Clostridium chrysemydis sp. nov., isolated from the faecal material of a painted turtle.

A strict anaerobic, Gram-stain-positive rod-shaped bacterium, designated PTT, was isolated from the faecal material of a painted turtle (Chrysemys picta). Based on a comparative 16S rRNA gene sequence analysis, the isolate was assigned to Clostridium sensu stricto with the highest sequence similarities to Clostridium moniliforme (97.4 %), Clostridium sardiniense (97.2 %) and the misclassified organism Eubacterium multiforme (97.1 %). The predominant cellular fatty acids of strain PTT were C14 : 0, C16 : 0 and an unidentified product with an equivalent chain length of 14.969. The G+C content determined from the genome was 28.8 mol%. The fermentation end products from glucose were acetate and butyrate with no alcohols detected and trace amounts of CO2 and H2 also detected; no respiratory quinones were detected. Based on biochemical, phylogenetic, genotypic and chemotaxonomic criteria, the isolate represents a novel species of the genus Clostridium for which the name Clostridium chrysemydis sp. nov. is proposed. The type strain is strain PTT (=CCUG 74180T=ATCC TSD-219T).

Membrane and Actin Tethering Transitions Help IQGAP1 Coordinate GTPase and Lipid Messenger Signaling.

The coordination of lipid messenger signaling with cytoskeletal regulation is central to many organelle-specific regulatory processes. This coupling often depends on the function of multidomain scaffolds that orchestrate transient interactions among multiple signaling intermediates and regulatory proteins on organelles. The number of possible scaffold interaction partners and the ability for these interactions to occur at different timescales makes investigations of scaffold functions challenging. This work employs live cell imaging to probe how the multidomain scaffold IQ motif containing GTPase activating protein 1 (IQGAP1) coordinates the activities of proteins affecting local actin polymerization, membrane processing, and phosphoinositide signaling. Using endosomes that are confined by a local actin network as a model system, we demonstrate that IQGAP1 can transition between different actin and endosomal membrane tethered states. Fast scaffold binding/disassociation transitions are shown to be driven by interactions between C-terminal scaffold domains and Rho GTPases at the membrane. Fluctuations in these binding modes are linked to negative regulation of actin polymerization. Although this control governs core elements of IQGAP1 dynamics, actin binding by the N-terminal calponin homology domain of the scaffold is shown to help the scaffold track the temporal development of endosome membrane markers, implying actin associations bolster membrane and actin coordination. Importantly, these effects are not easily distilled purely through standard (static) co-localization analyses or traditional pathway perturbations methods and were resolved by performing dynamic correlation and multiple regression analyses of IQGAP1 scaffold mutants. Using these capabilities with pharmacological inhibition, we provide evidence that membrane tethering is dependent on the activities of the lipid kinase phosphoinositide 3-kinase in addition to the Rho GTPases Rac1 and Cdc42. Overall, these methods and results point to a scaffold tethering mechanism that allows IQGAP1 to help control the amplitude of phosphoinositide lipid messenger signaling by coordinating signaling intermediate activities with the development and disassembly of local actin cytoskeletal networks.

Pseudomonas aeruginosa PcrV and Psl, the Molecular Targets of Bispecific Antibody MEDI3902, Are Conserved Among Diverse Global Clinical Isolates.

Background: Bispecific antibody MEDI3902, targeting the Pseudomonas aeruginosa type 3 secretion system (PcrV) and Psl exopolysaccharide, is currently in phase 2b development for prevention of nosocomial pneumonia in patients undergoing mechanical ventilation. We surveyed a diverse collection of isolates to study MEDI3902 epitope conservation and protective activity. Methods: P. aeruginosa clinical isolates (n = 913) were collected from diverse patients and geographic locations during 2003-2014. We conducted whole-genome sequencing; performed PcrV and Psl expression analyses via immunoblotting and enzyme-linked immunosorbent assay, respectively; performed crystallography to determine the MEDI3902 PcrV epitope, using anti-PcrV Fab and PcrV components (resolved at 2.8 Å); and evaluated MEDI3902 protective activity against select isolates in vitro and in vivo. Results: Intact psl operon and pcrV genes were present in 94% and 99% of isolates, respectively, and 99.9% of isolates contained at least one of the genetic elements. Anti-Psl binding was confirmed in tested isolates harboring a complete Psl operon or lacking nonessential psl genes. We identified 46 PcrV variant sequences, and MEDI3902-PcrV contact residues were preserved. MEDI3902 maintained potent in vivo activity against various strains, including strains expressing only a single target. Conclusions: Psl and PcrV are highly prevalent in global clinical isolates, suggesting MEDI3902 can mediate broad coverage against P. aeruginosa.

