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BackgroundMany individuals with type 1 diabetes retain residual beta-cell function. Sustained endogenous insulin and C-peptide secretion is associated with reduced diabetes related complications, but underlying mechanisms remain unclear. Lower circulating numbers of endothelial and hematopoietic progenitor cells (EPCs and HPCs), and the inability to increase the count of these cells in response to exercise, are also associated with increased diabetes complications and cardiovascular disease. It is unknown whether residual beta-cell function influences HPCs and EPCs. Thus, this study examined the influence of residual beta-cell function in type 1 diabetes upon exercise-induced changes in haematopoietic (HPCs) and endothelial progenitor cells (EPCs).MethodsParticipants with undetectable stimulated C-peptide (n=11; Cpepund), 10 high C-peptide (Cpephigh; >200 pmol/L), and 11 non-diabetes controls took part in this observational exercise study, completing 45 minutes of intensive walking at 60% V˙O2peak. Clinically significant HPCs (CD34+) and EPCs (CD34+VEGFR2+) phenotypes for predicting future adverse cardiovascular outcomes, and subsequent cell surface expression of chemokine receptor 4 (CXCR4) and 7 (CXCR7), were enumerated at rest and immediately post-exercise by flow cytometry.ResultsExercise increased HPCs and EPCs phenotypes similarly in the Cpephigh and control groups (+34-121% across phenotypes, pund group did not significantly increase from rest, even after controlling for diabetes duration. Strikingly, the post-exercise Cpepund counts were still lower than Cpephigh at rest.ConclusionsResidual beta-cell function is associated with an intact exercise-induced HPCs and EPCs mobilisation. As key characteristics (age, fitness, HbA1c) were similar between groups, the mechanisms underpinning the absent mobilisation within those with negative C-peptide, and the vascular implications, require further investigation.

5030 Background: Up to 30% of patients with germ cell tumor of the testis (TGCT) develop recurrent disease after initial treatment. The majority of recurrences occur in the first 2 years after treatment. Very late recurrence (LR), i.e. > 5 years after initial presentation, occurs in about 1% of patients with TGCT and is associated with poor prognosis. Current guideline does not require follow-up after 5 years to detect LR, except in those presenting with metastatic NSGCT. Methods: We retrospectively reviewed the records of patients from the Genitourinary Medical Oncology clinic at the M. D. Anderson Cancer Center, who developed recurrent disease > 5 years after their initial diagnosis of TGCT. Specifically, we examined the pathology and location of their primary and recurrent tumors, treatments rendered (e.g., surgery, radiotherapy, chemotherapy), and overall survival after LR. Overall survival from the time of LR was estimated using Kaplan-Meier estimates and compared for patient subgroups with log rank tests. Fisher’s exact test was used to compare proportions in patient subgroups. Results: We identified 25 patients who developed LR between July 2007 and August 2020. Age at time of LR: median 46 years (range, 29-61); time of late LR: median 16.1 years (range, 6.8-33.1 years) after diagnosis. Stage at time of diagnosis: I – 5, II-IIIA – 13, IIIB-C – 7. Pathology of primary: nonseminoma with yolk sac tumor or teratoma – 15, nonseminoma without yolk sac tumor or teratoma – 1, not available – 9. Pathology of LR: somatic transformation to carcinoma – 9, somatic transformation to sarcoma – 2, nonseminoma with yolk sac tumor or teratoma – 10, nonseminoma without yolk sac tumor or teratoma – 2, not available – 2. Overall, 5 patients (20%) had LR in retroperitoneum alone, 6 patients (24%) had non-retroperitoneal nodal or pulmonary metastases, and 14 patients (56%) had non-pulmonary visceral metastases. Nine patients (36%) are deceased, ten patients (40%) are alive without evidence of disease (NED), and 6 patients are alive with disease (24%). With a median follow-up of 42 months, 68% of patients are alive 3 years after LR. Patients with prior post-chemotherapy consolidation surgery have longer survival, 80% vs. 53% at 3 years, respectively (p = 0.01). Additionally, at their last follow-up 9/12 vs. 1/13 patients were NED with vs. without prior post-chemotherapy consolidation surgery, respectively (p = 0.001). Conclusions: Patients with LR > 5 years after initial presentation tend to harbor nonseminoma (with yolk sac tumor and or teratoma). Among these patients, a majority who did not undergo surgery to remove residual disease after chemotherapy developed somatic transformation and succumbed to their LR. Further investigation into rates of LR among all patients may be warranted given the poor survival after LR.

The speckled dace (Rhinichthys osculus) is small cyprinid fish that is widespread in the Western USA. Currently treated as a single species, speckled dace consists of multiple evolutionary lineages that can be recognized as species and subspecies throughout its range. Recognition of taxonomic distinctiveness of speckled dace populations is important for developing conservation strategies. In this study, we collected samples of speckled dace from 38 locations in the American West, with a focus on California. We used RAD sequencing to extract thousands of SNPs across the genome from samples to identify genetic differences among seven California populations informally recognized as speckled dace subspecies: Amargosa, Owens, Long Valley, Lahontan, Klamath, Sacramento, and Santa Ana speckled dace. We performed principal component analysis, admixture analysis, estimated pairwise Fst, and constructed a phylogeny to explore taxonomic relationships among these groups and test if these subspecies warrant formal recognition. Our analyses show that the seven subspecies fit into three major lineages equivalent to species: western (Sacramento-Klamath), Santa Ana, and Lahontan speckled dace. Death Valley speckled dace were determined to be two lineages (Amargosa and Long Valley) within Lahontan speckled dace. Western and Lahontan speckled dace lineages had branches that can be designated as subspecies. These designations fit well with the geologic history of the region which has promoted long isolation of populations. This study highlights the importance of genetic analysis for conservation and management of freshwater fishes.

