Sex ratio bias and shared paternity reduce individual fitness and population viability in a critically endangered parrot

Sex‐biased mortality can lead to altered adult sex ratios (ASRs), which may in turn lead to harassment and lower fitness of the rarer sex and changes in the mating system. Female critically endangered swift parrots (Lathamus discolor) suffer high predation while nesting due to an introduced mammalian predator, the sugar glider (Petaurus breviceps). High predation on females is causing severe population decline alongside strongly biased adult sex ratios (≥73% male). Our 6‐year study showed that 50.5% of critically endangered swift parrot nests had shared paternity although the birds remained socially monogamous. Shared paternity increased significantly with the local rate of predation on breeding females, suggesting that rates of shared paternity increased when the ASR became more biased. Nests that were not predated produced fewer fledglings as the local ASR became more male‐biased possibly due to higher interference during nesting from unpaired males. Population viability analyses showed that part of the predicted decline in the swift parrot population is due to reduced reproductive success when paternity is shared. The models predicted that the population would decline by 89.4% over three generations if the birds maintained the lowest observed rate of shared paternity. This compares with predicted population reductions of 92.1–94.9% under higher rates of shared paternity. We conclude that biases in the ASR, in this case caused by sex‐specific predation from an introduced predator, can lead to changes in the mating system and negative impacts on both individual fitness and long‐term population viability.This research was funded by an Australian Research Council Discovery Grant (DP140104202)

A multiwavelength campaign of active stars with intermediate rotation rates

Near-to-simultaneous ultraviolet and visual spectroscopy of two moderate nu(sin i) RS CVn systems, V815 Herculis (nu(sin i) = 27 km s(exp -1)) and LM Pegasi (nu(sin i) = 24 km s(exp -1)), are presented along with contemporaneous UBV (RI)(sub c) - band photometry. These data were used to probe inhomogeneities in the chromospheres and photospheres, and the possible relationship between them. Both systems show evidence for rotationally modulated chromospheric emission, generally varying in antiphase to the photospheric brightness. A weak flare was observed at Mg II for V815 Her. In the case of IM Peg, we use photometry and spectra to estimate temperatures, sizes, and locations of photospheric spots. Further constraints on the spot temperature is provided by TiO observations. For IM Peg, the anticorrelation between chromospheric emission and brightness is discussed in the context of a possible solar-like spot cycle

The data facility of the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS)

AVIRIS operations at the Jet Propulsion Laboratory include a significant data task. The AVIRIS data facility is responsible for data archiving, data calibration, quality monitoring and distribution. Since 1987, the data facility has archived over one terabyte of AVIRIS data and distributed these data to science investigators as requested. In this paper we describe recent improvements in the AVIRIS data facility

Comparison of three techniques for genetic estimation ofeffective population size in a critically endangered parrot

Understanding the current population size of small, spatially aggregating populations of species is essential for their conservation. Reliable estimates of the effective population size (Ne) can be used to provide an early warning for conservation managers of the risks to genetic viability of small populations. Critically endangered, migratory swift parrots Lathamus discolor exist in a single panmictic population in Australia. In their Tasmanian breeding range, they are at severe risk of predation by introduced sugar gliders, exacerbated by deforestation. We used three genetic approaches to estimate Ne using DNA samples genotyped by microsatellite markers and existing life-history data of swift parrots. Based on all samples, we revealed small contemporary Ne estimates across methods (range: 44-140), supporting the need to urgently address threatening processes. Using the 0.5 Ne/N ratio calculated from demographic data suggests that the minimum potential contemporary population size is below 300 individual swift parrots. This is considerably lower than the published estimates derived from expert elicitation, and accords with modeled estimates of extinction risk in this species. Our study has important implications for other threatened species with unknown population sizes and demonstrates that by utilizing available genetic data, reasonable estimates of Ne can be derived.This work was funded by the Loro Parque Fundaci on, theAustralian Research Council (DP140104202), and a crowd-funding campaign“The parrot, the possum and the parda-lote”. This research also received support from theAustralian Government’s National Environmental ScienceProgram through the Threatened Species Recovery Hub, andfrom Australia Awards through the Endeavour Scholarshipsand Fellowships (ERF-PDR-6086-2017

Toy Models of Superposition

Neural networks often pack many unrelated concepts into a single neuron - a puzzling phenomenon known as 'polysemanticity' which makes interpretability much more challenging. This paper provides a toy model where polysemanticity can be fully understood, arising as a result of models storing additional sparse features in "superposition." We demonstrate the existence of a phase change, a surprising connection to the geometry of uniform polytopes, and evidence of a link to adversarial examples. We also discuss potential implications for mechanistic interpretability.Comment: Also available at https://transformer-circuits.pub/2022/toy_model/index.htm

Stem cell factor receptor (c-KIT) codon 816 mutations predict development of bilateral testicular germ-cell tumors

Testicular germ-cell tumors (TGCTs) of adolescents and adults originate from intratubular germ cell neoplasia (ITGCN), which is composed of the malignant counterparts of embryonal germ cells. ITGCN cells are characterized, among others, by the presence of stem cell factor receptor c-KIT. Once established, ITGCN will always progress to invasiveness. Approximately 2.5-5% of patients with a TGCT will develop bilateral disease and require complete castration, resulting in infertility, a need for lifelong androgen replacement, and psychological stress. To date, the only way to predict a contralateral tumor is surgical biopsy of the contralateral testis to demonstrate ITGCN. We did a retrospective study of 224 unilateral and 61 proven bilateral TGCTs (from 46 patients, in three independently collected series in Europe) for the presence of activating c-KIT codon 816 mutations. A c-KIT codon 816 mutation was found in three unilateral TGCT (1.3%), and in 57 bilateral TGCTs (93%; P < 0.0001). In the two wild-type bilateral tumors for which ITGCN was available, the preinvasive cells contained the mutation. The mutations were somatic in origin and identical in both tumors. We conclude that somatic activating codon 816 c-KIT mutations are associated with development of bilateral TGCT. Detection of c-KIT codon 816 mutations in unilateral TGCT identifies patients at risk for bilateral disease. These patients may undergo tailored treatment to prevent the development of bilateral disease, with retention of testicular hormonal function