Correction to: Breast cancer subtype discordance: impact on post-recurrence survival and potential treatment options.

It has been highlighted that the original manuscript [1] contains a typesetting error regarding the authorship.

Breast cancer subtype discordance: impact on post-recurrence survival and potential treatment options.

BACKGROUND: Recent studies have shown that breast cancer subtype can change from the primary tumour to the recurrence. Discordance between primary and recurrent breast cancer has implications for further treatment and ultimately prognosis. The aim of the study was to determine the rate of change between primary and recurrence of breast cancer and to assess the impact of these changes on survival and potential treatment options. METHODS: Patient demographics were collected on those who underwent surgery for breast cancer between 2001 and 2014 and had a recurrence with biopsy results and pathology scoring of both the primary and recurrence. RESULTS: One hundred thirty two consecutive patients were included. There were 31 (23.5%) changes in subtype. Discordance occurred most frequently in luminal A breast cancer (n = 20), followed by triple negative (n = 4), luminal B (n = 3) and HER2 (n = 3). Patients who changed from luminal A to triple negative (n = 18) had a significantly worse post-recurrence survival (p < 0.05) with overall survival approaching significance (p = 0.064) compared to concordant luminal A cases (n = 46). Overall receptor discordance rates were: estrogen receptor 20.4% (n = 27), progesterone receptor 37.7% (n = 50) and HER2 3% (n = 4). Loss of estrogen receptor and progesterone receptor was more common than gain (21 vs. 6 (p = 0.04) and 44 vs. 6 (p = 0.01) respectively). Nine patients (6.8%) gained receptor status potentially impacting treatment options. CONCLUSION: Discordance in subtype and receptor status occurs between primary and recurrent breast cancer, ultimately affecting survival and potentially impacting treatment options.

Patients' attitude towards travelling for breast services versus waiting longer for local services

Geographical access is a cornerstone of health care provision. However, prolonged waiting for breast clinic appointments in local services results in delayed diagnosis and excessive anxiety for patients. In this study, we present a patient satisfaction survey results of an initiative to offer out-patient clinic appointments for non-urgent patients referred to the breast unit in Letterkenny General Hospital (LGH), Ireland, and exceeded the recommended waiting period of 12 weeks. These patients were offered appointment in University Hospital Galway (UCHG), which is an average travel time of about 3.5-4.5 hours away from LGH. 163 patients out of 336 (48.5%) patients actively waiting more than 12 weeks for appointments in LGH accepted alternative appointments in UCHG. Despite the long travel distance for these patients, 100% of them reported high satisfaction and 97.3% said they would accept further UCHG appointments if a similar situation of prolonged waiting in LGH arises. None of these patients were diagnosed with cancer, and only one had a benign lumpectomy. This study showed that if offered alternative appointments, just under half of the patients would accept. The initiative provides a feasible solution for long waiters, and the survey shows that patients' satisfaction remains high despite long travel.

Prospective comparison of outcome after treatment for triple-negative and non-triple-negative breast cancer.

INTRODUCTION: Triple-negative breast cancers (TNBC) are associated with a poor prognosis owing to an aggressive phenotype. We aimed to carry out a prospective study comparing management strategies and response to therapy in TNBC and non-TNBC patients. METHODS: Data were obtained from a prospectively maintained database of patients treated for breast cancer. RESULTS: A total of 142 TNBC and 142 age-, stage- and NPI-matched non-TNBC patients were treated. The difference in overall survival between the 2 groups was statistically significant (77% of TNBC patients alive at a mean follow-up of 32 months, versus 92% of non-TNBC patients at a mean follow-up of 38 months, P = 0.0 Log rank test). This survival difference was found to be independent of NPI (P = 0.0 Log rank test). Locoregional recurrence rates were similar between TNBC patients who were treated with wide local excision versus mastectomy (P = 0.449 Log rank test). A significant difference in survival was noted between TNBC patients who responded differentially to neoadjuvant chemotherapy (P = 0.035 Log rank test). CONCLUSION: Patients with TNBC have adverse outcomes despite aggressive treatment. The development of effective targeted therapies is essential for this breast cancer subtype.

Human islets and dendritic cells generate post-translationally modified islet autoantigens.

