Search

PurposePolymorphisms in complement genes are risk-associated for age-related macular degeneration (AMD). Functional analysis revealed a common deficiency to control the alternative complement pathway by risk-associated gene polymorphisms. Thus, we investigated the levels of terminal complement complex (TCC) in the plasma of wet AMD patients with defined genotypes and the impact of the complement activation of their plasma on second-messenger signaling, gene expression, and cytokine/chemokine secretion in retinal pigment epithelium (RPE) cells.DesignCollection of plasma from patients with wet AMD (n = 87: 62% female and 38% male; median age 77 years) and controls (n = 86: 39% female and 61% male; median age 58 years), grouped for risk factor smoking and genetic risk alleles CFH 402HH and ARMS2 rs3750846, determination of TCC levels in the plasma, in vitro analysis on RPE function during exposure to patients’ or control plasma as a complement source.MethodsGenotyping, measurement of TCC concentrations, ARPE-19 cell culture, Ca2+ imaging, gene expression by qPCR, secretion by multiplex bead analysis of cell culture supernatants.Main outcome measuresTCC concentration in plasma, intracellular free Ca2+, relative mRNA levels, cytokine secretion.ResultsTCC levels in the plasma of AMD patients were five times higher than in non-AMD controls but did not differ in plasma from carriers of the two risk alleles. Complement-evoked Ca2+ elevations in RPE cells differed between patients and controls with a significant correlation between TCC levels and peak amplitudes. Comparing the Ca2+ signals, only between the plasma of smokers and non-smokers, as well as heterozygous (CFH 402YH) and CFH 402HH patients, revealed differences in the late phase. Pre-stimulation with complement patients’ plasma led to sensitization for complement reactions by RPE cells. Gene expression for surface molecules protective against TCC and pro-inflammatory cytokines increased after exposure to patients’ plasma. Patients’ plasma stimulated the secretion of pro-inflammatory cytokines in the RPE.ConclusionTCC levels were higher in AMD patients but did not depend on genetic risk factors. The Ca2+ responses to patients’ plasma as second-messenger represent a shift of RPE cells to a pro-inflammatory phenotype and protection against TCC. We conclude a substantial role of high TCC plasma levels in AMD pathology.

The broiler industry supplies high-quality animal protein to the world. The ban of antibiotics as growth promoters has opened the way for plenty of phytochemicals and antioxidants to be explored. This study summarizes the use of natural antioxidants in a broiler diet as a way through which to deal with stressors, as well as their effects on the expression of various genes. The transcriptional factors and genes involved in the regulation of redox homeostasis are described and emphasis is placed on nuclear factor erythroid 2-related factor 2 and nuclear factor kappa B. Sources such as fruits, vegetables, spices, mushrooms, and algae contain numerous natural antioxidant compounds. The antioxidant activity of these compounds has also been confirmed at the genome level. This study focuses on the regulation of oxidative stress-related genes, as well as on genes that regulate the inflammatory response, apoptosis, response to heat stress, lipid metabolism, and the intestinal barrier status. The natural compounds presented include, but are not limited to, the following: rutin, lycopene, magnolol, genistein, hesperidin, naringin, quercetin, curcumin, bisdemethoxycurcumin, resveratrol, astaxanthin, squalene, pterostilbene, protocatechuic acid, taraxasterol, myricetin, and proanthocyanidins. Several studies have revealed a dose-dependent action. Future studies should focus on the role of phytogenic compounds as antibiotic alternatives in relation to gut microbiota and their role in eubiosis.

Pathogenic platelet factor 4 (PF4) antibodies contributed to the abnormal coagulation profiles in COVID-19 and vaccinated patients. However, the mechanism of what triggers the body to produce these antibodies has not yet been clarified. Similar patterns and many comparable features between the COVID-19 virus and heparin-induced thrombocytopenia (HIT) have been reported. Previously, we identified a new mechanism of autoimmunity in HIT in which PF4-antibodies self-clustered PF4 and exposed binding epitopes for other pathogenic PF4/eparin antibodies. Here, we first proved that the SARS-CoV-2 spike protein (SP) also binds to PF4. The binding was evidenced by the increase in mass and optical intensity as observed through quartz crystal microbalance and immunosorbent assay, while the switching of the surface zeta potential caused by protein interactions and binding affinity of PF4-SP were evaluated by dynamic light scattering and isothermal spectral shift analysis. Based on our results, we proposed a mechanism for the generation of PF4 antibodies in COVID-19 patients. We further validated the changes in zeta potential and interaction affinity between PF4 and SP and found that their binding mechanism differs from ACE2–SP binding. Importantly, the PF4/SP complexes facilitate the binding of anti-PF4/Heparin antibodies. Our findings offer a fresh perspective on PF4 engagement with the SARS-CoV-2 SP, illuminating the role of PF4/SP complexes in severe thrombotic events.

M-type stars are the most abundant stars in our Galaxy. Their visible spectra are characterized by strong TiO and VO absorption bands with occasional ScO bands near 6000–6100 Å. This region corresponds to the A ^2 Π–X ^2 Σ ^+ band system and can be used to measure the abundance of ScO. In this work, a new Doppler-limited resolution spectrum of ScO obtained in a hollow-cathode experiment is presented. The A ^2 Π–X ^2 Σ ^+ electronic transition is analyzed with special care dedicated to fitting the ${{\rm{A}}}^{{\prime} 2}{\rm{\Delta }}(v+2)$ ∼ A ^2 Π( v ) perturbation. Spectroscopic constants of the A ^2 Π( v ) states are reported for v ≤ 9, and a partial fit of spectroscopic constants is made for the ${{\rm{A}}}^{{\prime} 2}{\rm{\Delta }}(v)$ states 2 ≤ v ≤ 6. The modeled interaction of the two states reproduces the experimental data remarkably well. New equilibrium constants are extracted from the fit. Band strengths are calculated with the help of a scaled transition dipole moment function, previously calculated with ab initio methods. Finally, a line list of the A ^2 Π–X ^2 Σ ^+ band system is provided, including Einstein A coefficients and oscillator strengths. Using this line list, the spectrum of ScO can be simulated for different temperature and pressure conditions in stellar atmospheres.

ZrO is a well-studied metal monoxide because of its astrophysical importance in characterizing S stars. The bands of the d ^3 Φ–a ^3 Δ system ( γ system) with ${v}^{{\prime} }\leqslant 4$ and v ″ ≤ 5 are rotationally analyzed using the PGOPHER program to provide spectroscopic constants. The high-resolution ZrO emission spectrum was recorded with a Fourier transform spectrometer using a high-temperature carbon furnace source. New ab initio calculations of the transition dipole moment were carried out in order to determine the vibronic band strengths. The spectroscopic constants, along with the band strengths, are used to calculate a line list for the γ system. This line list can be used to determine Zr abundances in S stars. We also correct the line strengths for the B ^1 Π– A ^1 Δ transition calculated in our previous work.

YO bands are conspicuous in the spectra of S stars. The laboratory spectrum of the A ^2 Π–X ^2 Σ ^+ electronic transition has been recorded with a Fourier transform spectrometer using a composite-wall hollow cathode lamp source. The A ^2 Π–X ^2 Σ ^+ transition with ${v}^{{\prime} }\leqslant 4$ and v ″ ≤ 4 has been rotationally analyzed using the modern spectral fitting program PGOPHER. Vibronic band strengths were calculated using an ab initio transition dipole moment function. A line list for the A ^2 Π–X ^2 Σ ^+ transition is provided and can be utilized in the modeling of S stars.