We used restriction-site associated DNA sequencing for SNP discovery and genotyping of known-sex green sunfish Lepomis cyanellus DNA samples to search for sex-diagnostic single nucleotide polymorphisms (SNPs) and restriction-site associated sequences present in one sex and absent in the other. The bioinformatic analyses discovered candidate SNPs and sex-specific restriction-site associated sequences that fit patterns of male or female heterogametic sex determination systems. However, when primers were developed and tested, no candidates reliably identified phenotypic sex. The top performing SNP candidate (ZW_218) correlated with phenotypic sex 63.0% of the time and the presence-absence loci universally amplified in both sexes. We recommend further investigations that interrogate a larger fraction of the L. cyanellus genome. Additionally, studies on the effect of temperature and rearing density on sex determination, as well as breeding of sex-reversed individuals, could provide more insights into the sex determination system of L. cyanellus.

Shatavari has long been used as an Ayurvedic herb for women’s health, but empirical evidence for its effectiveness has been lacking. Shatavari contains phytoestrogenic compounds that bind to the estradiol receptor. Postmenopausal estradiol deficiency contributes to sarcopenia and osteoporosis. In a randomised double-blind trial, 20 postmenopausal women (68.5 ± 6 years) ingested either placebo (N = 10) or shatavari (N = 10; 1000 mg/d, equivalent to 26,500 mg/d fresh weight shatavari) for 6 weeks. Handgrip and knee extensor strength were measured at baseline and at 6 weeks. Vastus lateralis (VL) biopsy samples were obtained. Data are presented as difference scores (Week 6—baseline, median ± interquartile range). Handgrip (but not knee extensor) strength was improved by shatavari supplementation (shatavari +0.7 ± 1.1 kg, placebo −0.4 ± 1.3 kg; p = 0.04). Myosin regulatory light chain phosphorylation, a known marker of improved myosin contractile function, was increased in VL following shatavari supplementation (immunoblotting; placebo −0.08 ± 0.5 a.u., shatavari +0.3 ± 1 arbitrary units (a.u.); p = 0.03). Shatavari increased the phosphorylation of Aktser473 (Aktser473 (placebo −0.6 ± 0.6 a.u., shatavari +0.2 ± 1.3 a.u.; p = 0.03) in VL. Shatavari supplementation did not alter plasma markers of bone turnover (P1NP, β-CTX) and stimulation of human osteoblasts with pooled sera (N = 8 per condition) from placebo and shatavari supplementation conditions did not alter cytokine or metabolic markers of osteoblast activity. Shatavari may improve muscle function and contractility via myosin conformational change and further investigation of its utility in conserving and enhancing musculoskeletal function, in larger and more diverse cohorts, is warranted.

Anthropogenic factors have been identified as major stressors of nearshore environments such as estuaries, sea grass meadows and mangroves. We hypothesize that aquatic organisms functionally dependent on these habitats as nurseries respond to disturbances with subtle changes in their habitat-use patterns. We used a novel approach coupling behavioural change point analysis with fish otolith microchemistry to analyse continuous life history information independent of climate and physiological variability. Here we show that pre-industrial (1430–1640 CE) land use and fishing practices had little influence on the well synchronized migration behaviour of juvenile snapper Chrysophrys auratus in the Hauraki Gulf, New Zealand. In contrast, modern human disturbances have resulted in snapper spending less time in brackish nurseries and moving chaotically between habitats. Today, nearshore habitats have largely lost their nursery function for the species. Temporal comparison of habitat-use patterns is a powerful tool to evaluate past and present nursery habitat quality.

Paraneoplastic pemphigus (PNP) is a rare, highly fatal autoimmune blistering disease occurring in the setting of occult or confirmed neoplasms. The clinical hallmark of PNP is recalcitrant, painful mucositis, which may be accompanied by polymorphic cutaneous eruptions.1 In the era of oncodermatology, manifestations of PNP or PNP-like immune-related adverse events (irAE) are rare in patients receiving immune checkpoint inhibitor (ICI) therapy.2 The diagnosis of PNP is confirmed by skin biopsy with histopathologic evaluation and immunologic studies.1 We present a case of PNP associated with the administration of the ICI, pembrolizumab, in the treatment of metastatic urothelial carcinoma.

The Shoshone sculpin Cottus greenei is a micro-endemic species and an extreme habitat specialist, geographically restricted to the spring outlets that flow from the Snake River Plain Aquifer into the Snake River within the Hagerman Valley of south central Idaho. Although previous studies documented the range of the species and its relative abundance, no studies have assessed genetic diversity and structure. We sampled 20 populations from throughout the species range and genotyped 1311 with a panel of 12 microsatellite loci. Results indicate very high levels of genetic differentiation among most populations (average pairwise FST = 0.24), indicating limited gene flow. Preservation of the genetic diversity of this species will require the protection and preservation of multiple isolated populations.

Diabetes disrupts one in six pregnancies, bestowing immediate and long-term health risks to mother and child. Diet and exercise are commonly prescribed to control dysglycemia, but their effectiveness across sub-populations and types of diabetes (type-1; type-2; or gestational diabetes mellitus, GDM) is uncertain. Therefore, a systematic review and meta-analysis on the effect of diet and/or exercise on glycemia in pregnant women with diabetes was conducted. Random effects models were used to evaluate effect sizes across studies and anticipated confounders (e.g., age, ethnicity, BMI). Of the 4845 records retrieved, 26 studies (8 nutritional supplements, 12 dietary, and 6 exercise interventions) were included. All studies were conducted in patients with GDM. Overall, supplement- and exercise-based interventions reduced fasting glucose (−0.30 mmol/L; 95% CI = −0.55, −0.06; p = 0.02; and 0.10 mmol/L; 95% CI = −0.20, −0.01; p = 0.04); and supplement- and diet-based interventions reduced HOMA-IR (−0.40; 95% CI = −0.58, −0.22; p < 0.001; and −1.15; 95% CI = −2.12, −0.17; p = 0.02). Subgroup analysis by confounders only confirmed marginal changed effect sizes. Our results suggest a favorable role of certain nutritional supplements, diet, and exercise practices on glycemia in women with GDM and underline a lack of evidence in ~20% of other diabetes-related pregnancies (i.e., women with pre-existing diabetes).