The initiation of type 1 diabetes (T1D) requires a break in peripheral tolerance. New insights into neoepitope formation indicate that post-translational modification of islet autoantigens, for example via deamidation, may be an important component of disease initiation or exacerbation. Indeed, deamidation of islet autoantigens increases their binding affinity to the T1D highest-risk human leucocyte antigen (HLA) haplotypes HLA-DR3/DQ2 and -DR4/DQ8, increasing the chance that T cells reactive to deamidated autoantigens can be activated upon T cell receptor ligation. Here we investigated human pancreatic islets and inflammatory and tolerogenic human dendritic cells (DC and tolDC) as potential sources of deamidated islet autoantigens and examined whether deamidation is altered in an inflammatory environment. Islets, DC and tolDC contained tissue transglutaminase, the key enzyme responsible for peptide deamidation, and enzyme activity increased following an inflammatory insult. Islets treated with inflammatory cytokines were found to contain deamidated insulin C-peptide. DC, heterozygous for the T1D highest-risk DQ2/8, pulsed with native islet autoantigens could present naturally processed deamidated neoepitopes. HLA-DQ2 or -DQ8 homozygous DC did not present deamidated islet peptides. This study identifies both human islets and DC as sources of deamidated islet autoantigens and implicates inflammatory activation of tissue transglutaminase as a potential mechanism for islet and DC deamidation.

Influence of complications following immediate breast reconstruction on breast cancer recurrence rates.

BACKGROUND: The rate of immediate breast reconstruction is rising. Postoperative infections are more frequent in patients who undergo reconstruction. The inflammatory response to a postoperative infection can increase the risk of tumour recurrence in other forms of cancer through the release of proinflammatory mediators. The aim of this study was to assess the relationship between complications and breast cancer recurrence in patients undergoing immediate reconstruction. METHODS: This was a review of a prospectively maintained database of all patients who had immediate breast reconstruction between 2004 and 2009 at Galway University Hospital, a tertiary breast cancer referral centre serving the west of Ireland. All patients had a minimum follow-up of 5 years. Outcomes assessed included the development of wound complications and breast cancer recurrence. The data were evaluated by univariable and multivariable Cox regression analysis. RESULTS: A total of 229 patients who underwent immediate reconstruction were identified. The overall 5-year recurrence-free survival rate was 85·6 per cent. Fifty-three patients (23·1 per cent) had wound complications, of whom 44 (19·2 per cent) developed a wound infection. There was a significantly greater risk of developing systemic recurrence among patients who experienced a postoperative wound complication compared with those without a complication (hazard ratio 4·94, 95 per cent c.i. 2·72 to 8·95; P < 0·001). This remained significant after adjusting for Nottingham Prognostic Index group in the multivariable analysis. The 5-year recurrence-free survival rate for patients who had a wound complication was 64 per cent, compared with 89·2 per cent in patients without a complication (P < 0·001). CONCLUSION: This study has demonstrated that wound complications after immediate breast reconstructive surgery have significant implications for patients with breast cancer. Strategies are required to minimize the risk of postoperative wound complications in patients with breast cancer undergoing immediate reconstruction.

Collective dynamics of processive cytoskeletal motors.

Major cellular processes are supported by various biomolecular motors that usually operate together as teams. We present an overview of the collective dynamics of processive cytokeletal motor proteins based on recent experimental and theoretical investigations. Experimental studies show that multiple motors function with different degrees of cooperativity, ranging from negative to positive. This effect depends on the mechanical properties of individual motors, the geometry of their connections, and the surrounding cellular environment. Theoretical models based on stochastic approaches underline the importance of intermolecular interactions, the properties of single motors, and couplings with cellular medium in predicting the collective dynamics. We discuss several features that specify the cooperativity in motor proteins. Based on this approach a general picture of collective dynamics of motor proteins is formulated, and the future directions and challenges are discussed.

Avibactam and class C ß-lactamases: mechanism of inhibition, conservation of the binding pocket, and implications for resistance.