Cool red giant stars exhibit absorption bands of calcium monochloride (CaCl) in the optical region. In this work, the bands of CaCl corresponding to the A ^2 Π − X ^2 Σ ^+ transition with ${v}^{{\prime} }\leqslant $ 4 and v ″ ≤ 4, and B ^2 Σ ^+ − X ^2 Σ ^+ transition with ${v}^{{\prime} }\leqslant $ 2 and v ″ ≤ 2 are rotationally analyzed with PGOPHER, a multipurpose program for simulating and fitting molecular spectra. All bands were analyzed using high-resolution absorption spectra collected at the National Solar Observatory in 1985, calibrated with atomic lines from a high-resolution emission spectrum obtained in a separate hollow cathode experiment. The results are compared with previous laser-induced fluorescence measurements. Overall, the accuracy of spectroscopic constants for the A ^2 Π and B ^2 Σ ^+ states is improved. Scaled transition dipole moment calculations were used to obtain line strengths. Line lists are provided with Einstein A coefficients and oscillator strengths, which can be used to determine CaCl stellar abundances. Additionally, isotope splittings allowed us to estimate band origins for the ^40 Ca ^37 Cl isotopologue based on band-head positions.

The magnetic topology of erupting regions on the Sun is a key factor in the energy buildup and release, and the subsequent evolution of flares and coronal mass ejections (CMEs). The presence/absence of null points and separatrices dictates whether and where current sheets form and magnetic reconnection occurs. Numerical simulations show that energy buildup and release via reconnection in the simplest configuration with a null, the embedded bipole, is a universal mechanism for solar eruptions. Here we demonstrate that a magnetic topology with nested bipoles and two nulls can account for more complex dynamics, such as failed eruptions and CME–jet interactions. We investigate the stalled eruption of a nested configuration on 2013 July 13 in NOAA Active Region 11791, in which a small bipole is embedded within a large transequatorial pseudo-streamer containing a null. In the studied event, the inner active region erupted, ejecting a small flux rope behind a shock accompanied by a flare; the flux rope then reconnected with pseudo-streamer flux and, rather than escaping intact, mainly distorted the pseudo-streamer null into a current sheet. EUV and coronagraph images revealed a weak shock and a faint collimated outflow from the pseudo-streamer. We analyzed Solar Dynamics Observatory and Solar TErrestrial RElations Observatory observations and compared the inferred magnetic evolution and dynamics with three-dimensional magnetohydrodynamics simulations of a simplified representation of this nested fan-spine system. The results suggest that the difference between breakout reconnection at the inner null and at the outer null naturally accounts for the observed weak jet and stalled ejection. We discuss the general implications of our results for failed eruptions.

Inflammation is a vital defense mechanism, creating hostile conditions for pathogens, preventing the spread of tissue infection and repairing damaged tissues in humans and animals. However, when inflammation resolution is delayed or compromised as a result of its misregulation, the process proceeds from the acute phase to chronic inflammation, leading to the development of various chronic illnesses. It is proven that redox balance disturbances and oxidative stress are among major factors inducing NF-κB and leading to over-inflammation. Therefore, the anti-inflammatory properties of various natural antioxidants have been widely tested in various in vitro and in vivo systems. Accumulating evidence indicates that silymarin (SM) and its main constituent silibinin/silybin (SB) have great potential as an anti-inflammation agent. The main anti-inflammatory mechanism of SM/SB action is attributed to the inhibition of TLR4/NF-κB-mediated signaling pathways and the downregulated expression of pro-inflammatory mediators, including TNF-α, IL-1β, IL-6, IL-12, IL-23, CCL4, CXCL10, etc. Of note, in the same model systems, SM/SB was able to upregulate anti-inflammatory cytokines (IL-4, IL-10, IL-13, TGF-β, etc.) and lipid mediators involved in the resolution of inflammation. The inflammatory properties of SM/SB were clearly demonstrated in model systems based on immune (macrophages and monocytes) and non-immune (epithelial, skin, bone, connective tissue and cancer) cells. At the same time, the anti-inflammatory action of SM/SB was confirmed in a number of in vivo models, including toxicity models, nonalcoholic fatty liver disease, ischemia/reperfusion models, stress-induced injuries, ageing and exercising models, wound healing and many other relevant model systems. It seems likely that the anti-inflammatory activities of SM/SB are key elements on the health-promoting properties of these phytochemicals.

Lymphoma is the most common haematological malignancy affecting dogs and has a high incidence in the Bullmastiff breed. The aim of this study was to identify risk loci predisposing this breed to the disease. The average age of lymphoma diagnosis in 55 cases was less than 6 years, similar to the median age of 64 cases from our clinical and pathology databases. When fine-scale population structure was explored using NETVIEW, cases were distributed throughout an extended pedigree. When genotyped cases (n = 49) and dogs from the control group (n = 281) were compared in a genome-wide association analysis of lymphoma risk, the most prominent associated regions were detected on CFA13 and CFA33. The top SNPs in a 5.4 Mb region on CFA13 were significant at a chromosome-wide level, and the region was fine-mapped to ~1.2 Mb (CFA13: 25.2–26.4 Mb; CanFam3.1) with four potential functional candidates, including the MYC proto-oncogene bHLH transcription factor (MYC) and a region syntenic with the human and mouse lncRNA Pvt1 oncogene (PVT1). A 380 Kb associated region at CFA33: 7.7–8.1 Mb contained the coding sequence for SUMO specific peptidase7 (SENP7) and NFK inhibitor zeta (NFKBIZ) genes. These genes have annotations related to cancer, amongst others, and both have functional links to MYC regulation. Genomic signatures identified in lymphoma cases suggest that increased risk contributed by the regions identified by GWAS may complement a complex predisposing genetic background.

Synaptopodin-2 (SYNPO2) is a protein associated with the Z-disc in striated muscle cells. It interacts with α-actinin and filamin C, playing a role in Z-disc maintenance under stress by chaperone-assisted selective autophagy (CASA). In smooth muscle cells, SYNPO2 is a component of dense bodies. Furthermore, it has been proposed to play a role in tumor cell proliferation and metastasis in many different kinds of cancers. Alternative transcription start sites and alternative splicing predict the expression of six putative SYNPO2 isoforms differing by extended amino- and/or carboxy-termini. Our analyses at mRNA and protein levels revealed differential expression of SYNPO2 isoforms in cardiac, skeletal and smooth muscle cells. We identified synemin, an intermediate filament protein, as a novel binding partner of the PDZ-domain in the amino-terminal extension of the isoforms mainly expressed in cardiac and smooth muscle cells, and demonstrated colocalization of SYNPO2 and synemin in both cell types. A carboxy-terminal extension, mainly expressed in smooth muscle cells, is sufficient for association with dense bodies and interacts with α-actinin. SYNPO2 therefore represents an additional and novel link between intermediate filaments and the Z-discs in cardiomyocytes and dense bodies in smooth muscle cells, respectively. In pathological skeletal muscle samples, we identified SYNPO2 in the central and intermediate zones of target fibers of patients with neurogenic muscular atrophy, and in nemaline bodies. Our findings help to understand distinct functions of individual SYNPO2 isoforms in different muscle tissues, but also in tumor pathology.