The use of permeabilized muscle fibers (PMF) has emerged as a gold standard for assessing skeletal muscle mitochondrial function. PMF provide an intermediate approach between in vivo strategies and isolated mitochondria that allows the mitochondria to be maintained in close to their native morphology in the myofiber while allowing greater control of substrate and inhibitor concentrations. However, like mitochondrial isolation, the primary drawback to PMF is disruption of the cellular environment during the muscle biopsy and preparation. Despite all the benefits of permeabilized muscle fibers in evaluating mitochondrial respiration and dynamics one of the major drawbacks is increased variability introduced during a muscle biopsy as well as intrinsic variation that exists due to sex and age. This study was designed to evaluate how age, sex, and biopsy preparations affect mitochondrial respiration in extensor digitorum longus, soleus, and gastrocnemius muscle of mice. Here we detail a modified approach to skeletal muscle biopsy of the gastrocnemius muscle of mice focused on maintenance of intact fibers that results in greater overall respiration compared to cut fibers. The improved respiration of intact fibers is sex specific as are some of the changes in mitochondrial respiration with age. This study shows the need for standard practices when measuring mitochondrial respiration in permeabilized muscle and provides a protocol to control for variation introduced during a typical mouse muscle biopsy.

Enfortumab vedotin (EV) is a novel antibody-drug conjugate approved for advanced urothelial cancer (aUC) refractory to prior therapy. In the Urothelial Cancer Network to Investigate Therapeutic Experiences (UNITE) study, the authors looked at the experience with EV in patient subsets of interest for which activity had not been well defined in clinical trials.UNITE was a retrospective study of patients with aUC treated with recently approved agents. This initial analysis focused on patients treated with EV. Patient data were abstracted from chart reviews by investigators at each site. The observed response rate (ORR) was investigator-assessed for patients with at least 1 post-baseline scan or clear evidence of clinical progression. ORRs were compared across subsets of interest for patients treated with EV monotherapy.The initial UNITE analysis included 304 patients from 16 institutions; 260 of these patients were treated with EV monotherapy and included in the analyses. In the monotherapy cohort, the ORR was 52%, and it was40% in all reported subsets of interest, including patients with comorbidities previously excluded from clinical trials (baseline renal impairment, diabetes, and neuropathy) and patients with fibroblast growth factor receptor 3 (FGFR3) alterations. Progression-free survival and overall survival were 6.8 and 14.4 months, respectively. Patients with a pure urothelial histology had a higher ORR than patients with a variant histology component (58% vs 42%; P = .06).In a large retrospective cohort, responses to EV monotherapy were consistent with data previously reported in clinical trials and were also observed in various patient subsets, including patients with variant histology, patients with FGFR3 alterations, and patients previously excluded from clinical trials with an estimated glomerular filtration rate30 mL/min and significant comorbidities.Enfortumab vedotin, approved by the Food and Drug Administration in 2019, is an important new drug for the treatment of patients with advanced bladder cancer. This study looks at the effectiveness of enfortumab vedotin as it has been used at multiple centers since approval, and focuses on important patient populations previously excluded from clinical trials. These populations include patients with decreased kidney function, diabetes, and important mutations. Enfortumab vedotin is effective for treating these patients. Previously reported clinical trial data have been replicated in this real-world setting, and support the use of this drug in broader patient populations.

Parvoviruses (family Parvoviridae) are small DNA viruses that cause numerous diseases of medical, veterinary, and agricultural significance and have important applications in gene and anticancer therapy. DNA sequences derived from ancient parvoviruses are common in animal genomes and analysis of these endogenous parvoviral elements (EPVs) has demonstrated that the family, which includes twelve vertebrate-specific genera, arose in the distant evolutionary past. So far, however, such ‘paleovirological’ analysis has only provided glimpses into biology of parvoviruses and their long-term evolutionary interactions with hosts. Here, we comprehensively map EPV diversity in 752 published vertebrate genomes, revealing defining aspects of ecology and evolution within individual parvovirus genera. We identify 364 distinct EPV sequences and show these represent ∼200 unique germline incorporation events, involving at least five distinct parvovirus genera, that took place at points throughout the Cenozoic Era. We use the spatiotemporal and host range calibrations provided by these sequences to infer defining aspects of long-term evolution within individual parvovirus genera, including mammalian vicariance for genus Protoparvovirus, and inter-class transmission for genus Dependoparvovirus. Moreover, our findings support a model of virus evolution in which the long-term co-circulation of multiple parvovirus genera in vertebrates reflects the adaptation of each viral genus to fill a distinct ecological niche. Our discovery that parvovirus diversity can be understood in terms of genus-specific adaptations acquired over millions of years has important implications for their development as therapeutic tools - we show that these endeavours can now be approached from a rational foundation based on comparative evolutionary analysis. To support this, we published our data in the form of an open, extensible, and cross-platform database designed to facilitate the wider utilisation of evolution-related domain knowledge in parvovirus research.

Multiple therapies with novel mechanisms have been explored in clinical trials for the treatment of metastatic pheochromocytomas and paragangliomas. We review current and future therapies for this disease and provide guidance on how and when to prescribe them based on tumor progression, clinical manifestations, molecular features, and social factors.Approximately 60-70% of metastatic pheochromocytomas and paragangliomas express the noradrenaline transporter in their cell membranes. High specific activity iodine-131 metaiodobenzylguanidine has been recently approved by the US Food and Drug Administration for the treatment of metastatic pheochromocytomas and paragangliomas that express the noradrenaline transporter, in patients aged ≥ 12 years. More than 90% of patients treated with this medication exhibit clinical benefits. However, other therapies with novel mechanisms of action are needed to help all patients with this disease. Treatment of metastatic pheochromocytomas and paragangliomas is recommended based on the severity of symptoms, the progression of the disease, and the patient's performance status. Currently available therapies include surgery; systemic chemotherapy with cyclophosphamide, vincristine, and dacarbazine, or with temozolomide; high specific activity iodine-131 metaiodobenzylguanidine; peptide receptor radionuclide therapy; immunotherapy; tyrosine kinase inhibitors; and hypoxia-inducible factor 2 alpha inhibitors. Financial and social factors such as health insurance coverage and disparities also impact current clinical practice in the USA.