Avibactam is a novel non-ß-lactam ß-lactamase inhibitor that inhibits a wide range of ß-lactamases. These include class A, class C, and some class D enzymes, which erode the activity of ß-lactam drugs in multidrug-resistant pathogens like Pseudomonas aeruginosa and Enterobacteriaceae spp. Avibactam is currently in clinical development in combination with the ß-lactam antibiotics ceftazidime, ceftaroline fosamil, and aztreonam. Avibactam has the potential to be the first ß-lactamase inhibitor that might provide activity against class C-mediated resistance, which represents a growing concern in both hospital- and community-acquired infections. Avibactam has an unusual mechanism of action: it is a covalent inhibitor that acts via ring opening, but in contrast to other currently used ß-lactamase inhibitors, this reaction is reversible. Here, we present a high-resolution structure of avibactam bound to a class C ß-lactamase, AmpC, from P. aeruginosa that provided insight into the mechanism of both acylation and recyclization in this enzyme class and highlighted the differences observed between class A and class C inhibition. Furthermore, variants resistant to avibactam that identified the residues important for inhibition were isolated. Finally, the structural information was used to predict effective inhibition by sequence analysis and functional studies of class C ß-lactamases from a large and diverse set of contemporary clinical isolates (P. aeruginosa and several Enterobacteriaceae spp.) obtained from recent infections to understand any preexisting variability in the binding pocket that might affect inhibition by avibactam.

Emergency surgery preoperative delays: realities, economic impacts and gains of a second emergency operating theatre.

INTRODUCTION: Time-to-theatre (TTT) is a key performance indicator of theatre efficiency and delayed TTT incurs significant costs and poor clinical outcomes. An increasing Irish population in conjunction with an ageing population puts increasing pressure on emergency surgical services across Ireland. We examined our institution's experience with introducing a second emergency theatre and semi-elective theatre lists for acute surgical patients. METHODS: A retrospective review of electronic, prospectively maintained databases was performed between 1 February 2018 and 31 January 2020. A cost analysis was conducted to assess the economic impact of delayed TTT. The cost-saving benefit of introducing a second emergency theatre and semi-elective Kaizen lists was then calculated and compared with 2012-2014 figures from our institution. RESULTS: In total, 6,679 procedures were performed. Overall mean TTT was 16h, 10h shorter than before the introduction of a second emergency theatre and Kaizen theatre lists (p < 0.001). Patients aged >65 years, who are historically a significantly disadvantaged group, had a shorter TTT following the introduction of a second emergency theatre. The economic advantage of a second emergency theatre resulted in a cost saving of €3,674,538 over 24 months. CONCLUSION: Investment in emergency surgical services resulted in more efficient access to emergency theatres. There was a reduction in out-of-hours operating across all specialties and across the more at-risk groups such as those over the age of 65, who had an overall reduction in TTT. This had significant financial benefits and likely reduced the clinical risk associated with delayed TTT and out-of-hours operating.

Continuous spatial field confocal thermometry using lanthanide doped tellurite glass.

Distinguishing between microscopic variances in temperature in both space and time with high precision can open up new opportunities in optical sensing. In this paper, we present a novel approach to optically measure temperature from the fluorescence of erbium:ytterbium doped tellurite glass, with fast temporal resolution at micron-scale localisation over an area with sub millimetre spatial dimensions. This confocal-based approach provides a micron-scale image of temperature variations over a 200 µ m × 200 µ m field of view at sub-1 second time intervals. We test our sensing platform by monitoring the real-time evaporation of a water droplet over a wide field of view and track it's evaporative cooling effect on the glass where we report a net temperature change of 6.97 K ± 0.03 K. This result showcases a confocal approach to thermometry to provide high temporal and spatial resolution over a microscopic field of view with the goal of providing real-time measures of temperature on the micro-scale.

Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy).

Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.

Extreme seasonal water-level changes and hydraulic modeling of deep, high-altitude, glacial-carved, Himalayan lakes.

Himalayan lakes represent critical water resources, culturally important waterbodies, and potential hazards. Some of these lakes experience dramatic water-level changes, responding to seasonal monsoon rains and post-monsoonal draining. To address the paucity of direct observations of hydrology in retreating mountain glacial systems, we describe a field program in a series of high altitude lakes in Sagarmatha National Park, adjacent to Ngozumba, the largest glacier in Nepal. In situ observations find extreme (>12 m) seasonal water-level changes in a 60-m deep lateral-moraine-dammed lake (lacking surface outflow), during a 16-month period, equivalent to a 5 [Formula: see text] m[Formula: see text] volume change annually. The water column thermal structure was also monitored over the same period. A hydraulic model is constructed, validated against observed water levels, and used to estimate hydraulic conductivities of the moraine soils damming the lake and improves our understanding of this complex hydrological system. Our findings indicate that lake level compared to the damming glacier surface height is the key criterion for large lake fluctuations, while lakes lying below the glacier surface, regulated by surface outflow, possess only minor seasonal water-level fluctuations. Thus, lakes adjacent to glaciers may exhibit very different filling/draining dynamics based on presence/absence of surface outflows and elevation relative to retreating glaciers, and consequently may have very different fates in the next few decades as the climate warms.

Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

Accurately identifying somatic mutations is essential for precision oncology and crucial for calculating tumor-mutational burden (TMB), an important predictor of response to immunotherapy. For tumor-only variant calling (i.e., when the cancer biopsy but not the patient's normal tissue sample is sequenced), accurately distinguishing somatic mutations from germline variants is a challenging problem that, when unaddressed, results in unreliable, biased, and inflated TMB estimates. Here, we apply machine learning to the task of somatic vs germline classification in tumor-only solid tumor samples using TabNet, XGBoost, and LightGBM, three machine-learning models for tabular data. We constructed a training set for supervised classification using features derived exclusively from tumor-only variant calling and drawing somatic and germline truth labels from an independent pipeline using the patient-matched normal samples. All three trained models achieved state-of-the-art performance on two holdout test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (AUC > 94%), and a metastatic melanoma dataset (AUC > 85%). Concordance between matched-normal and tumor-only TMB improves from R2 = 0.006 to 0.71-0.76 with the addition of a machine-learning classifier, with LightGBM performing best. Notably, these machine-learning models generalize across cancer subtypes and capture kits with a call rate of 100%. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of white patients due to the racial biases of germline databases. We show that our approach with XGBoost and LightGBM eliminates this significant racial bias in tumor-only variant calling.

The stoned age: Sex differences in the effects of adolescent cannabinoid exposure on prefrontal cortex structure and function in animal models.

Cannabis is the most used drug during adolescence, which is a period of enhanced cortical plasticity and synaptic remodeling that supports behavioral, cognitive, and emotional maturity. In this chapter, we review preclinical studies indicating that adolescent exposure to cannabinoids has lasting effects on the morphology and synaptic organization of the prefrontal cortex and associated circuitry, which may lead to cognitive dysfunction later in life. Additionally, we reviewed sex differences in the effects of adolescent cannabinoid exposure with a focus on brain systems that support cognitive functioning. The body of evidence indicates enduring sex-specific effects in behavior and organization of corticolimbic circuitry, which appears to be influenced by species, strain, drug, route of administration, and window/pattern of drug exposure. Caution should be exercised when extrapolating these results to humans. Adopting models that more closely resemble human cannabis use will provide more translationally relevant data concerning the long-term effects of cannabis use on the adolescent brain.

Ultrathin side-viewing needle probe for optical coherence tomography.

We present the smallest reported side-viewing needle probe for optical coherence tomography (OCT). Design, fabrication, optical characterization, and initial application of a 30-gauge (outer diameter 0.31 mm) needle probe are demonstrated. Extreme miniaturization is achieved by using a simple all-fiber probe design incorporating an angle-polished and reflection-coated fiber-tip beam deflector. When inserted into biological tissue, aqueous interstitial fluids reduce the probe's inherent astigmatism ratio to 1.8, resulting in a working distance of 300 µm and a depth-of-field of 550 µm with beam diameters below 30 µm. The needle probe was interfaced with an 840 nm spectral-domain OCT system and the measured sensitivity was shown to be only 7 dB lower than that of a comparable galvo-scanning sample arm configuration. 3D OCT images of lamb lungs were acquired over a depth range of ~600 µm, showing individual alveoli and bronchioles.

Detection of Helicobacter in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis.

In animals, infection by the Epsilonproteobacteria Helicobacter spp. and H. cetorum is widespread. It has been suggested that H. cetorum may cause gastritis in cetaceans. The aim of our study was to investigate the presence of Helicobacter spp. in the fecal material of the endangered Yangtze finless porpoise Neophocaena phocaenoides asiaeorientalis. The fecal material of 12 porpoises living in the wild in Poyang Lake and 1 porpoise living in captivity at the Wuhan Baiji Dolphinarium were examined by PCR for the presence of Helicobacter spp. The fecal material of 8 of 12 wild porpoises and the captive porpoise were positive for Helicobacter spp. as determined by PCR using Helicobacter-specific primers, which target the 16S rRNA gene. A 16S rRNA clone library was then prepared from 1 sample isolated from a female porpoise living in the wild. DNA sequence analysis from 3 of the clones showed 98 to 99% identity to the H. cetorum 16S rRNA gene. These results demonstrate the prevalence of Helicobacter spp. and H. cetorum in endangered freshwater finless porpoises.