Plain English Summary Community engagement or community involvement in Aboriginal health research is a process that involves partnering with Aboriginal and Torres Strait Islander people or potential research participants to empower them to have a say in how research with Aboriginal communities is carried out. In the context of Aboriginal health, this is particularly important so that researchers can respond to the priorities of the community and conduct research in a way that respectful of Aboriginal cultural values and beliefs. One approach to community engagement in research is to form a community reference group to provide input to the research project. Although using a community reference group is considered to be an effective way to involve community members in research, often there are practical challenges in setting up and sustaining such a group. In this paper, we set out to describe an approach used to set up a community reference group for a new Aboriginal health research project exploring joint pain in Aboriginal and Torres Strait Islander people. This involved interviewing 13 health professionals and researchers (12 who identified as Aboriginal and one who identified as Aboriginal and Torres Strait Islander) about how to best go about setting up a community reference group. We used recommendations from these participants to inform who we approached to be members of the group and how the group would function. In describing the process we used to establish a community reference group, we were able to design a 10-step practical guide which may help other research groups who are looking to conduct new, ethical Aboriginal health research projects.

Abstract Transfemoral transcatheter aortic valve implantation (TAVI) under conscious sedation is the most widely used method of implantation. Echocardiography is used to detect complications and to assess the implantation result. The aim of this paper is to provide a time-efficient protocol when transthoracic echocardiography (TTE) is used to guide TAVI procedures.

Abstract Immunization with radiation-attenuated Plasmodium falciparum (Pf) sporozoites (SPZ) in PfSPZ Vaccine, has provided better vaccine efficacy (VE) against controlled human malaria infection (CHMI) with the same parasites as in the vaccine (homologous) than with genetically distant parasites (heterologous). We sought to identify an immunization regimen that provided similar VE against CHMI with homologous and heterologous Pf for at least 9 weeks in malaria-naïve adults. Such a regimen was identified in part 1 (optimization), an open label study, and confirmed in part 2 (verification), a randomized, double-blind, placebo-controlled study in which VE was assessed by cross-over repeat CHMI with homologous (PfNF54) and heterologous (Pf7G8) PfSPZ at 3 and 9–10 weeks. VE was calculated using Bayesian generalized linear regression. In part 1, vaccination with 9 × 105 PfSPZ on days 1, 8, and 29 protected 5/5 (100%) subjects against homologous CHMI at 3 weeks after the last immunization. In part 2, the same 3-dose regimen protected 5/6 subjects (83%) against heterologous CHMI at both 3 and 9–10 weeks after the last immunization. Overall VE was 78% (95% predictive interval: 57–92%), and against heterologous and homologous was 79% (95% PI: 54–95%) and 77% (95% PI: 50–95%) respectively. PfSPZ Vaccine was safe and well tolerated. A 4-week, 3-dose regimen of PfSPZ Vaccine provided similar VE for 9–10 weeks against homologous and heterologous CHMI. The trial is registered with ClinicalTrials.gov, NCT02704533.

Abstract Anti-IL17A therapies have proven effective for numerous inflammatory diseases including psoriasis, axial spondylitis and psoriatic arthritis. Modulating and/or antagonizing protein–protein interactions of IL17A cytokine binding to its cell surface receptors with oral therapies offers the promise to bring forward biologics-like efficacy in a pill to patients. We used an NMR-based fragment screen of recombinant IL17A to uncover starting points for small molecule IL17A antagonist discovery. By examining chemical shift perturbations in 2D [1H, 13C-HSQC] spectra of isotopically labeled IL17A, we discovered fragments binding the cytokine at a previously undescribed site near the IL17A C-terminal region, albeit with weak affinity (> 250 µM). Importantly this binding location was distinct from previously known chemical matter modulating cytokine responses. Subsequently through analog screening, we identified related compounds that bound symmetrically in this novel site with two copies. From this observation we employed a linking strategy via structure-based drug design and obtained compounds with increased binding affinity (

Accurate classification of genetic variants is critical for research and patient care. Here, the authors report that population-based associations between rare variants and quantitative endophenotypes for monogenic diseases can provide support for variant pathogenicity.

Abstract In neuroblastoma, MYCN amplification and 11q-deletion are important, although incomplete, markers of high-risk disease. It is therefore relevant to characterize additional alterations that can function as prognostic and/or predictive markers. Using SNP-microarrays, a group of neuroblastoma patients showing amplification of one or multiple 12q loci was identified. Two loci containing CDK4 and MDM2 were commonly co-amplified, although amplification of either locus in the absence of the other was observed. Pharmacological inhibition of CDK4/6 with ribociclib or abemaciclib decreased proliferation in a broad set of neuroblastoma cell lines, including CDK4/MDM2-amplified, whereas MDM2 inhibition by Nutlin-3a was only effective in p53wild-type cells. Combined CDK4/MDM2 targeting had an additive effect in p53wild-type cell lines, while no or negative additive effect was observed in p53mutated cells. Most 12q-amplified primary tumors were of abdominal origin, including those of intrarenal origin initially suspected of being Wilms’ tumor. An atypical metastatic pattern was also observed with low degree of bone marrow involvement, favoring other sites such as the lungs. Here we present detailed biological data of an aggressive neuroblastoma subgroup hallmarked by 12q amplification and atypical clinical presentation for which our in vitro studies indicate that CDK4 and/or MDM2 inhibition also could be beneficial.

Abstract Background Cutaneous epitheliotropic T-cell lymphoma is a malignant tumour of the skin already reported in humans, dogs, cats, horses, and other species, but not previously in donkeys. The standard diagnosis is based on clinical, morphological and immunophenotypic data. Differentiation of malignant versus benign proliferation of lymphocytes is crucial; in ambiguous cases T-cell receptor gamma (TRG) molecular clonality should be tested. In the present paper, we report a case of mycosis fungoides diagnosed in a donkey whose diagnosis was based on clinical, histological and immunohistochemical aspects and a positive TRG clonality test. Case presentation A twenty-five-year-old donkey gelding was referred with a mildly pruritic, generalised and severe exfoliative dermatosis. Otherwise, the animal was clinically healthy, though mildly underweight. Dermatological examination revealed severe generalised alopecic and exfoliative dermatitis, occasionally eroded, with high number of large, thin, greyish scales. All mucocutaneous junctions except the hoofs were affected. Ectoparasites and dermatophytes were ruled out. The complete blood count and blood smear evaluation revealed mild normocytic normochromic anemia. The biochemistry panel showed mild hyperproteinemia with albumin within the normal range. Protein electrophoresis showed moderate polyclonal hypergammaglobulinemia. Histological findings were characterised by interface dermatitis with massive exocytosis in the epidermis of a homogenous population of lymphoid cells showing atypia. Clusters of neoplastic cells were present within the epidermis forming Pautrier “microabscesses”. These findings are consistent with cutaneous epitheliotropic lymphoma. Immunohistochemical staining revealed uniform labelling of the neoplastic cells for CD3, and lack of expression of CD20 (a B cell lineage associated marker). Molecular clonality PCR (PARR) was performed using equine TRG primers; this revealed a clonal rearrangement in a heavy polyclonal background. Transmission electronic microscopy showed multiple lymphocytes with convoluted or cerebriform nuclei. Conclusions This case report provides the first evidence of clinical, histopathological, immunophenotypic features, electron microscopy findings and molecular analysis of a cutaneous epitheliotropic T-cell lymphoma (mycosis fungoides) in a donkey. Our observations suggest that cutaneous T-cell lymphoma should be included in the differential diagnoses of exfoliative dermatitis, even those progressing in a chronic pattern and/or with few or no pruritus.