BRCA2 polymorphic stop codon K3326X and the risk of breast, prostate, and ovarian cancers

Background: The K3326X variant in BRCA2 (BRCA2*c.9976A&gt;T; p.Lys3326*; rs11571833) has been found to be associated with small increased risks of breast cancer. However, it is not clear to what extent linkage disequilibrium with fully pathogenic mutations might account for this association. There is scant information about the effect of K3326X in other hormone-related cancers. Methods: Using weighted logistic regression, we analyzed data from the large iCOGS study including 76 637 cancer case patients and 83 796 control patients to estimate odds ratios (ORw) and 95% confidence intervals (CIs) for K3326X variant carriers in relation to breast, ovarian, and prostate cancer risks, with weights defined as probability of not having a pathogenic BRCA2 variant. Using Cox proportional hazards modeling, we also examined the associations of K3326X with breast and ovarian cancer risks among 7183 BRCA1 variant carriers. All statistical tests were two-sided. Results: The K3326X variant was associated with breast (ORw = 1.28, 95% CI = 1.17 to 1.40, P = 5.9x10- 6) and invasive ovarian cancer (ORw = 1.26, 95% CI = 1.10 to 1.43, P = 3.8x10-3). These associations were stronger for serous ovarian cancer and for estrogen receptor–negative breast cancer (ORw = 1.46, 95% CI = 1.2 to 1.70, P = 3.4x10-5 and ORw = 1.50, 95% CI = 1.28 to 1.76, P = 4.1x10-5, respectively). For BRCA1 mutation carriers, there was a statistically significant inverse association of the K3326X variant with risk of ovarian cancer (HR = 0.43, 95% CI = 0.22 to 0.84, P = .013) but no association with breast cancer. No association with prostate cancer was observed. Conclusions: Our study provides evidence that the K3326X variant is associated with risk of developing breast and ovarian cancers independent of other pathogenic variants in BRCA2. Further studies are needed to determine the biological mechanism of action responsible for these associations

Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers

Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 x 10(53)). In BRCA2 carriers, the strongest association with BC risk was seen for the overall BC PRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 x 10(-20)). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management

Probiotic prophylaxis in patients with predicted severe acute pancreatitis (PROPATRIA): design and rationale of a double-blind, placebo-controlled randomised multicenter trial [ISRCTN38327949]

BACKGROUND: Infectious complications are the major cause of death in acute pancreatitis. Small bowel bacterial overgrowth and subsequent bacterial translocation are held responsible for the vast majority of these infections. Goal of this study is to determine whether selected probiotics are capable of preventing infectious complications without the disadvantages of antibiotic prophylaxis; antibiotic resistance and fungal overgrowth. METHODS/DESIGN: PROPATRIA is a double-blind, placebo-controlled randomised multicenter trial in which 200 patients will be randomly allocated to a multispecies probiotic preparation (Ecologic 641) or placebo. The study is performed in all 8 Dutch University Hospitals and 7 non-University hospitals. The study-product is administered twice daily through a nasojejunal tube for 28 days or until discharge. Patients eligible for randomisation are adult patients with a first onset of predicted severe acute pancreatitis: Imrie criteria 3 or more, CRP 150 mg/L or more, APACHE II score 8 or more. Exclusion criteria are post-ERCP pancreatitis, malignancy, infection/sepsis caused by a second disease, intra-operative diagnosis of pancreatitis and use of probiotics during the study. Administration of the study product is started within 72 hours after onset of abdominal pain. The primary endpoint is the total number of infectious complications. Secondary endpoints are mortality, necrosectomy, antibiotic resistance, hospital stay and adverse events. To demonstrate that probiotic prophylaxis reduces the proportion of patients with infectious complications from 50% to 30%, with alpha 0,05 and power 80%, a total sample size of 200 patients was calculated. CONCLUSION: The PROPATRIA study is aimed to show a reduction in infectious complications due to early enteral use of multispecies probiotics in severe acute pancreatitis

Genome-wide linkage screen for testicular germ cell tumour susceptibility loci

A family history of disease is a strong risk factor for testicular germ cell tumour (TGCT). In order to identify the location of putative TGCT susceptibility gene(s) we conducted a linkage search in 237 pedigrees with two or more cases of TGCT. One hundred and seventy-nine pedigrees were evaluated genome-wide with an average inter-marker distance of 10 cM. An additional 58 pedigrees were used to more intensively investigate several genomic regions of interest. Genetic linkage analysis was performed with the ALLEGRO software using two model-based parametric analyses and a non-parametric analysis. Six genomic regions on chromosomes 2p23, 3p12, 3q26, 12p13-q21, 18q21-q23 and Xq27 showed heterogeneity LOD (HLOD) scores of greater than 1, with a maximum HLOD of 1.94 at 3q26. Genome-wide simulation studies indicate that the observed number of HLOD peaks greater than one does not differ significantly from that expected by chance. A TGCT locus at Xq27 has been previously reported. Of the 237 pedigrees examined in this study, 66 were previously unstudied at Xq27, no evidence for linkage to this region was observed in this new pedigree set. Overall, the results indicate that no single major locus can account for the majority of the familial aggregation of TGCT, and suggests that multiple susceptibility loci with weak effects contribute to the diseas