GlycoStore ( http://www.glycostore.org ) is an open access chromatographic and electrophoretic retention database of glycans characterized from glycoproteins, glycolipids, and biotherapeutics. It is a continuation of the GlycoBase project (Oxford Glycobiology Institute and National Institute for Bioprocessing Research and Training, Ireland) but addresses many of the technological limitations that impacted the growth of GlycoBase, in particular, improvements to the bioinformatics architecture, enhancing data annotations and coverage, and improving connectivity with external resources. The first release of GlycoStore (October 2017) contains over 850 glycan entries accompanied by 8500+ retention positions including data from: (1) fluorescently labelled released glycans determined using hydrophilic interaction chromatography (HILIC) ultrahigh-performance liquid chromatography (U/HPLC) and reversed phase (RP)-U/HPLC; (2) porous graphitized carbon chromatography (PGC) interfaced with ESI-MS/MS; and (3) capillary electrophoresis with laser induced fluorescence detection (CE-LIF). In this chapter, we outline the objectives of GlycoStore, and describe a selection of step-by-step workflows for navigating and browsing the information available. We also provide a short description of informatics tools available to query the database using Semantic technologies. The information presented in this chapter supplements our documentation knowledge base that describes interface improvements, new features and tools, and content updates ( https://unicarbkb.freshdesk.com/ ).

GlycoStore ( http://www.glycostore.org ) is an open access chromatographic and electrophoretic retention database of glycans characterized from glycoproteins, glycolipids, and biotherapeutics. It is a continuation of the GlycoBase project (Oxford Glycobiology Institute and National Institute for Bioprocessing Research and Training, Ireland) but addresses many of the technological limitations that impacted the growth of GlycoBase, in particular, improvements to the bioinformatics architecture, enhancing data annotations and coverage, and improving connectivity with external resources. The first release of GlycoStore (October 2017) contains over 850 glycan entries accompanied by 8500+ retention positions including data from: (1) fluorescently labelled released glycans determined using hydrophilic interaction chromatography (HILIC) ultrahigh-performance liquid chromatography (U/HPLC) and reversed phase (RP)-U/HPLC; (2) porous graphitized carbon chromatography (PGC) interfaced with ESI-MS/MS; and (3) capillary electrophoresis with laser induced fluorescence detection (CE-LIF). In this chapter, we outline the objectives of GlycoStore, and describe a selection of step-by-step workflows for navigating and browsing the information available. We also provide a short description of informatics tools available to query the database using Semantic technologies. The information presented in this chapter supplements our documentation knowledge base that describes interface improvements, new features and tools, and content updates ( https://unicarbkb.freshdesk.com/ ).

Funder: University of Leeds, PURPOSE: Findings from randomized controlled trials (RCTs) evaluating the effect of pulse intake on glycemic control are inconsistent and conclusive evidence is lacking. The aim of this study was to systematically review the impact of pulse consumption on post-prandial and long-term glycemic control in adults with and without type 2 diabetes (T2D). METHODS: Databases were searched for RCTs, reporting outcomes of post-prandial and long-term interventions with different pulse types on parameters of glycemic control in normoglycemic and T2D adults. Effect size (ES) was calculated using random effect model and meta-regression was conducted to assess the impact of various moderator variables such as pulse type, form, dose, and study duration on ES. RESULTS: From 3334 RCTs identified, 65 studies were eligible for inclusion involving 2102 individuals. In acute RCTs, pulse intake significantly reduced peak post-prandial glucose concentration in participants with T2D (ES - 2.90; 95%CI - 4.60, - 1.21; p ≤ 0.001; I2 = 93%) and without T2D (ES - 1.38; 95%CI - 1.78, - 0.99; p ≤ 0.001; I2 = 86%). Incorporating pulse consumption into long-term eating patterns significantly attenuated fasting glucose in normoglycemic adults (ES - 0.06; 95%CI - 0.12, 0.00; p ≤ 0.05; I2 = 30%). Whereas, in T2D participants, pulse intake significantly lowered fasting glucose (ES - 0.54; 95%CI - 0.83, - 0.24; p ≤ 0.001; I2 = 78%), glycated hemoglobin A1c (HbA1c) (ES - 0.17; 95%CI - 0.33, 0.00; p ≤ 0.05; I2 = 78) and homeostatic model assessment of insulin resistance (HOMA-IR) (ES - 0.47; 95%CI - 1.25, - 0.31; p ≤ 0.05; I2 = 79%). CONCLUSION: Pulse consumption significantly reduced acute post-prandial glucose concentration > 1 mmol/L in normoglycemic adults and > 2.5 mmol/L in those with T2D, and improved a range of long-term glycemic control parameters in adults with and without T2D. PROSPERO REGISTRY NUMBER: (CRD42019162322).

BackgroundShatavari has long been used as an Ayurvedic herb for women’s health, but empirical evidence for its effectiveness has been lacking. Shatavari contains phytoestrogenic compounds that bind to the estradiol receptor, and may therefore benefit postmenopausal women since postmenopausal estradiol deficiency contributes to sarcopenia and osteoporosis.MethodsIn a randomised double-blind trial, 20 postmenopausal women (68.5 ± 6 y) ingested either placebo (N=10) or shatavari (N=10; 1000 mg/d, equivalent to 26,500 mg/d fresh weight shatavari) for 6 weeks. Handgrip and knee extensor strength were measured at baseline and at 6 weeks. Vastus lateralis (VL) biopsy samples were obtained. Data are presented and analysed (t test/Mann Whitney U) as difference scores (Week 6 – baseline, median ± interquartile range).ResultsHandgrip, (but not knee extensor) strength was improved by shatavari supplementation (shatavari +0.7 ± 1.1 kg, placebo -0.4 ± 1.3 kg; p=0.04). Myosin regulatory light chain phosphorylation, a known marker of improved myosin contractile function, was increased in VL following shatavari supplementation (immunoblotting; placebo -0.08 ± 0.5 a.u. shatavari +0.3 ± 1 arbitrary units (a.u.); p=0.03). Shatavari increased phosphorylation of Aktser473 (Aktser473 (placebo -0.6 ± 0.6 a.u. shatavari +0.2 ± 1.3 a.u; p=0.03) in VL. Shatavari supplementation did not alter plasma markers of bone turnover (P1NP, β-CTX) and stimulation of human osteoblasts with pooled sera (N=8 per condition) from placebo and shatavari supplementation conditions did not alter cytokine or metabolic markers of osteoblast activity.ConclusionsShatavari may improve muscle function and contractility via myosin conformational change and warrants further investigation of its utility in conserving musculoskeletal function in postmenopausal women.Trial RegistrationRetrospectively registered at clinicaltrials.gov as NCT05025917 on 30/08/21.