Abstract Background Calling germline SNP variants from bisulfite-converted sequencing data poses a challenge for conventional software, which have no inherent capability to dissociate true polymorphisms from artificial mutations induced by the chemical treatment. Nevertheless, SNP data is desirable both for genotyping and to understand the DNA methylome in the context of the genetic background. The confounding effect of bisulfite conversion however can be conceptually resolved by observing differences in allele counts on a per-strand basis, whereby artificial mutations are reflected by non-complementary base pairs. Results Herein, we present a computational pre-processing approach for adapting sequence alignment data, thus indirectly enabling downstream analysis on a per-strand basis using conventional variant calling software such as GATK or Freebayes. In comparison to specialised tools, the method represents a marked improvement in precision-sensitivity based on high-quality, published benchmark datasets for both human and model plant variants. Conclusion The presented “double-masking” procedure represents an open source, easy-to-use method to facilitate accurate variant calling using conventional software, thus negating any dependency on specialised tools and mitigating the need to generate additional, conventional sequencing libraries alongside bisulfite sequencing experiments. The method is available at https://github.com/bio15anu/revelio and an implementation with Freebayes is available at https://github.com/EpiDiverse/SNP

Study Design Retrospective cohort study. Purpose To determine whether implant density impact three-dimensional deformity correction in posterior spinal fusion (PSF) without Ponte osteotomies (POs) for patients with Lenke 1 and 2 adolescent idiopathic scoliosis (AIS). Overview of Literature Currently, the optimal pedicle screw (PS) density for flexible moderate-sized thoracic AIS curve correction is still controversial. There are limited data regarding the impact of implant density on three-dimensional correction in PSF without the use of PO for thoracic AIS surgery. Methods A database of patients with AIS with Lenke 1 and 2 curves treated with PSF without PO and instrumented with PSs and ≥2-year follow-up was reviewed. The preoperative, immediate, and final follow-up postoperative radiographs were analyzed. The correlation between PS density and the following factors were determined: major curve correction (MCC), correction index (CI; MCC/curve flexibility), kyphosis angle change, and rib index (RI) correction. Then, patients were divided into low-density (LD) and high-density (HD) groups according to mean PS density for the entire cohort (1.5 PS per level). Demographics and radiographic and clinical outcomes were compared between groups. Results The study included 99 patients with Lenke 1 and 23 patients with Lenke 2 AIS. The average MCC was 67.2%. There was no correlation between screw density and these parameters: MCC (r=0.10, p=0.26), CI (r=0.16, p=0.07), change in T2–T12 kyphosis angle (r=−0.13, p=0.14), and RI correction (r=−0.09, p=0.37). Demographic and preoperative radiographic parameters were similar between the LD and HD groups. At the latest follow-up, there were no differences between the two groups in regard to MCC, CI, change in T2–T12 kyphosis angle, RI correction, and Scoliosis Research Society-30 scores (all p>0.05). Conclusions This study revealed no significant correlation between screw density and curve correction in any planes. HD construct may not provide better deformity correction in patients with flexible and moderate thoracic AIS undergoing PSF without PO.

Abstract Analysis of stool offers simple, non-invasive monitoring for many gastrointestinal (GI) diseases and access to the gut microbiome, however adherence to stool sampling protocols remains a major challenge because of the prevalent dislike of handling one’s feces. We present a technology that enables individual stool specimen collection from toilet wastewater for fecal protein and molecular assay. Human stool specimens and a benchtop test platform integrated with a commercial toilet were used to demonstrate reliable specimen collection over a wide range of stool consistencies by solid/liquid separation followed by spray-erosion. The obtained fecal suspensions were used to perform occult blood tests for GI cancer screening and for microbiome 16S rRNA analysis. Using occult blood home test kits, we found overall 90% agreement with standard sampling, 96% sensitivity and 86% specificity. Microbiome analysis revealed no significant difference in within-sample species diversity compared to standard sampling and specimen cross-contamination was below the detection limit of the assay. Furthermore, we report on the use of an analogue turbidity sensor to assess in real time loose stools for tracking of diarrhea. Implementation of this technology in residential settings will improve the quality of GI healthcare by facilitating increased adherence to routine stool monitoring.

IntroductionThe rising global burden of metabolic disease impacts the control of endemic tuberculosis (TB) in many regions, as persons with diabetes mellitus (DM) are up to three times more likely to develop active TB than those without DM. Active TB can also promote glucose intolerance during both acute infection and over a longer term, potentially driven by aspects of the immune response. Identifying patients likely to have persistent hyperglycemia following TB treatment would enable closer monitoring and care, and an improved understanding of underlying immunometabolic dysregulation.MethodsWe measured the relationship of plasma cytokine levels, T cell phenotypes and functional responses with the change in hemoglobin A1c (HbA1c) before and after treatment of pulmonary TB in a prospective observational cohort in Durban, South Africa. Participants were stratified based on stable/increased HbA1c (n = 16) versus decreased HbA1c (n = 46) levels from treatment initiation to 12 month follow-up.ResultsCD62 P-selectin was up- (1.5-fold) and IL-10 downregulated (0.85-fold) in plasma among individuals whose HbA1c remained stable/increased during TB treatment. This was accompanied by increased pro-inflammatory TB-specific IL-17 production (Th17). In addition, Th1 responses were upregulated in this group, including TNF-α production and CX3CR1 expression, with decreased IL-4 and IL-13 production. Finally, the TNF-α+ IFNγ+ CD8+ T cells were associated with stable/increased HbA1c. These changes were all significantly different in the stable/increased HbA1c relative to the decreased HbA1c group.DiscussionOverall, these data suggest that patients with stable/increased HbA1c had an increased pro-inflammatory state. Persistent inflammation and elevated T cell activity in individuals with unresolved dysglycemia following TB treatment may indicate failure to fully resolve infection or may promote persistent dysglycemia in these individuals, and further studies are needed to explore potential mechanisms.

IntroductionA key skill for dental professionals to master is their ability to have effective preventive oral health conversations. On qualifying, UK dentists undertake a one-year foundation training programme in general practice. This study explored with Foundation Dentists, the barriers and facilitators to undertaking oral health conversations with parents/caregivers and their children, aged 0–11 years old.Materials and methodsApproximately 100 Foundation Dentists from the Yorkshire and Humber region attended a series of focus groups. They discussed how they and their wider dental team undertake oral health conversations with parents/caregivers of young children, aged 0–11 years old. The data was analysed using thematic analysis.ResultsFive themes were identified as barriers and facilitators to providing oral health advice: (1) Lack of knowledge around parenting skills and child development; (2) Parental receptivity; (3) Motivation for changing behaviours; (4) Information content and inconsistency; and (5) Current National Health Service (NHS) structures of general dental practice.DiscussionA multi-faceted approach is needed to develop the training of Foundation Dentists to undertake preventive oral health conversations with parents/caregivers and children. Such an approach has the potential to improve the patient-practitioner relationship and increase effective behaviour change conversations taking place in general dental care, thus improving children's oral health.

