Search

We report a case of cerebral venous sinus thrombosis, bilateral adrenal hemorrhage, and thrombocytopenia in a 70-year-old man found dead. He had previously received the ChAdOx1 nCoV-19 vaccine (Vaxzevria®, AstraZeneca) 18 days before, and had since developed unspecific and undiagnosed characteristics of what proved to be a rare case of vaccine-associated thrombocytopenia with thrombosis syndrome (TTS). He was found dead 1 week after the beginning of symptoms (day 25 post-vaccine). Autopsy yielded venous hemorrhagic infarction with the presence of thrombi within dural venous sinuses, and extensive hemorrhagic necrosis of the central part of the adrenal glands. Antibodies against platelet factor 4 (PF4) were strongly positive in postmortem fluids, as measured with an enzyme-linked immunosorbent assay (ELISA). This difficult diagnosis is usually made during the patient's lifetime. After eliminating differential diagnoses, we concluded on a fatal case of vaccine-induced immune TTS with positive anti-PF4 antibodies in cadaveric blood, 3 weeks after ChAdOx1 nCoV-19 vaccination. Specific search for anti-PF4 antibodies in cadaveric blood appears therefore paramount to assess postmortem cases of TTS associated with anti-COVID vaccines.

Silvopastoral systems (SPSs) are sustainable alternatives for pasture intensification. Management practices such as thinning are options to diminish competition for resources between pasture and trees, ensuring appropriate forage production. The objective of this study was to evaluate the productive and nutritive traits of Piatã palisadegrass (Urochloa brizantha cv. BRS Piatã) after thinning the forest component of a SPS. Forage production and nutritive value, along with microclimate variables were assessed in a SPS and in an intensive system (INT) in São Carlos-SP, Brazil, from 2016 to 2018. The INT was a full sun pasture of Piatã palisadegrass, while the SPS was established with Piatã palisadegrass shaded by eucalyptus (Eucalyptus urograndis clone GG100) spaced 15 × 2 m but thinned to 15 × 4 m before the onset of the experiment. In the SPS, measurements were made under the tree row (SPS_1), 3.75-m (SPS_2), 7.5-m (SPS_3) and 11.25-m (SPS_4) distant from the North row. Forage accumulation in the two systems were similar, whereas the pre-grazing forage mass in most of the SPS positions were smaller than that of the INT during the autumn of 2017 and summer of 2018. Crude protein (CP) content was greater in the SPS than in the INT in most positions and seasons. Forage production was favoured by the thinning of the trees mainly in the seasons close to the event, while forage CP was consistently greater in the understory pasture. Thinning of trees in SPSs can be adopted to provide forage production similar to intensive pastures with higher protein content.

Soil organic matter (SOM) plays a key role in the global carbon and nitrogen cycles. Soil biogeochemistry is regularly studied by extracting the base-soluble fractions of SOM: acidinsoluble humic acid (HA) and acid-soluble fulvic acid (FA). Electrospray ionization−Fourier transform−ion cyclotron resonance−mass spectrometry (ESI-FT-ICR-MS) is commonly utilized for molecularly characterizing these fractions. Different sample preparation techniques exist for the analysis of HA and FA though questions remain regarding data comparability following different preparations. Comparisons of different sample preparation techniques here revealed that the negative-mode ESI-FT-ICRMS analytical window can be skewed to detect different groups of molecules, with primary differences in oxygenation, aromaticity, and molecular weight. It was also observed that HA and FA from soils versus an aquatic matrix behaved very differently. Thus, we conclude that sample preparation techniques determined to be ?most optimal? in our study are in no way universal. We recommend that future studies of HA and FA involve similar comparative studies for determining the most suitable sample preparation technique for their particular type of HA or FA matrices. This will enhance data comparability among different studies and environmental systems and ultimately allow us to better understand the complex composition of environmental matrices. Made available in DSpace on 2022-09-28T18:06:04Z (GMT). No. of bitstreams: 1 P-Comparison-of-Sample-Preparation-Techniques-for-the-8722ESI-FTICR-MS-Analysis-of-Humic-and-Fulvic-Acids.pdf: 4440230 bytes, checksum: b5f1ae1f920e91892bfd9853652654d3 (MD5) Previous issue date: 2022