INTRODUCTION AND OBJECTIVE:Tumor shrinkage of ≥10% with presurgical targeted molecular therapy (TMT) in renal cell carcinoma (RCC) was associated with improved overall survival (OS). We characteriz...

Fisheries managers routinely use hatcheries to increase angling opportunity. Many hatcheries operate as segregated programs where hatchery-origin fish are not intended to spawn with natural-origin conspecifics in order to prevent potential negative effects on the natural-origin population. Currently available techniques to monitor the frequency with which hatchery-origin strays successfully spawn in the wild rely on either genetic differentiation between the hatchery- and natural-origin fish or extensive sampling of fish on the spawning grounds. We present a method to infer grandparent-grandchild trios using only genotypes from two putative grandparents and one putative grandchild. We developed estimators of false positive and false negative error rates and showed that genetic panels containing 500 - 700 single nucleotide polymorphisms or 200 - 300 microhaplotypes are expected to allow application of this technique for monitoring segregated hatchery programs. We discuss the ease with which this technique can be implemented by pre-existing parentage-based tagging programs and provide an R package that applies the method.

Many micro-aerial vehicles can benefit from having compact and robust pre-deployment configurations that can later transform into larger and more capable forms. We demonstrate parylene-covered silicon frames that can be folded into origami-inspired aerodynamic shapes for structural applications in centimeter-scale aircraft. By changing the spacing between the frames, we can control the conformality of the parylene deposition, which determines the directionality of the fold (mountain or valley). We fabricated a foldable propeller from such polymer-coated frames and characterized its mass and thrust. [2020-0095]

Objectives This report describes the surgical implantation of a novel bilateral hypoglossal nerve stimulator (Genio system®, Nyxoah S.A., Belgium) and the successful treatment of a patient with moderate obstructive sleep apnea (OSA). Study Design Surgical technique description and case study report. Methods The bilateral implantable stimulator (IS) simultaneously stimulates both genioglossus (GG) muscles to reduce airway obstruction. At night, patients wear an activation chip under their chin that wirelessly transmits energy to the implant and enables the nerve stimulation. Surgical implantation of the IS is performed under general anesthesia by making a small incision above the hyoid bone and dissecting through the platysma, mylohyoid, and geniohyoid muscles to the GG muscle. The hypoglossal nerve branches are then identified, followed by suturing the IS in place. The system was evaluated in an otherwise healthy, 60-year-old woman with moderate OSA (apnea hypopnea index (AHI): 25/hr, nadir O2 saturation: 78%). Appropriate stimulation settings were determined at 2-, 3-, and 6-months post implantation during polysomnography (PSG) and changes in apnea and hypopnea events and oxygen desaturation recorded. Results The surgery was well tolerated by the patient with an uneventful recovery. The PSG at 6 months showed that AHI per hour, obstructive apnea events per hour, hypopnea events per hour, and oxygen desaturation index have been reduced by 88%, 92%, 88%, and 97%, respectively, and nadir O2 saturation improved to 91%. Conclusions The absence of complications and considerable reduction of apnea and hypopnea events in this case study help demonstrate the potential safety and efficacy of the bilateral hypoglossal nerve stimulator. Level of Evidence 4.

This article estimated the weight of annual discards in the Queensland east coast otter trawl fishery. Discards data were analysed using three generalized linear mixed models to derive adjusted discard rates, expressed as kg per retained catch, kg per boat day, and kg per area swept by trawls, respectively. Model explanatory terms included trawl fishing sector, presence/absence of bycatch reduction devices (BRDs), lunar phase, and whether the data were obtained from commercial vessels during their normal fishing activities or during research charters. Adjusted discard rates were then used to derive three estimates of annual discards and the average used to examine a long-term discard trends from 1988 to 2014. Total discards declined significantly from a peak of approximately 67 000 t in 1997 to approximately 21 000 t from 2011 to 2014, largely due to a decline in fishing effort, and to a lesser degree, the effects of BRDs that were mandated in the fishery in the early 2000s.

Males and females often differ in their fitness optima for shared traits that have a shared genetic basis, leading to sexual conflict. Morphologically differentiated sex chromosomes can resolve this conflict and protect sexually antagonistic variation, but they accumulate deleterious mutations. However, how sexual conflict is resolved in species that lack differentiated sex chromosomes is largely unknown. Here we present a chromosome-anchored genome assembly for rainbow trout (Oncorhynchus mykiss) and characterize a 55-Mb double-inversion supergene that mediates sex-specific migratory tendency through sex-dependent dominance reversal, an alternative mechanism for resolving sexual conflict. The double inversion contains key photosensory, circadian rhythm, adiposity and sex-related genes and displays a latitudinal frequency cline, indicating environmentally dependent selection. Our results show sex-dependent dominance reversal across a large autosomal supergene, a mechanism for sexual conflict resolution capable of protecting sexually antagonistic variation while avoiding the homozygous lethality and deleterious mutations associated with typical heteromorphic sex chromosomes.

The development of sex-specific genetic assays in a species provides both a method for identifying the system of sex determination and a valuable tool to address questions of conservation and management importance. In this study, we focused on the identification of single nucleotide polymorphisms (SNPs) that differentiate genetic sex in burbot Lota lota. Burbot are the only true freshwater representative of the cod family and a species of conservation and management importance throughout Eurasia and North America. To identify sex-specific SNPs, we utilized restriction site-associated DNA sequencing (RADseq) to interrogate thousands of SNPs in burbot samples of known phenotypic sex. We discovered 170,569 biallelic SNPs, none of which fit the pattern expected under female heterogamety. However, we identified 22 SNPs that fit the pattern expected under male heterogamety (males heterozygous XY, females fixed XX) and, from these, developed two genetic assays that robustly (~ 97% genotyping success) and accurately (> 99% correct) sexed burbot samples. These sex-specific genetic assays will benefit growing conservation aquaculture programs for this species and allow future assessments of sex-specific migration, growth, and mortality.