Senescent cells release a variety of cytokines, proteases, and growth factors collectively known as the senescence-associated secretory phenotype (SASP). Sustained SASP contributes to a pattern of chronic inflammation associated with aging and implicated in many age-related diseases. Here, we investigated the expression and function of the immunomodulatory cytokine BAFF (B-cell activating factor; encoded by the TNFSF13B gene), a SASP protein, in multiple senescence models. We first characterized BAFF production across different senescence paradigms, including senescent human diploid fibroblasts (WI-38, IMR-90) and monocytic leukemia cells (THP-1), and tissues of mice induced to undergo senescence. We then identified IRF1 (interferon regulatory factor 1) as a transcription factor required for promoting TNFSF13B mRNA transcription in senescence. We discovered that suppressing BAFF production decreased the senescent phenotype of both fibroblasts and monocyte-like cells, reducing IL6 secretion and SA-β-Gal staining. Importantly, however, the influence of BAFF on the senescence program was cell type-specific: in monocytes, BAFF promoted the early activation of NF-κB and general SASP secretion, while in fibroblasts, BAFF contributed to the production and function of TP53 (p53). We propose that BAFF is elevated across senescence models and is a potential target for senotherapy.

Background: Extremity sarcoma surgery entails significant costs for patients, governments and insurers. Multiple studies have described individual costs, however, the overall impact of cost on the quality of surgical care remains unclear. Objectives: A narrative review with a systematic approach was undertaken to compare the impact of cost on the quality of extremity sarcoma care across low-middle-income and high-income countries. Data Sources: MEDLINE, EMBASE, Cochrane, PsycInfo, DARE, NHS-EED, HTA. Methods: A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines. Inclusion criteria were: discussion of costs and the surgical management of primary extremity sarcoma. There were no restrictions on study design, publication type, date, geographic location or publication status. A data extraction table was used to identify study location, type and findings. Results: 1012 studies were retrieved and 44 met the inclusion criteria. Four additional studies were identified from the reference lists of included articles. 27 studies were published in high-income countries (HIC) including all four full health economic analyses and 20 studies were published in low-middle income countries (LMC). Within LMC, cost impeded access to diagnosis, resection and options for reconstruction. In HIC, cost varied with choice of management, particularly during the long-term postoperative period. Conclusions: Within LMC, cost impaired the provision of quality, curative care for patients with extremity sarcoma. Within HIC, while costs varied with chosen management, they were not prohibitive to the provision of quality care. Further research is required, specific to both socioeconomic contexts, to further describe the long-term cost-utility of different methods for the surgical management of extremity sarcoma.

The joint statement is a synergistic action between HyperChildNET and the European Academy of Pediatrics about the diagnosis and management of hypertension in youth, based on the European Society of Hypertension Guidelines published in 2016 with the aim to improve its implementation. Arterial hypertension is not only the most important risk factor for cardiovascular morbidity and mortality, but also the most important modifiable risk factor. Early hypertension-mediated organ damage may already occur in childhood. The duration of existing hypertension plays an important role in risk assessment, and structural and functional organ changes may still be reversible or postponed with timely treatment. Therefore, appropriate therapy should be initiated in children as soon as the diagnosis of arterial hypertension has been confirmed and the risk factors for hypertension-mediated organ damage have been thoroughly evaluated. Lifestyle measures should be recommended in all hypertensive children and adolescents, including a healthy diet, regular exercise, and weight loss, if appropriate. If lifestyle changes in patients with primary hypertension do not result in normalization of blood pressure within six to twelve months or if secondary or symptomatic hypertension or hypertension-mediated organ damage is already present, pharmacologic therapy is required. Regular follow-up to assess blood pressure control and hypertension-mediated organ damage and to evaluate adherence and side effects of pharmacologic treatment is required. Timely multidisciplinary evaluation is recommended after the first suspicion of hypertension. A grading system of the clinical evidence is included.

The joint statement is a synergistic action between HyperChildNET and the European Academy of Pediatrics about the diagnosis and management of hypertension in youth, based on the European Society of Hypertension Guidelines published in 2016 with the aim to improve its implementation. The first and most important requirement for the diagnosis and management of hypertension is an accurate measurement of office blood pressure that is currently recommended for screening, diagnosis, and management of high blood pressure in children and adolescents. Blood pressure levels should be screened in all children starting from the age of 3 years. In those children with risk factors for high blood pressure, it should be measured at each medical visit and may start before the age of 3 years. Twenty-four-hour ambulatory blood pressure monitoring is increasingly recognized as an important source of information as it can detect alterations in circadian and short-term blood pressure variations and identify specific phenotypes such as nocturnal hypertension or non-dipping pattern, morning blood pressure surge, white coat and masked hypertension with prognostic significance. At present, home BP measurements are generally regarded as useful and complementary to office and 24-h ambulatory blood pressure for the evaluation of the effectiveness and safety of antihypertensive treatment and furthermore remains more accessible in primary care than 24-h ambulatory blood pressure. A grading system of the clinical evidence is included.

BackgroundBlack Americans, particularly in the southern United States, are disproportionately affected by the US HIV epidemic. Patient-reported outcome (PRO) data collection can improve patient outcomes and provide oft-overlooked data on mental health, substance use, and patient adherence to antiretroviral therapy. ObjectiveWe piloted the use of an electronic tablet to collect PRO data on social and behavioral determinants of health among people with HIV at the Meharry Community Wellness Center, an HIV clinic affiliated with a Historically Black Medical College in Nashville, Tennessee. Our primary objective was to better understand patients’ experiences and comfort with using an electronic PRO tool through patient interviews. MethodsWe enrolled 100 people with HIV in care at the Meharry Community Wellness Center consecutively to completely validate PRO tools using the Research Electronic Data Capture platform on a hand-held tablet. Using a purposive sampling strategy, we enrolled 20 of the 100 participants in an in-depth interview (IDI). Interview guide development was grounded in the cognitive-behavioral model, in which thoughts, feelings, and behaviors are interrelated. IDIs were audio recorded, transcribed, deidentified, and formatted for coding. A hierarchical coding system was developed and refined using an inductive-deductive approach. ResultsAmong the 100 people with HIV enrolled, the median age was 50 (IQR 42-54) years; 89% (n=89) were Black, 60% (n=60) were male, and 82% (n=82) were living below 100% of the federal poverty level in 2016. Five major interview themes emerged: overall experience, question content, sensitive topics, clinic visit impact, and future recommendations. IDI participants felt that the tablet was easy to use and that the question content was meaningful. Question content related to trauma, sexual and drug use behaviors, mental health, stigma, and discrimination elicited uncomfortable or distressing feelings in some participants. Patients expressed a strong desire to be truthful, and most would complete these surveys without compensation at future visits if offered. ConclusionsThe use of an electronic tablet to complete PRO data collection was well received by this cohort of vulnerable persons in HIV care in the southern United States. Despite some discomfort related to question content, our cohort overwhelmingly believed this was a meaningful part of their medical experience and expressed a high desire for truthfulness. Future research will focus on scaling up the implementation and evaluation of PRO data collection in a contextually appropriate manner while obtaining input from providers and staff to ensure that the collected data are both applicable and actionable.

Influential models of causal learning assume that learning about generative and preventive relationships are symmetrical to each other. That is, a preventive cue directly prevents an outcome from occurring (i.e., “direct” prevention) in the same way a generative cue directly causes an outcome to occur. However, previous studies from our lab have shown that many participants do not infer a direct prevention causal structure after feature-negative discrimination (A+/AB–) with a unidirectional outcome (Lee & Lovibond, 2021). Melchers et al. (2006) suggested that the use of a bidirectional outcome that can either increase or decrease from baseline, encourages direct prevention learning. Here we test an alternative possibility that a bidirectional outcome encourages encoding of a 'generative' relationship in the 'opposite' direction, where B directly causes a decrease in the outcome. Thus, previous evidence of direct prevention learning using bidirectional outcomes may instead be explained by some participants inferring an “Opposite Causal” structure. In two experiments, participants did indeed report an opposite causal structure. In Experiment 1, these participants showed the lowest outcome predictions when B was combined with a novel cause in a summation test, and lowest outcome predictions when B was presented alone. In Experiment 2, B successfully blocked learning to a novel cue that was directly paired with a reduction in the outcome, and this effect was strongest among participants who endorsed an Opposite Causal structure. We conclude that previous evidence of direct prevention learning using bidirectional outcomes may be a product of excitatory rather than inhibitory learning.