Mammalian orthoreoviruses (reoviruses) serve as potential triggers of celiac disease and have oncolytic properties, making these viruses potential cancer therapeutics. Primary attachment of reovirus to host cells is mainly mediated by the trimeric viral protein, σ1, which engages cell-surface glycans, followed by high-affinity binding to junctional adhesion molecule-A (JAM-A). This multistep process is thought to be accompanied by major conformational changes in σ1, but direct evidence is lacking. By combining biophysical, molecular, and simulation approaches, we define how viral capsid protein mechanics influence virus-binding capacity and infectivity. Single-virus force spectroscopy experiments corroborated by in silico simulations show that GM2 increases the affinity of σ1 for JAM-A by providing a more stable contact interface. We demonstrate that conformational changes in σ1 that lead to an extended rigid conformation also significantly increase avidity for JAM-A. Although its associated lower flexibility impairs multivalent cell attachment, our findings suggest that diminished σ1 flexibility enhances infectivity, indicating that fine-tuning of σ1 conformational changes is required to successfully initiate infection. Understanding properties underlying the nanomechanics of viral attachment proteins offers perspectives in the development of antiviral drugs and improved oncolytic vectors.

The conversion of native vegetation into agricultural lands is often associated with a decrease in soil C. The soils from the Brazilian savannah (named Cerrado), with 200 million hectares, are rich in Fe and Al (hydr)oxides, which could result in more organo-mineral associations and lead to particularly high C storage. The changes in the C stocks from the conversion of native forest into degraded pasture (DP), and the adoption of proper management to recover DP and increase C stocks in such Ferralsols are not well understood. To provide insights into the drivers of C storage, this study compared the C stocks across depth in the top 1m and the distribution of C in the soil fractions 24 years after the adoption of different management systems in degraded pastures in the Brazilian Cerrado.A DP area located in São Carlos, São Paulo, Brazil was converted into different management systems: (i) RMS: rainfed pasture with moderate animal stocking rate, (ii) RHS: rainfed pasture with higher animal stocking rate, and (iii) IHS: irrigated pasture with higher stocking rate. As a control, the adjacent native vegetation (FO) was also evaluated. The adoption of management started in 1996 with RMS and in 2002 for RHS and IHS. Except for the DP, all areas were limed and N-fertilized. RMS with 200 kg N ha, RHS 400 kg N ha, and IHS with 600 kg N ha. Soil sampling was carried out in 2020 and the C stocks were evaluated up to 1 m deep. To state vegetation change from C3 (native forest) to C4 (introduced pasture) the isotopic natural abundance of 13C was analyzed. To evaluate the contribution of mineral-associated and particulate organic matter forms to C storage, we performed a physical fractionation by size and density with SPT 1.8 g cm-3, respectively.Our results showed that the conversion of FO into DP decreased soil C stocks. Otherwise, the adoption of management in DP with RMS and RHS increased C stocks achieving levels similar to FO. RMS showed the highest C stocks with the lower dosage of N-fertilizer and animal stocking rate. IHS area did not increase their C stocks compared to DP, which may be related to limited root growth after irrigation decreasing the C input. Around 50% of the C stocks in RHS and RMS systems are pasture-derived (C4 plants) according to the 13C abundance. This shows that half of C stocks from rainfed pastures is of preserved organic matter from previous FO. While in the IHS and DP systems, the organic matter composition is mainly pasture-derived. Our preliminary data showed that the RMS topsoil contained more free particulate organic matter than the FO, suggesting that the C stocks were enhanced mainly by pasture-derived biomass input. The contribution of mineral-associated organic matter still will be evaluated.Our study shows that the recovery of degraded pasture soils by management leads to increased OC stocks derived from fertilized pasture but also higher maintenance of OC from FO.