Background Immune checkpoint inhibitors (ICIs) are being increasingly utilised in the front-line (1L) setting of metastatic clear-cell renal cell carcinoma (mccRCC). Limited data exist on responses and survival on second-line (2L) vascular endothelial growth factor–receptor tyrosine kinase inhibitor (VEGFR-TKI) therapy after 1L ICI therapy. Patients and methods This is a retrospective study of mccRCC patients treated with 2L VEGFR-TKI after progressive disease (PD) with 1L ICI. Patients were treated at MD Anderson Cancer Center or Memorial Sloan Kettering Cancer Center between December 2015 and February 2018. Objective response was assessed by blinded radiologists' review using Response Evaluation Criteria in Solid Tumours v1.1. Descriptive statistics and Kaplan–Meier method were used. Results Seventy patients were included in the analysis. Median age at mccRCC diagnosis was 59 years; 8 patients (11%) had international metastatic database consortium favourable-risk disease, 48 (69%) had intermediate-risk disease and 14 (20%) had poor-risk disease. As 1L therapy, 12 patients (17%) received anti–programmed death ligand-1 (PD-(L)1) monotherapy with nivolumab or atezolizumab, 33 (47%) received nivolumab plus ipilimumab and 25 (36%) received combination anti–PD-(L)1 plus bevacizumab. 2L TKI therapies included pazopanib, sunitinib, axitinib and cabozantinib. On 2L TKI therapy, one patient (1.5%) achieved a complete response, 27 patients (39.7%) a partial response and 36 patients (52.9%) stable disease. Median progression-free survival (mPFS) was 13.2 months (95% confidence interval: 10.1, NA). Forty-five percent of subjects required a dose reduction, and twenty-seven percent of patients discontinued treatment because of toxicity. Conclusions In this retrospective study of patients with mccRCC receiving 2L TKI monotherapy after 1L ICI, we observed 2L antitumour activity and tolerance comparable to historical data for 1L TKI.

Internally enhanced surfaces such as micro-fins are an important class of heat transfer enhancement in commercial applications. Many research papers discuss the design and optima of these surfaces. However, most previous studies have demonstrated only the macro relationship between the geometries of the micro-fins and heat transfer. The need for a deeper understanding of these fins arose from some currently unsolved problems that limit future development of enhanced surfaces. First, why are increases of heat transfer larger than area increases in micro-finned tubes in most cases? Second, why do internally micro-finned tubes typically have lower heat-transfer-enhanced ratios in laminar and transition flows? This work presents a novel method to analyze the detailed relationship between flow characteristics and heat transfer for one type of micro-fin. The goal of the paper was not to find a new Reynolds number-based correlation, but to find flow patterns responsible for heat transfer enhancement and understand the mechanisms that cause this. First, this paper introduces comprehensive experimental measurements including particle image velocimetry (PIV), measurement of the heat transfer coefficient and accuracy of pressure-drop measurements, all used to validate numerical approaches. Validated large eddy simulations (LES) are then used to predict flow characteristics and coherent structures (Q criterion). The numerical simulation includes both heat conduction in the metal structure and heat convection on the solid–fluid interface. Finally, the paper documents how the flow structures link with the enhancement of heat transfer in the micro-finned duct.

This study offers an analysis of teacher attrition patterns at charter schools in Nashville and Memphis, Tennessee. Using survey data from 121 teachers, the study reports teacher opinion regarding four common causes of teacher attrition, examines the role of demography and school organization on future attrition plans, and offers various regression models in an attempt to predict future plans for the teachers within the sample. Overall, teachers reported lukewarm feelings regarding common causes of teacher attrition, and no background characteristic or school organizational structure held significance for future plans.

Background Emergency medicine (EM) pharmacists are increasingly recognized as integral team members in the care of emergency department (ED) patients but there is variability in the scope of direct patient care services. Objectives The primary objective was to categorize direct patient care activities and drug therapy recommendations. The secondary objectives were to categorize recommendations based on drug class and to determine the proportion of recommendations associated with Institute for Safe Medication Practices (ISMP) high-alert medications. Methods This retrospective, single-center, chart review was conducted in an academic ED with 65,000 annual visits. EM pharmacists documented direct patient care activities in the electronic health record. Documented activities from 1/1/2015 through 3/31/2015 were abstracted electronically for analysis by a trained reviewer. Results There were 3567 interventions and direct patient care activities documented. The most common activities were facilitation of medication histories (n = 1300) and drug therapy recommendations (n = 1165). Of 1165 drug therapy recommendations, 986 were linked to a drug class such as antimicrobial agents (31.9%), cardiovascular agents (16.6%), and analgesic agents (13.2%) and 20% of these interventions were associated with ISMP high-alert medications. Conclusion EM pharmacists documented several types of direct patient care activities with the majority being drug therapy recommendations and medication histories.

Whole-genome duplications (WGDs) have occurred repeatedly and broadly throughout the evolutionary history of eukaryotes. However, the effects of WGD on genome function and evolution remain unclear. The salmonid WGD that occurred approximately 88 million years ago presents an excellent opportunity for studying the effects of WGD as ∼10–15% of each salmonid genome still exhibits tetrasomic inheritance. Herein, we utilized the rainbow trout (Oncorhynchus mykiss) genome assembly and brain transcriptome data to examine the fate of gene pairs (ohnologs) following the salmonid whole-genome duplication. We find higher sequence identity between ohnologs located within known tetrasomic regions than between ohnologs found in disomic regions, and that tetrasomically inherited ohnologs showed greater similarity in patterns of gene expression and per ohnolog were lower expressed, than disomically inherited ohnologs. Enrichment testing for Gene Ontology terms identified 49 over-represented terms in tetrasomically inherited ohnologs compared to disomic ohnologs. However, why these ohnologs are retained as tetrasomic is difficult to answer. It could be that we have identified salmonid specific “dangerous duplicates”, that is, genes that cannot take on new roles following WGD. Alternatively, there may be adaptive advantages for retaining genes as functional duplicates in tetrasomic regions, as presumably, movement of these genes into disomic regions would affect both their sequence identity and their gene expression patterns.