During a 2-year period, eight cases of a distinct illness were seen among 1,424 neonates admitted to a newly established neonatal care unit in southern Haiti. The newborns presented with a picture of sepsis with shock, vomiting, hypotonia, lethargy, and abdominal distention. Five cases proved fatal and another case left the hospital against advice in extremis with little chance of survival. In each case, the illness was associated with a history of ingestion of teas that included castor oil, known as lok in Haitian Creole. The presumptive cause of the illness was established by the presence of a dark, oily substance in drainage from the nares and nasogastric tubes and by subsequent admission on direct questioning of the caregivers, who said that the infants had been given large amounts of lok. The castor oil tea had been given to three infants in the immediate neonatal period where its use is attributed to encouraging the passage of meconium. The five remaining infants were between 15 and 30 days of life when they were given lok shortly before admission to the neonatal unit for treatment of an undefined illness. All of them were term infants with no identified risks at birth. As nasogastric tubes are not routinely placed in sick neonates, and the parents did not volunteer information about lok administration, the practice may be more widespread than that recorded here. Although our data are confined to observations in Haiti, the use of traditional medicines is a globally widespread phenomenon. Attention must be drawn to the potential toxicity of such preparations and means found to ban their use in neonates.

Abstract Background Commonly, sequence and structure elements are assumed to evolve congruently, such that homologous sequence positions correspond to homologous structural features. Assuming congruent evolution, alignments based on sequence and structure similarity can therefore optimize both similarities at the same time in a single alignment. To model incongruent evolution, where sequence and structural features diverge positionally, we recently introduced bi-alignments. This generalization of sequence and structure-based alignments is best understood as alignments of two distinct pairwise alignments of the same entities: one modeling sequence similarity, the other structural similarity. Results Optimal bi-alignments with affine gap costs (or affine shift cost) for two constituent alignments can be computed exactly in quartic space and time. Even bi-alignments with affine shift and gap cost, as well as bi-alignment with sub-additive gap cost are optimized efficiently. Affine gap-cost bi-alignment of large proteins ( $$\sim 930$$ ∼ 930 aa) can be computed. Conclusion Affine cost bi-alignments are of practical interest to study shifts of protein sequences and protein structures relative to each other. Availability The affine cost bi-alignment algorithm has been implemented in Python 3 and Cython. It is available as free software from https://github.com/s-will/BiAlign/releases/tag/v0.3 and as bioconda package bialign.

Abstract Sialic acids as the terminal caps of the cellular glycocalyx play an essential role in self-recognition and were shown to modulate complement processes via interaction between α2,3-linked sialic acids and complement factor H. Previously, it was suggested that low molecular weight α2,8-linked polysialic acid (polySia avDP20) interferes with complement activation, but the exact molecular mechanism is still unclear. Here, we show that soluble polySia avDP20 (molecular weight of ~ 6 kDa) reduced the binding of serum-derived alternative pathway complement activator properdin to the cell surface of lesioned Hepa-1c1c7 and PC-12 neuroblastoma cells. Furthermore, polySia avDP20 added to human serum blocked the alternative complement pathway triggered by plate-bound lipopolysaccharides. Interestingly, no inhibitory effect was observed with monosialic acid or oligosialic acid with a chain length of DP3 and DP5. In addition, polySia avDP20 directly bound properdin, but not complement factor H. These data show that soluble polySia avDP20 binds properdin and reduces the alternative complement pathway activity. Results strengthen the previously described concept of self-recognition of sialylation as check-point control of complement activation in innate immunity.

Aim: To investigate the clinical relevance of the radiotherapy (RT) dose bath in patients treated for lower grade glioma (LGG). Methods: Patients (n = 17) treated with RT for LGG were assessed with neurocognitive function (NCF) tests and structural Magnetic Resonance Imaging (MRI) and categorized in subgroups based on tumour lateralisation. RT dose, volumetric results and cerebral microbleed (CMB) number were extracted for contralateral cerebrum, contralateral hippocampus, and cerebellum. The RT clinical target volume (CTV) was included in the analysis as a surrogate for focal tumour and other treatment effects. The relationships between RT dose, CTV, NCF and radiological outcome were analysed per subgroup. Results: The subgroup with left-sided tumours (n = 10) performed significantly lower on verbal tests. The RT dose to the right cerebrum, as well as CTV, were related to poorer performance on tests for processing speed, attention, and visuospatial abilities, and more CMB.In the subgroup with right-sided tumours (n = 7), RT dose in the left cerebrum was related to lower verbal memory performance, (immediate and delayed recall, r = −0.821, p = 0.023 and r = −0.937, p = 0.002, respectively), and RT dose to the left hippocampus was related to hippocampal volume (r = −0.857, p = 0.014), without correlation between CTV and NCF. Conclusion: By using a novel approach, we were able to investigate the clinical relevance of the RT dose bath in patients with LGG more specifically. We used combined MRI-derived and NCF outcome measures to assess radiation-induced brain damage, and observed potential RT effects on the left-sided brain resulting in lower verbal memory performance and hippocampus volume.

Abstract A new diazo derivative of a pyrrolidine-2,5-dione (8) fused at position-3,4 to a dibenzobarrelene backbone has been prepared by coupling the previously reported N-arylsuccinimid (5) precursor with aryldiazonium ion of aniline. The initial step of the reaction involved the preparation of the intermediate 9,10-dihydro-9,10-ethanoanthracene-11,12-dicarboxylic anhydride (3) through [4 + 2]-cycloaddition between anthracene and maleic anhydride in refluxing xylene which was then condensed with para-aminophenol to give compound 5. Compounds 5 and 8 were characterized by their physical, elemental, and spectroscopic data. 2D-NMR (COSY, HSQC, and HMBC) techniques were used to confirm the structure of compound 5. Compounds 5 (MIC = 32–128 μg/mL) and 8 (MIC = 16–256 μg/mL) along with the precursor 3 (MIC = 64–128 μg/mL) displayed moderate to low antimicrobial activities against selected bacterial and fungal species when compared with those of nystatin (MIC = 0.50–2 μg/mL) and ciprofloxacin (MIC = 0.50–16 μg/mL) used as reference drugs. Graphical Abstract

