the effectiveness of post-fire management operations to mitigate these responses. In this study, the effectiveness of two post-fire treatments (hydromulch and natural pine needle mulch) in reducing post-fire runoff and soil erosion was evaluated against control conditions (i.e. untreated conditions), at different spatial scales. The main objective of this study was to use field data to evaluate the ability of different erosion models: (i) empirical (RUSLE), (ii) semi-empirical (MMF), and (iii) physically-based (PESERA), to predict the hydrological and erosive response as well as the effectiveness of different mulching techniques in fire-affected areas. The results of this study showed that all three models were reasonably able to reproduce the hydrological and erosive processes occurring in burned forest areas. In addition, it was demonstrated that the models can be calibrated at a small spatial scale (0.5 m2) but provide accurate results at greater spatial scales (10 m2). From this work, the RUSLE model seems to be ideal for fast and simple applications (i.e. prioritization of areas-at-risk) mainly due to its simplicity and reduced data requirements. On the other hand, the more complex MMF and PESERA models would be valuable as a base of a possible tool for assessing the risk of water contamination in fire-affected water bodies and for testing different land management scenarios.

Comparison of three different extenders on Murrah buffaloes (Bubalus bubalis) semen freezability.

The use of frozen semen for artificial insemination is the main approach utilised for the genetic improvement of most domesticated species. The advantages include lower transportation costs, continuous availability of semen, fewer occurrences of sexually transmitted diseases and the incorporation of desirable genes in a relatively short amount of time. Nevertheless, the use of frozen semen in buffalo herds remains limited due to the loss of sperm quality when buffalo semen is frozen. So, the goal of this study was to evaluate the pre- and post-cryopreservation quality of buffalo semen diluted in three distinct freezing media: Tris-egg yolk, Botu-bov® (BB) and ACP-111®. Thirty-two ejaculates from four bulls were analysed in terms of kinetics, morphology and sperm viability by epifluorescence microscope. Thawed samples were also evaluated for capacitation-like damage, DNA fragmentation and plasma and acrosomal membrane integrity using flow cytometry. The Tris-egg yolk and BB® extenders yielded better results than the ACP-111® extender for kinetics parameter (total motility, progressive motility and percentage of rapid cells). However, semen samples were similar for parameters evaluated by flow cytometry. Taken together, the data indicate that in comparison with Tris-egg yolk and BB extender, ACP-111® can also be used as an extender for buffalo semen cryopreservation.

Helminths Infecting the Cat-eyed Snake Leptodeira Annulata Linnaeus 1758 (Squamata: Dipsadidae) in a Semiarid Region of Brazil.

Snakes have diverse feeding and living habits, being exposed to a variety of endoparasite communities. However, more studies are still necessary to document these relationships. We examined 18 specimens of the cat-eyed snake Leptodeira annulata from a semi-arid region in Northeast Brazil. Eight taxa of parasites were found, with higher prevalence of cystacanths (Acanthocephala). Five nematode species (Hexametra boddaertii, Oswaldocruzia sp., Oxyascaris sp., Physaloptera sp. and Raillietnema spectans) and the pentastome Raillietiella furcocerca represent a new parasitism record for the host studied. Our results also showed that L. annulata could act as paratenic host for acanthocephalans. These results contribute to the knowledge of the helminth fauna of L. annulata.

SISSY: An efficient and automatic algorithm for the analysis of EEG sources based on structured sparsity.

Over the past decades, a multitude of different brain source imaging algorithms have been developed to identify the neural generators underlying the surface electroencephalography measurements. While most of these techniques focus on determining the source positions, only a small number of recently developed algorithms provides an indication of the spatial extent of the distributed sources. In a recent comparison of brain source imaging approaches, the VB-SCCD algorithm has been shown to be one of the most promising algorithms among these methods. However, this technique suffers from several problems: it leads to amplitude-biased source estimates, it has difficulties in separating close sources, and it has a high computational complexity due to its implementation using second order cone programming. To overcome these problems, we propose to include an additional regularization term that imposes sparsity in the original source domain and to solve the resulting optimization problem using the alternating direction method of multipliers. Furthermore, we show that the algorithm yields more robust solutions by taking into account the temporal structure of the data. We also propose a new method to automatically threshold the estimated source distribution, which permits to delineate the active brain regions. The new algorithm, called Source Imaging based on Structured Sparsity (SISSY), is analyzed by means of realistic computer simulations and is validated on the clinical data of four patients.

Waist-to-height ratio is independently related to whole and central body fat, regardless of the waist circumference measurement protocol, in non-alcoholic fatty liver disease patients.

BACKGROUND: Waist-to-height ratio (WHtR) has been reported as a preferable risk related body fat (BF) marker, although no standardised waist circumference measurement protocol (WCmp) has been proposed. The present study aimed to investigate whether the use of a different WCmp affects the strength of relationship between WHtR and both whole and central BF in non-alcoholic fatty liver disease (NAFLD) patients. METHODS: BF was assessed with dual energy X-ray absorptiometry (DXA) in 28 NAFLD patients [19 males, mean (SD) 51 (13) years and nine females, 47 (13) years]. All subjects also underwent anthropometric evaluation including height and waist circumference (WC) measurement using four different WCmp (WC1, minimal waist; WC2, iliac crest; WC3, mid-distance between iliac crest and lowest rib; WC4, at the umbilicus) and WHtR was calculated using each WC measurements (WHtR1, WHtR2, WHtR3 and WHtR4, respectively). Partial correlations were conducted to assess the relation of WHtR and DXA assessed BF. RESULTS: All WHtR were particularly correlated with central BF, including abdominal BF (r = 0.80, r = 0.84, r = 0.84 and r = 0.78, respectively, for WHtR1, WHtR2, WHtR3 and WHtR4) and central abdominal BF (r = 0.72, r = 0.77, r = 0.76 and r = 0.71, respectively, for WHtR1, WHtR2, WHtR3 and WHtR4), after controlling for age, sex and body mass index. There were no differences between the correlation coefficients obtained between all studied WHtR and each whole and central BF variable. CONCLUSIONS: Waist-to-height ratio was found a suitable BF marker in the present sample of NAFLD patients and the strength of the relationship between WHtR and both whole and central BF was not altered by using different WCmp in the present sample of NAFLD patients.

Genetic diversity and relatedness between Canindé and British Alpine goat breeds in Northeastern Brazil accessed by microsatellite markers.

The aim of this study was to access the genetic diversity and relatedness between Canindé and British Alpine goat breeds in the States of Piauí and Ceará using microsatellite markers. Genomic DNA was isolated from hair samples of 99 goats belonging to six different flocks. A panel of polymorphic heterologous microsatellite loci was used to genotype individuals. The microsatellite markers resulted in a total number of 145 alleles, with an average of 8.5 alleles per locus. The observed and expected heterozygosities were ≥0.687 and ≥0.627, respectively, for all loci. The polymorphic information content showed that all loci were highly informative with an overall mean of 0.757. Overall FST across all populations and loci was 18%, which was consistent with the coefficient of gene differentiation (GST = 0.104). AMOVA revealed that 12.8% of the variation was captured between breeds. The Bayesian STRUCTURE clustering detected the maximum likelihood for a model of two genetically distinct groups, in agreement with the number of predefined studied breeds and the two-dimensional plot from the PCoA analysis. The exotic British Alpine breed and the naturalized Brazilian Canindé breed were clearly differentiated by the microsatellite markers, indicating that these two breeds have distant genetic identities, despite the phenotypic similarity.