Purpose The purpose of this paper is to explore the experiences of students and teachers who had participated in a postgraduate work-based praxis course within a Master of mental health practice qualification. Design/methodology/approach This qualitative study used an interpretative phenomenological approach to understand the lived experience of students and course convenors participating in a work-based praxis course. Seven students and two convenors were recruited. Interview and reflective portfolio data were analysed thematically. Findings The main themes identified were the importance of planning, the value of partnerships, the significance of learning in the workplace and how the facilitation of work-based learning differs from coursework. Originality/value Work-based learning within postgraduate coursework qualifications can support higher-level learning, knowledge and skills has received limited attention in the literature. This study supported the value of providing postgraduate students with work-based learning opportunities, resulting in the application of new or advanced skills, within their existing work roles. This study is important, because it provides insights into the student experience of postgraduate work-based learning and the impact of this learning on professional practice.

Background Muscle strength loss following immobilisation has been predominantly attributed to rapid muscle atrophy. However, this cannot fully explain the magnitude of muscle strength loss, so changes in neuromuscular function (NMF) may be involved. Objectives We systematically reviewed literature that quantified changes in muscle strength, size and NMF following periods of limb immobilisation in vivo in humans. Methods Studies were identified following systematic searches, assessed for inclusion, data extracted and quality appraised by two reviewers. Data were tabulated and reported narratively. Results Forty eligible studies were included, 22 immobilised lower and 18 immobilised upper limbs. Limb immobilisation ranged from 12 h to 56 days. Isometric muscle strength and muscle size declined following immobilisation; however, change magnitude was greater for strength than size. Evoked resting twitch force decreased for lower but increased for upper limbs. Rate of force development either remained unchanged or slowed for lower and typically slowed for upper limbs. Twitch relaxation rate slowed for both lower and upper limbs. Central motor drive typically decreased for both locations, while electromyography amplitude during maximum voluntary contractions decreased for the lower and presented mixed findings for the upper limbs. Trends imply faster rates of NMF loss relative to size earlier in immobilisation periods for all outcomes. Conclusions Limb immobilisation results in non-uniform loss of isometric muscle strength, size and NMF over time. Different outcomes between upper and lower limbs could be attributed to higher degrees of central neural control of upper limb musculature. Future research should focus on muscle function losses and mechanisms following acute immobilisation. Registration PROSPERO reference: CRD42016033692. Electronic supplementary material The online version of this article (10.1007/s40279-019-01088-8) contains supplementary material, which is available to authorized users.

Spiny-rayed fishes (Acanthomorpha) dominate modern marine habitats and comprise more than a quarter of all living vertebrate species1–3. It is believed that this dominance resulted from explosive lineage and phenotypic diversification coincident with the Cretaceous-Paleogene (K-Pg) mass-extinction event4. It remains unclear, however, if living acanthomorph diversity is the result of a punctuated burst or gradual accumulation of diversity following the K-Pg. We assess these hypotheses with a time-calibrated phylogeny inferred using ultraconserved elements from a sampling of species that represent over 91% of all acanthomorph families, as well as an extensive body shape dataset of extant species. Our results indicate that several million years after the end-Cretaceous, acanthomorphs underwent a prolonged and significant expansion of morphological disparity primarily driven by changes in body elongation, and that acanthomorph lineages containing the bulk of the living species diversity originated throughout the Cenozoic. These acanthomorph lineages radiated into distinct regions of morphospace and retained their iconic phenotypes, including a large group of laterally compressed reef fishes, fast-swimming open-ocean predators, bottom-dwelling flatfishes, seahorses, and pufferfishes. The evolutionary success of spiny-rayed fishes is the culmination of a post K-Pg adaptive radiation in which rates of lineage diversification were decoupled from periods of high phenotypic disparity.

BackgroundRecent evidence suggests severe hypoglycaemia may pose a risk of premature mortality to individuals with type 2 diabetes. Evidence surrounding strategies to mitigate this risk is currently lacking as is evidence regarding risk stratification of such patients. MethodsWe performed a post-hoc analysis from a previously published RCT studying the impact of a structured nurse led intervention following severe hypoglycaemia. A Cox regression model was used to identify baseline characteristics associated with increased mortality and to adjust for differences between study groups. Kaplan Meier (KM) curves were created to demonstrate differences in outcome between study groups across a number of variables.Results124 participants (mean age 75, 57% male) were included in analysis. Diabetes severity score, age and insulin use were found to correlate with mortality, while other variables including HbA1c and presence of established cardiovascular disease showed no correlations. When comparing KM curves between study groups, the intervention appeared to be beneficial irrespective of glycaemic control, presence of vascular disease, diabetes severity score or age.ConclusionIn this analysis, only diabetes severity score, age and insulin use were significantly associated with death following severe hypoglycaemia in the community. A structured nurse-led intervention appears to reduce the risk of death irrespective of age, co-morbidities or type of treatment. Trial registrationData is taken from a previously published randomised controlled trial with trial registration NCT04422145.

Bisulfite sequencing detects 5mC and 5hmC at single-base resolution. However, bisulfite treatment damages DNA, which results in fragmentation, DNA loss, and biased sequencing data. To overcome these problems, enzymatic methyl-seq (EM-seq) was developed. This method detects 5mC and 5hmC using two sets of enzymatic reactions. In the first reaction, TET2 and T4-BGT convert 5mC and 5hmC into products that cannot be deaminated by APOBEC3A. In the second reaction, APOBEC3A deaminates unmodified cytosines by converting them to uracils. Therefore, these three enzymes enable the identification of 5mC and 5hmC. EM-seq libraries were compared with bisulfite-converted DNA, and each library type was ligated to Illumina adaptors before conversion. Libraries were made using NA12878 genomic DNA, cell-free DNA, and FFPE DNA over a range of DNA inputs. The 5mC and 5hmC detected in EM-seq libraries were similar to those of bisulfite libraries. However, libraries made using EM-seq outperformed bisulfite-converted libraries in all specific measures examined (coverage, duplication, sensitivity, etc.). EM-seq libraries displayed even GC distribution, better correlations across DNA inputs, increased numbers of CpGs within genomic features, and accuracy of cytosine methylation calls. EM-seq was effective using as little as 100 pg of DNA, and these libraries maintained the described advantages over bisulfite sequencing. EM-seq library construction, using challenging samples and lower DNA inputs, opens new avenues for research and clinical applications.