Abstract Background Progress towards malaria elimination has stagnated, partly because infections persisting at low parasite densities comprise a large reservoir contributing to ongoing malaria transmission and are difficult to detect. This study compared the performance of an ultrasensitive rapid diagnostic test (uRDT) designed to detect low density infections to a conventional RDT (cRDT), expert microscopy using Giemsa-stained thick blood smears (TBS), and quantitative polymerase chain reaction (qPCR) during a controlled human malaria infection (CHMI) study conducted in malaria exposed adults (NCT03590340). Methods Blood samples were collected from healthy Equatoguineans aged 18–35 years beginning on day 8 after CHMI with 3.2 × 103 cryopreserved, infectious Plasmodium falciparum sporozoites (PfSPZ Challenge, strain NF54) administered by direct venous inoculation. qPCR (18s ribosomal DNA), uRDT (Alere™ Malaria Ag P.f.), cRDT [Carestart Malaria Pf/PAN (PfHRP2/pLDH)], and TBS were performed daily until the volunteer became TBS positive and treatment was administered. qPCR was the reference for the presence of Plasmodium falciparum parasites. Results 279 samples were collected from 24 participants; 123 were positive by qPCR. TBS detected 24/123 (19.5% sensitivity [95% CI 13.1–27.8%]), uRDT 21/123 (17.1% sensitivity [95% CI 11.1–25.1%]), cRDT 10/123 (8.1% sensitivity [95% CI 4.2–14.8%]); all were 100% specific and did not detect any positive samples not detected by qPCR. TBS and uRDT were more sensitive than cRDT (TBS vs. cRDT p = 0.015; uRDT vs. cRDT p = 0.053), detecting parasitaemias as low as 3.7 parasites/µL (p/µL) (TBS and uRDT) compared to 5.6 p/µL (cRDT) based on TBS density measurements. TBS, uRDT and cRDT did not detect any of the 70/123 samples positive by qPCR below 5.86 p/µL, the qPCR density corresponding to 3.7 p/µL by TBS. The median prepatent periods in days (ranges) were 14.5 (10–20), 18.0 (15–28), 18.0 (15–20) and 18.0 (16–24) for qPCR, TBS, uRDT and cRDT, respectively; qPCR detected parasitaemia significantly earlier (3.5 days) than the other tests. Conclusions TBS and uRDT had similar sensitivities, both were more sensitive than cRDT, and neither matched qPCR for detecting low density parasitaemia. uRDT could be considered an alternative to TBS in selected applications, such as CHMI or field diagnosis, where qualitative, dichotomous results for malaria infection might be sufficient.

Female embryonic stem cells (ESCs) are the ideal model to study X chromosome inactivation (XCI) establishment; however, these cells are challenging to keep in culture. Here the authors create fluorescent ‘Xmas’ reporter mice as a renewable source of ESCs and show nucleosome remodelers Smarcc1 and Smarca4 create a nucleosome-free promoter region prior to the establishment of silencing.

Grooved liquid annular seals have a significant influence on the design of turbomachines. Corresponding lubrication film models need to account for the different friction behavior of the grooves compared to plain seals. However, there is a lack of reliable and validated models for this purpose. Thus, the applicability of a friction factor model is explored and a calibration method is presented. A single square groove is investigated by means of 96 steady-state RANS simulations for different operation conditions and groove geometries. The results are used to calibrate the friction model and successfully verify it in terms of the pressure drop over the groove. For validation, two full grooved seals with relatively large square grooves were investigated by experiment. The friction model was incorporated in a lubrication model and compared to the measurement data for the pressure difference and the resulting force for specified leakage and eccentricity. The model predictions for the pressure difference can be considered very good. The force predictions show significant deviation, but can be considered acceptable given the low force magnitudes and measurement uncertainty. The results offer a general validity to our friction model approach, assumptions and the calibration method.

The class II hydrophobin group (HFBII) is an extracellular group of proteins that contain the HFBII domain and eight conserved cysteine residues. These proteins are exclusively secreted by fungi and have multiple functions with a probable role as effectors. In the present study, a total of 45 amino acid sequences of hydrophobin class II proteins from different phytopathogenic fungi were retrieved from the NCBI database. We used the integration of well-designed bioinformatic tools to characterize and predict their physicochemical parameters, novel motifs, 3D structures, multiple sequence alignment (MSA), evolution, and functions as effector proteins through molecular docking. The results revealed new features for these protein members. The ProtParam tool detected the hydrophobicity properties of all proteins except for one hydrophilic protein (KAI3335996.1). Out of 45 proteins, six of them were detected as GPI-anchored proteins by the PredGPI server. Different 3D structure templates with high pTM scores were designed by Multifold v1, AlphaFold2, and trRosetta. Most of the studied proteins were anticipated as apoplastic effectors and matched with the ghyd5 gene of Fusarium graminearum as virulence factors. A protein–protein interaction (PPI) analysis unraveled the molecular function of this group as GTP-binding proteins, while a molecular docking analysis detected a chitin-binding effector role. From the MSA analysis, it was observed that the HFBII sequences shared conserved 2 Pro (P) and 2 Gly (G) amino acids besides the known eight conserved cysteine residues. The evolutionary analysis and phylogenetic tree provided evidence of episodic diversifying selection at the branch level using the aBSREL tool. A detailed in silico analysis of this family and the present findings will provide a better understanding of the HFBII characters and evolutionary relationships, which could be very useful in future studies.

Exposure to repeated mild blast traumatic brain injury (mbTBI) is common in combat soldiers and the training of Special Forces. Evidence suggests that repeated exposure to a mild or subthreshold blast can cause serious and long-lasting impairments, but the mechanisms causing these symptoms are unclear. In this study, we characterise the effects of single and tightly coupled repeated mbTBI in Sprague–Dawley rats exposed to shockwaves generated using a shock tube. The primary outcomes are functional neurologic function (unconsciousness, neuroscore, weight loss, and RotaRod performance) and neuronal density in brain regions associated with sensorimotor function. Exposure to a single shockwave does not result in functional impairments or histologic injury, which is consistent with a mild or subthreshold injury. In contrast, exposure to three tightly coupled shockwaves results in unconsciousness, along with persistent neurologic impairments. Significant neuronal loss following repeated blast was observed in the motor cortex, somatosensory cortex, auditory cortex, and amygdala. Neuronal loss was not accompanied by changes in astrocyte reactivity. Our study identifies specific brain regions particularly sensitive to repeated mbTBI. The reasons for this sensitivity may include exposure to less attenuated shockwaves or proximity to tissue density transitions, and this merits further investigation. Our novel model will be useful in elucidating the mechanisms of sensitisation to injury, the temporal window of sensitivity and the evaluation of new treatments.

Abstract Background Transcription factors (TFs) are proteins controlling the flow of genetic information by regulating cellular gene expression. A better understanding of TFs in a bacterial community context may open novel revenues for exploring gene regulation in ecosystems where bacteria play a key role. Here we describe PredicTF, a platform supporting the prediction and classification of novel bacterial TF in single species and complex microbial communities. PredicTF is based on a deep learning algorithm. Results To train PredicTF, we created a TF database (BacTFDB) by manually curating a total of 11,961 TF distributed in 99 TF families. Five model organisms were used to test the performance and the accuracy of PredicTF. PredicTF was able to identify 24–62% of the known TFs with an average precision of 88% in our five model organisms. We demonstrated PredicTF using pure cultures and a complex microbial community. In these demonstrations, we used (meta)genomes for TF prediction and (meta)transcriptomes for determining the expression of putative TFs. Conclusion PredicTF demonstrated high accuracy in predicting transcription factors in model organisms. We prepared the pipeline to be easily implemented in studies profiling TFs using (meta)genomes and (meta)transcriptomes. PredicTF is an open-source software available at https://github.com/mdsufz/PredicTF .