Frankia actinobacteria occur in northwest Patagonian steppe soils and form nitrogen-fixing actinorhizal symbiotic root nodules with Ochetophila trinervis (Rhamnaceae). Soil disturbances affect soilborne Frankia, reducing the likelihood of establishing symbiosis, as found for Pinus ponderosa plantations in the region. The effect on local actinorhizal symbionts of other kinds of disturbance such as the ash that was deposited by the eruption of the Puyehue-Cordon Caulle (PCC) volcanic complex was unknown. We studied the initial succession steps for the Frankia colonization process and the soil change that might affect the establishment of symbiosis as a result of the combined action of volcanic ash deposition and P. ponderosa afforestation by comparing pre- and post-eruption time points. We collected soil and ash samples at three depths to use in plant bioassays with O. trinervis. These samples were also used to determine chemical properties (soil and ashes) and elemental composition (soil). Infective Frankia gradually colonized the ash deposited in steppe soils via soil legacy and immigration. The higher nodulation frequency found in plants inoculated with buried soil and deep ash than in plants inoculated with surface ash suggests that the colonization process was mainly due to soil legacy, but also, though at a slower rate, to immigration of Frankia from elsewhere. Nevertheless, the colonization process seemed to be hindered by the pine plantation establishment processes. C, N and P increased over time, favoring the establishment of Frankia and therefore the nodulation capacity of ash. The chemical and elemental characteristics of soils under natural vegetation seemed to be closer to pre-eruptive conditions than those of soils under the afforestation, and to favor nodulation capacity. The combination of ash deposition and the pine plantation appeared to have the strongest effect in impairing the restoration of previous conditions for the establishment of symbiosis with Frankia.

Viruses mutate under a variety of selection pressures, allowing them to continuously adapt to their hosts. Mutations in SARS-CoV-2 have shown effective evasion of population immunity and increased affinity to host factors, in particular to the cellular receptor ACE2. However, in the dynamic environment of the respiratory tract forces act on the binding partners, which raises the question whether not only affinity, but also force-stability of the SARS-CoV-2:ACE2 bond, might be a selection factor for mutations. Here, we use magnetic tweezers (MT) to study the effect of amino acid substitutions in variants of concern (VOCs) on RBD:ACE2 bond kinetics with and without external load. We find higher affinity for all VOCs compared to wt, in good agreement with previous affinity measurements in bulk. In contrast, Alpha is the only VOC that shows significantly higher force stability compared to wt. Investigating the RBD:ACE2 interactions with molecular dynamics simulations, we are able to rationalize the mechanistic molecular origins of this increase in force-stability. Our study emphasizes the diversity of contributions to the assertiveness of variants and establishes force-stability as one of several factors for fitness. Understanding fitness-advantages opens the possibility for prediction of likely mutations allowing rapid adjustment of therapeutics, vaccination, and intervention measures.

Agriculture can stock carbon on soil increasing the organic matter content, and mitigating greenhouse gas emissions. LIBS and LIFS were used to evaluate different pasture systems, which showed that well-managed pastures can increase soil carbon stock.

Purpose: During the juvenile stage, such areas as the hippocampus and corpus callosum (CC) are still immature and sensitive to stress exposure. The present study investigated whether two different types of stressors in the juvenile stage of life have a long-lasting impact on behavior and biological outcomes in adult rats. Methods: Male juvenile rats were exposed to restraint or predator stress on postnatal day 25 (P25) for 3 days. Thirty-two days later (P60-74), behavioral and biological analyses were conducted. The behavioral analysis included measures of anxiety-like behavior and recognition memory. The biological analysis investigated gross cerebral morphology, based on volume analysis of the CC and hippocampus, perirhinal cortex thickness, and dendritic spine density. Results: Neither restraint stress nor predator stress affected anxiety-like behavior or object recognition memory in adulthood. Body weight and adrenal gland weight were unaffected by both types of stress. Overall, volumetric measures of the CC and hippocampus were not significant, with no changes in perirhinal cortex thickness. Spine density in the medial prefrontal cortex also was unaffected, but a decrease in dendritic spine density was found in the hippocampus in response to restraint stress and an increase to predator stress. Conclusion: Short-term and daily restraint and predator stress during the juvenile stage had no long-lasting effects on anxiety-like behavior, object memory, volume of the CC or hippocampus, or perirhinal cortex thickness, but a decrease in dendritic spine density was found in the hippocampus. These findings suggest that different types of stressors have different impacts on microstructures in the brain without affecting behavior or the gross morphology of stress-sensitive brain areas.