Cytosine methylation (5mC) is an important regulator of gene expression. Bisulfite sequencing is most commonly used to study 5mCs but it is frequently associated with DNA damage and fragmentation. This can prove problematic when using low amounts of DNA as the damage results in uneven genome coverage as well as biased sequencing data. Here we show data generated using NEBNext® Enzymatic Methyl-Seq (EM-Seq™), an enzymatic alternative to bisulfite conversion. The method has been optimized for low input DNAs ranging from 10 ng to 100 pg. NA12878 DNA was used to demonstrate that the modifications to the protocol permitted accurate representation of global CpG, CHG and CHH methylation. These libraries also displayed similar basic metrics to standard input EM-seq libraries. The GC bias plot was even and there was high CpG coverage with strong correlation between replicates. In addition, the possibility of introducing unique molecular identifiers into this system would be useful for many researchers who use DNA originating from single cells, plasma (cfDNA) and formalin fixed paraffin embedded (FFPE) sections. This low input method is robust and reproducible and gives researchers a new tool to tackle studies where DNA has traditionally been limiting. Citation Format: Louise Williams, V. K. Chaithanya Ponnaluri, Vaishnavi Panchapakesa, Romualdas Vaisvila, Matthew A. Campbell, Bradley W. Langhorst, Eileen T. Dimalanta, Theodore B. Davis. Enzymatic methyl-seq: Cytosine methylation detection using picograms of DNA [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2101.

A number of immunotherapies have been developed and adopted for the treatment of urothelial cancer (encompassing cancers arising from the bladder, urethra, or renal pelvis). For these immunotherapies to positively impact patient outcomes, optimal selection of agents and treatment scheduling, especially in conjunction with existing treatment paradigms, is paramount. Immunotherapies also warrant specific and unique considerations regarding patient management, emphasizing both the prompt identification and treatment of potential toxicities. In order to address these issues, the Society for Immunotherapy of Cancer (SITC) convened a panel of experts in the field of immunotherapy for urothelial cancer. The expert panel developed this clinical practice guideline (CPG) to inform healthcare professionals on important aspects of immunotherapeutic treatment for urothelial cancer, including diagnostic testing, treatment planning, immune-related adverse events (irAEs), and patient quality of life (QOL) considerations. The evidence- and consensus-based recommendations in this CPG are intended to give guidance to cancer care providers treating patients with urothelial cancer.

BackgroundImmune checkpoint therapy (ICT) prolongs survival in subsets of patients with cancer but can also trigger immune-related adverse events (irAEs) requiring treatment discontinuation. Recent studies have investigated safety of ICT rechallenge after irAEs, and evidence suggests that rechallenge may be associated with improved antitumor responses. However, data are limited on response duration after ICT rechallenge, particularly after severe irAEs.ObjectiveTo evaluate safety and efficacy of ICT rechallenge after moderate-to-severe irAEs in patients with renal cell carcinoma (RCC), urothelial carcinoma (UC), and prostate cancer.MethodsIn this retrospective cohort study, medical records from September 25, 2013, to June 1, 2020, for patients with genitourinary (GU) cancers at MD Anderson Cancer Center who were rechallenged with the same or different ICT following irAEs were reviewed. Demographics, ICT exposure, irAEs (grade and treatment), ICT discontinuation or rechallenge, rates of subsequent irAEs (new or recurrent) and antitumor activity (objective response rates and response duration) were reviewed.ResultsSixty-one patients with RCC, UC, and prostate cancer were rechallenged with ICT after experiencing 105 total irAEs. Objective response rates after rechallenge, that is, upgrade in response, were 14% in RCC (4/28), 21% in UC (3/14), and 0% in prostate cancer. All seven patients who achieved upgrade in response had initial grade 2 or 3 irAEs. Responses were durable among these seven patients, with median radiographic progression-free survival not reached (range: 3.7–66.4 months) as of the March 8, 2021, data cut-off (median follow-up 40.9 months (95% CI 35.3 to 46.5)). All achieved complete response except one patient who was lost to follow-up. The rate of subsequent grade 3 or 4 irAEs after rechallenge was 30%, with no fatal irAEs. The rate of recrudescence of the same irAE was 26% (16/61). 54% of patients received corticosteroids (33/61), and 21% received targeted immunosuppression (13/61) for the initial irAEs.Conclusions and relevanceICT rechallenge after moderate-to-severe irAEs was associated with deep and durable responses in a subset of patients with RCC and UC, with acceptable safety and no fatal events. Strategies to enable ICT resumption after moderate-to-severe irAEs, such targeted immunosuppression, warrant further study.

BackgroundMutations in the mitochondrial genome (mtDNA) can cause devastating maternally inherited diseases, while the accumulation of somatic mtDNA mutations is linked to common diseases of aging. Although mtDNA mutations impact human health, the process(es) that give rise to these mutations are unclear and are under considerable debate. We analyzed the distribution of naturally occurring somatic mutations across the mouse and human mtDNA obtained by Duplex Sequencing to provide clues to the mechanism by which de novo mutations arise as well as how the genome is replicated.ResultsWe observe two distinct mutational gradients in G→A and T→C transitions, but not their complements, that are delimited by the light-strand origin and the control region (CR). The gradients increase with age and are lost in the absence of DNA polymerase γ proofreading activity. A nearly identical pattern is present in human mtDNA somatic mutations. The distribution of mtDNA single nucleotide polymorphisms (SNPs) in the human population and genome base composition across >3,000 vertebrate species mirror this gradient pattern, pointing to evolutionary conservation of this phenomenon. Lastly, high-resolution analysis of the mtDNA control region highlights mutational ‘hotspots’ and ‘cold-spots’ that strongly align with important regulatory regions.ConclusionsCollectively, these patterns support an asymmetric strand-displacement mechanism with key regulatory structures in the CR and argue against alternative replication models. The mutational gradient is a fundamental consequence of mtDNA replication that drives somatic mutation accumulation and influences inherited polymorphisms and, over evolutionary timescales, genome composition.

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