Abstract Background While antibodies can provide significant protection from SARS-CoV-2 infection and disease sequelae, the specific attributes of the humoral response that contribute to immunity are incompletely defined. Methods We employ machine learning to relate characteristics of the polyclonal antibody response raised by natural infection to diverse antibody effector functions and neutralization potency with the goal of generating both accurate predictions of each activity based on antibody response profiles as well as insights into antibody mechanisms of action. Results To this end, antibody-mediated phagocytosis, cytotoxicity, complement deposition, and neutralization were accurately predicted from biophysical antibody profiles in both discovery and validation cohorts. These models identified SARS-CoV-2-specific IgM as a key predictor of neutralization activity whose mechanistic relevance was supported experimentally by depletion. Conclusions Validated models of how different aspects of the humoral response relate to antiviral antibody activities suggest desirable attributes to recapitulate by vaccination or other antibody-based interventions.

Ruiz-Molina et al. design a synthetic protein, MFHR13, as a multi-target complement regulator. They demonstrate that it protects sheep erythrocytes from complement attack exhibiting 26 and 4-fold the regulatory activity of eculizumab and human Factor H, respectively, which highlights its therapeutic potential.

Abstract The ability to cryopreserve mosquitoes would revolutionize work on these vectors of major human infectious diseases by conserving stocks, new isolates, lab-bred strains, and transgenic lines that currently require continuous life cycle maintenance. Efforts over several decades to develop a method for cryopreservation have, until now, been fruitless: we describe here a method for the cryopreservation of Anopheles stephensi embryos yielding hatch rates of ~ 25%, stable for > 5 years. Hatched larvae developed into fertile, fecund adults and blood-fed females, produced fully viable second generation eggs, that could be infected with Plasmodium falciparum at high intensities. The key components of the cryopreservation method are: embryos at 15–30 min post oviposition, two incubation steps in 100% deuterated methanol at − 7 °C and − 14.5 °C, and rapid cooling. Eggs are recovered by rapid warming with concomitant dilution of cryoprotectant. Eggs of genetically modified A. stephensi and of A. gambiae were also successfully cryopreserved. This enabling methodology will allow long-term conservation of mosquitoes as well as acceleration of genetic studies and facilitation of mass storage of anopheline mosquitoes for release programs.

Abstract Background Interferon regulatory factor-8 (IRF8) and nuclear factor-activated T cells c1 (NFATc1) are two transcription factors that have an important role in osteoclast differentiation. Thanks to ChIP-seq technology, scientists can now estimate potential genome-wide target genes of IRF8 and NFATc1. However, finding target genes that are consistently up-regulated or down-regulated across different studies is hard because it requires analysis of a large number of high-throughput expression studies from a comparable context. Method We have developed a machine learning based method, called, Cohort-based TF target prediction system (cTAP) to overcome this problem. This method assumes that the pathway involving the transcription factors of interest is featured with multiple “functional groups” of marker genes pertaining to the concerned biological process. It uses two notions, Gene-Present Sufficiently (GP) and Gene-Absent Insufficiently (GA), in addition to log2 fold changes of differentially expressed genes for the prediction. Target prediction is made by applying multiple machine-learning models, which learn the patterns of GP and GA from log2 fold changes and four types of Z scores from the normalized cohort’s gene expression data. The learned patterns are then associated with the putative transcription factor targets to identify genes that consistently exhibit Up/Down gene regulation patterns within the cohort. We applied this method to 11 publicly available GEO data sets related to osteoclastgenesis. Result Our experiment identified a small number of Up/Down IRF8 and NFATc1 target genes as relevant to osteoclast differentiation. The machine learning models using GP and GA produced NFATc1 and IRF8 target genes different than simply using a log2 fold change alone. Our literature survey revealed that all predicted target genes have known roles in bone remodeling, specifically related to the immune system and osteoclast formation and functions, suggesting confidence and validity in our method. Conclusion cTAP was motivated by recognizing that biologists tend to use Z score values present in data sets for the analysis. However, using cTAP effectively presupposes assembling a sizable cohort of gene expression data sets within a comparable context. As public gene expression data repositories grow, the need to use cohort-based analysis method like cTAP will become increasingly important.

A visibility-modelling based method is introduced to determine the elevation and azimuth angles for a signal received at a quasi-randomly arranged (2-D) array. The method is optimal for the number of antennas when the array is configured such that no antenna baselines are repeated. Simulation shows that our method has comparable accuracy to subspace-based acrlong doa algorithms like acrfull music and measured data shows that it is both more accurate and faster than visibility based methods like acrlong ra all-sky imaging.

The dog is valued as a companion animal and increasingly recognized as a model for human disorders. Given the importance of T cells in health and disease, comprehensive knowledge of canine T cells can contribute to our understanding of pathogenesis mechanisms and inform the development of new treatment strategies. However, the diversity of canine T cells is still poorly understood mainly due to the lack of species-reactive antibodies for use in flow cytometry. The aim of this study was to generate a detailed atlas of peripheral blood TCRαβ+ T cells of healthy dogs using single-cell RNA-sequencing (scRNAseq) combined with immune repertoire sequencing. A total of 22 TCRαβ+ T cell clusters were identified, which were classified into three major groups: CD4-dominant (11 clusters), CD8A-dominant (8 clusters), and CD4/CD8A-mixed (3 clusters). Based on differential gene expression, distinct differentiation states (naïve, effector, memory, exhausted) and lineages (e.g. CD4 T helper and regulatory T cells) could be distinguished. Importantly, several T cell populations were identified, which have not been described in dogs before. Of particular note, our data provide first evidence for the existence of canine mucosa-associated invariant T cell (MAIT)-like cells, representing one of three newly identified FCER1G+ innate-like CD8A+ T cell populations in the peripheral blood of healthy dogs. In conclusion, using scRNAseq combined with immune repertoire sequencing we were able to resolve canine TCRαβ+ T cell populations at unprecedented resolution. The peripheral blood TCRαβ+ T cell atlas of healthy dogs generated here represents an important reference data set for future studies and is of relevance for identifying new targets for T cell-specific therapies.

Abstract Carbon nanotube‐spandex textiles are rapidly gaining in popularity as sensors for human motion, yet their use as—and comparison to—viable clinical‐based instrumentation has not been thoroughly investigated. Herein, the use of novel yarn‐based sensors that show excellent characteristics, ideal for joint kinematic sensing, is described. Knee kinematic monitoring of nine healthy participants while walking on a treadmill is examined. This is enabled through a 3D‐printed knee brace integrated with a wireless transmission device. The design, development, and testing of the wearable device is presented along with wireless data capture and processing. Additionally, the findings are compared in vivo to those reported by a reference optoelectronic measurement system (KneeKG) for validation purposes. The results show a high correlation between both systems, with an average Pearson's r‐value of 0.89 across each corresponding knee. This study is the first to explore the use of these novel yarn sensors for sagittal knee kinematic monitoring on participants during trials and validate the findings via an optoelectronic measurement system.

In year one of the COVID-19 epidemic, the incidence of infection for US carceral populations was 5.5-fold higher than that in the community. Prior to the rapid roll out of a comprehensive jail surveillance program of Wastewater-Based Surveillance (WBS) and individual testing for SARS-CoV-2, we sought the perspectives of formerly incarcerated individuals regarding mitigation strategies against COVID-19 to inform acceptability of the new program. In focus groups, participants discussed barriers to their receiving COVID-19 testing and vaccination. We introduced WBS and individual nasal self-testing, then queried if wastewater testing to improve surveillance of emerging outbreaks before case numbers surged, and specimen self-collection, would be valued. The participants' input gives insight into ways to improve the delivery of COVID-19 interventions. Hearing the voices of those with lived experiences of incarceration is critical to understanding their views on infection control strategies and supports including justice-involved individuals in decision-making processes regarding jail-based interventions.