SARS-CoV-2 infections are initiated by attachment of the receptor-binding domain (RBD) on the viral Spike protein to angiotensin-converting enzyme-2 (ACE2) on human host cells. This critical first step occurs in dynamic environments, where external forces act on the binding partners and multivalent interactions play critical roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using magnetic tweezers and atomic force spectroscopy as highly complementary single-molecule force spectroscopy techniques, we investigate the RBD:ACE2 interaction over the whole physiologically relevant force range. We combine the experimental results with steered molecular dynamics simulations and observe and assign fully consistent unbinding and unfolding events across the three techniques, enabling us to establish ACE2 unfolding as a molecular fingerprint. Measuring at forces of 2-5 pN, we quantify the force dependence and kinetics of the RBD:ACE2 bond in equilibrium. We show that the SARS-CoV-2 RBD:ACE2 interaction has higher mechanical stability, larger binding free energy, and a lower dissociation rate in comparison to SARS-CoV-1, which helps to rationalize the different infection patterns of the two viruses. By studying how free ACE2 outcompetes tethered ACE2, we show that our assay is sensitive to prevention of bond formation by external binders. We expect our results to provide a novel way to investigate the roles of mutations and blocking agents for targeted pharmaceutical intervention.

Wasps are a diverse group of insects that possess a sting apparatus associated with a venom gland, which is used for predation and colony defense. The biochemistry of Hymenoptera venom has been evaluated in relation to allergy and immunology, and proteomics has been shown to be a powerful tool for the identification of compounds with pharmacological potential. Data on wasps venom the of genus Apoica are scarce, so the objective of the present work was to identify the venom proteins of the eusocial wasp Apoica pallens, as a first step towards further investigation of applied uses of the venom and its protein constituents. The venom proteins were separated by two-dimensional gel electrophoresis, followed by MALDI-TOF/TOF mass spectrometry. A total of 259 spots were detected, with molecular weights from 4.9 to 141 kDa. Thirty of these proteins were identified and classified into eight functional categories: allergen, enzyme, metabolism, structural, environmental response, proteoglycan, active in DNA and RNA, and unknown function. Due to the few available proteomic data for wasp venom, many proteins could not be identified, which makes studies with proteomic analysis of Hymenoptera venom even more important.

O conhecimento da variabilidade espacial das propriedades do solo é útil para o uso racional dos insumos, como na aplicação localizada de calcário e fertilizantes nos sistemas de integração lavoura-Pecuária-Floresta (ILPF). A agricultura de precisão (PA) é a ferramenta para melhorar a eficiência do uso destes insumos. O objetivo desta pesquisa foi avaliar a aplicação calagem e de fertilizante fosfatado a taxas variáveis em um sistema ILPF. O estudo de campo foi realizado em uma área de 30 ha da Embrapa Pecuária Sudeste, em São Carlos, SP. As amostras de solo foram coletadas a 0-0,2 m de profundidade, e cada amostra representou um piquete. A variabilidade espacial das propriedades do solo e das necessidades específicas de calcário e fertilizantes foram modeladas. Os resultados mostraram que a análise espacial das necessidades de calagem e adubação podem fornecer ferramentas de gestão para o manejo de pastagens. E a tecnologia da aplicação de calcário e fertilizante fosfatado à taxa variável pode ser utilizada como ferramenta de correção e adubação do solo levando à maior homogeneidade dos atributos químicos do solo.

Resume Dans les cas souvent complexes de demembrements criminels, il est tres important de tenter de determiner le type de scie qui a ete utilise. Le but de ce travail etait d’analyser des faux departs experimentaux sur des femurs humains avec deux scies a mains possedant des TPI (teeth per inch) eleves, respectivement 15 et 32. Ces scies ont rarement ete etudiees dans la litterature medicolegale. Nous presentons ici les resultats preliminaires (30 lesions experimentales, 15 pour chaque scie etudiee). La scie no 2 (scie a refendre, TPI 32, avoyage ondule) a montre des caracteres classiques (faible largeur minimum de la lesion, profil concave, stries fines et droites). Par contre, la scie no 1 (scie universelle a dents isoceles, TPI 15, avoyage alterne) a revele des caracteres inattendus : largeur minimum de la lesion faible, murs droits, stries droites et fines ; et surtout un profil tres particulier, avec une succession de pics et de depressions qui n’avait jamais ete decrite auparavant.

Background Intensive care unit (ICU) survivors often suffer from cognitive, physical and mental impairments, known as post-intensive care syndrome (PICS). ICU follow-up clinics may improve aftercare of these patients. There is a lack of evidence whether or which concept of an ICU follow-up clinic is effective. Within the PINA study, a concept for an ICU follow-up clinic was developed and will be tested in a pilot randomised controlled trial (RCT), primarily to evaluate the feasibility and additionally the potential efficacy. Methods/design Design: Pilot RCT with intervention and control (usual care) arms plus mixed-methods process evaluation. Participants: 100 ICU patients (50 per arm) of three ICUs in a university hospital (Regensburg, Germany), ≥ 18 years with an ICU stay of > 5 days, a sequential organ failure assessment (SOFA) score > 5 during the ICU stay and a life expectancy of more than 6 months. Intervention: The intervention will contain three components: information, consultation and networking. Information will be available in form of an intensive care guide for patients and next of kin at the ICU and phone support during follow-up. For consultation, patients will visit the ICU follow-up clinic at least once during the first 6 months after discharge from ICU. During these visits, patients will be screened for symptoms of PICS and, if required, referred to specialists for further treatment. The networking part (e.g. special referral letter from the ICU follow-up clinic) aims to provide a network of outpatient care providers for former ICU patients. Feasibility Outcomes: Qualitative and quantitative evaluation will be used to explore reasons for non-participation and the intervention´s acceptability to patients and caregivers. Efficacy Outcomes: Health-related quality of life (HRQOL) will be assessed as primary outcome by the physical component score (PCS) of the Short-Form 12 Questionnaire (SF-12). Secondary outcomes encompass further patient-reported outcomes. All outcomes are assessed at 6 months after discharge from ICU. Discussion The PINA study will determine feasibility and potential efficacy of a complex intervention in a pilot RCT to enhance follow-up care of ICU survivors. The pilot study is an important step for further studies in the field of ICU aftercare and especially for the implementation of a pragmatic multi-centre RCT. Trial registration ClinicalTrials.gov, NCT04186468. Submitted 2 December 2019

BackgroundThe anti-SARS2 vaccination is considered the best way to reduce the frequency and the subsequent effects of COVID19 pandemic. To this aim, the most used in western countries are mRNA vaccines BNT16162b2 (Pfizer-BioNT) and mRNA-1273 (Moderna). With both these vaccines the risk/benefits balance is largely favorable and severe adverse effects are almost rare. In keeping, although transient myalgia and arthralgia are frequently seen, myositis have been until now rarely reported.ObjectivesTo report two cases of myositis occurring in two patients after BNT16162b2 vaccine administration evaluated at the Center for Rheumatic Diseases in Venice, Italy.MethodsIn these patients clinical examination, blood and instrumental investigations for myositis and, in addition HLA typing, were performed. Patients were followed for at least six months after the onset of symptoms.ResultsThe first patient, a 54-year-old male, complained of high-grade fever 4 days after the I dose of BNT16162b2 (Pfizer-BioNT) followed, by mild fatigue, muscle soreness and increasing weakness. He was sent to the emergency department of the local Hospital. The physical examination confirmed the muscle weakness. Blood investigation revealed an increase of AST: 509 U/L (NV< 37), ALT:189 U/L (NV The second case was a 29-year-old female presented with a history of complaints appeared two days after the vaccination with BNT16162b2 administration (Pfizer-BioNT) characterized by three days of high-degree fever, followed by sever weakness, especially in the arms. The family doctor decide to hear our advise. At the initial presentation arm strenght was very decrease and the patient was accompanied. We required a serie of investigations which revealed: CPK 8950 U/L (NV 250), CRP 3.5 mg/dl increased; antinuclear and anti-myositis antibodies absent; cardiac (Ultrasound) and thoracic (CT) investigation and electromyography negative. HLA typing revealed the presence of haplotypes B*35 and DRB1*15. PN (50 mg orally day) was started; two weeks later she improved and both muscle indices and CRP negative. Thus, we reduce the dosage at 25 mg/day with tapering 5 mg weekly. She was completely remitted at end of PN cycle. At present, three month later she is well.ConclusionThe rare occurrence of some particular side effects is not predictable. Our cases of severe myositis which in both cases completely remitted in some months are associated with haplotypes HLA-B*35 and DRB1*15. These are both binding sites linked to high-affinity interactions to S-protein T-cell epitope which account for high potentials to trigger immunogenic responses to the S protein of SARS-CoV-2 (1). Furthermore classically, HLA-B35 is associated with reactive arthritis and self-limiting, unclassified rheumatism (2).References[1]Sarma VR, Olotu FA, Soliman MERS. Integrative immunoinformatics paradigm for predicting potential B-cell and T-cell epitopes as viable candidates for subunit vaccine design againts COVID-19 virulance. Biomed J 2021; 44:447-60[2]Dubost JJ, Demarquilly F, Soubrier M, Coussediere JM, Ristori JM, Sauvezie BJ. HLA and sel-limiting, unclassified rheumatism. A role for HLA-B35? J Rheumatol 1999; 26:2400-3Disclosure of InterestsNone declared

Additional file 1:. SPIRIT 2013 Checklist: Recommended items to address in a clinical trial protocol and related documents

Molecular interactions are essential for regulation of cellular processes from the formation of multi-protein complexes to the allosteric activation of enzymes. Identifying the essential residues and molecular features that regulate such interactions is paramount for understanding the biochemical process in question, allowing for suppression of a reaction through drug interventions or optimization of a chemical process using bioengineered molecules. In order to identify important residues and information pathways within molecular complexes, the dynamical network analysis method was developed and has since been broadly applied in the literature. However, in the dawn of exascale computing, this method is frequently limited to relatively small biomolecular systems. In this work, we provide an evolution of the method, application, and interface. All data processing and analysis are conducted through Jupyter notebooks, providing automatic detection of important solvent and ion residues, an optimized and parallel generalized correlation implementation that is linear with respect to the number of nodes in the system, and subsequent community clustering, calculation of betweenness of contacts, and determination of optimal paths. Using the popular visualization program visual molecular dynamics (VMD), high-quality renderings of the networks over the biomolecular structures can be produced. Our new implementation was employed to investigate three different systems, with up to 2.5M atoms, namely, the OMP-decarboxylase, the leucyl-tRNA synthetase complexed with its cognate tRNA and adenylate, and respiratory complex I in a membrane environment. Our enhanced and updated protocol provides the community with an intuitive and interactive interface, which can be easily applied to large macromolecular complexes.

International audience; NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on central processing unit (CPU)-and graphics processing unit (GPU)-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics, controlling the temperature, pressure and pH, applying external potentials on tailored grids, leveraging massively parallel resources in multiple-copy simulations, as well as hybrid QM/MM descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations, and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts towards achieving optimal performance on GPUbased architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.