Selecting single cell clustering parameter values using subsampling-based robustness metrics

Background Generating and analysing single-cell data has become a widespread approach to examine tissue heterogeneity, and numerous algorithms exist for clustering these datasets to identify putative cell types with shared transcriptomic signatures. However, many of these clustering workflows rely on user-tuned parameter values, tailored to each dataset, to identify a set of biologically relevant clusters. Whereas users often develop their own intuition as to the optimal range of parameters for clustering on each data set, the lack of systematic approaches to identify this range can be daunting to new users of any given workflow. In addition, an optimal parameter set does not guarantee that all clusters are equally well-resolved, given the heterogeneity in transcriptomic signatures in most biological systems. Results Here, we illustrate a subsampling-based approach (chooseR) that simultaneously guides parameter selection and characterizes cluster robustness. Through bootstrapped iterative clustering across a range of parameters, chooseR was used to select parameter values for two distinct clustering workflows (Seurat and scVI). In each case, chooseR identified parameters that produced biologically relevant clusters from both well-characterized (human PBMC) and complex (mouse spinal cord) datasets. Moreover, it provided a simple “robustness score” for each of these clusters, facilitating the assessment of cluster quality. Conclusion chooseR is a simple, conceptually understandable tool that can be used flexibly across clustering algorithms, workflows, and datasets to guide clustering parameter selection and characterize cluster robustness

Detection of superhumps in XTE J1118+480 approaching quiescence

We present the results of our monitoring of the halo black-hole soft X-ray transient (SXT) XTE J1118+480 during its decline to quiescence. The system has decayed 0.5 mags from December 2000 to its present near quiescent level at R=18.65 (June 2001). The ellipsoidal lightcurve is distorted by an additional modulation that we interpret as a superhump of P_sh=0.17049(1) d i.e. 0.3% longer than the orbital period. This implies a disc precession period P_prec= 52 d. After correcting the average phase-folded light curve for veiling, the amplitude difference between the minima suggests that the binary inclination angle lies in the range i=71-82 deg. However, we urge caution in the interpretation of these values because of residual systematic contamination of the ellipsoidal lightcurve by the complex form of the superhump modulation. The orbital--mean H-alpha profiles exhibit clear velocity variations with ~500 km/s amplitude. We interpret this as the first spectroscopic evidence of an eccentric precessing disc.Comment: Accepted for publication in MNRA

Exact sampling from non-attractive distributions using summary states

Propp and Wilson's method of coupling from the past allows one to efficiently generate exact samples from attractive statistical distributions (e.g., the ferromagnetic Ising model). This method may be generalized to non-attractive distributions by the use of summary states, as first described by Huber. Using this method, we present exact samples from a frustrated antiferromagnetic triangular Ising model and the antiferromagnetic q=3 Potts model. We discuss the advantages and limitations of the method of summary states for practical sampling, paying particular attention to the slowing down of the algorithm at low temperature. In particular, we show that such a slowing down can occur in the absence of a physical phase transition.Comment: 5 pages, 6 EPS figures, REVTeX; additional information at http://wol.ra.phy.cam.ac.uk/mackay/exac

Cervicovaginal and Rectal Fluid as a Surrogate Marker of Antiretroviral Tissue Concentration: Implications for Clinical Trial Design

Quantifying tissue drug concentrations can yield important information during drug development, but complicates pharmacokinetic study design. Mucosal fluids collected by direct aspiration(cervicovaginal fluid; CVF) or swab(rectal fluid; RF) might be used as tissue concentration surrogates, but these relationships are not well characterized

Do organizational climate and competitive strategy moderate the relationship between human resource management and productivity?

This study examined whether the effectiveness of human resource management (HRM)practices is contingent on organizational climate and competitive strategy The concepts of internol and external fit suggest that the positive relationship between HRM and subsequent productivity will be stronger for firms with a positive organizational climate and for firms using differentiation strategies. Resource allocation theories of motivation, on the other hand, predict that the relationship between HRM and productivity will be stronger for firms with a poor climate because employees working in these firms should have the greatest amount of spare capacity. The results supported the resource allocation argument

A Translational Pharmacology Approach to Predicting Outcomes of Preexposure Prophylaxis Against HIV in Men and Women Using Tenofovir Disoproxil Fumarate With or Without Emtricitabine

Background. A novel translational pharmacology investigation was conducted by combining an in vitro efficacy target with mucosal tissue pharmacokinetic (PK) data and mathematical modeling to determine the number of doses required for effective human immunodeficiency virus (HIV) preexposure prophylaxis (PrEP)

A clinical approach to the diagnosis of patients with leukodystrophies and genetic leukoencephelopathies

Leukodystrophies (LD) and genetic leukoencephalopathies (gLE) are disorders that result in white matter abnormalities in the central nervous system (CNS). Magnetic resonance (MR) imaging (MRI) has dramatically improved and systematized the diagnosis of LDs and gLEs, and in combination with specific clinical features, such as Addison’s disease in Adrenoleukodystrophy or hypodontia in Pol-III related or 4H leukodystrophy, can often resolve a case with a minimum of testing. The diagnostic odyssey for the majority LD and gLE patients, however, remains extensive – many patients will wait nearly a decade for a definitive diagnosis and at least half will remain unresolved. The combination of MRI, careful clinical evaluation and next generation genetic sequencing holds promise for both expediting the diagnostic process and dramatically reducing the number of unresolved cases. Here we present a workflow detailing the Global Leukodystrophy Initiative (GLIA) consensus recommendations for an approach to clinical diagnosis, including salient clinical features suggesting a specific diagnosis, neuroimaging features and molecular genetic testing. We also discuss recommendations on the use of broad-spectrum next-generation sequencing in instances of ambiguous MRI or clinical findings. We conclude with a proposal for systematic trials of genome-wide agnostic testing as a first line diagnostic in LDs and gLEs given the increasing number of genes associated with these disorders

A method for successful collection of multicores and gravity cores from Antarctic subglacial lakes

During the 2018–2019 Antarctic field season, the Subglacial Antarctic Lakes Scientific Access project team cleanly accessed Mercer Subglacial Lake, West Antarctica, to sample water and sediments beneath 1087 m of overlying ice. A multicorer was successful in sampling the sediment–water interface, with 4 deployments retrieving 10 cores between 0.3 and 0.4 m in length. Gravity coring was also successful, retrieving cores of 0.97 and 1.78 m in glacial diamict. However, sediment cores retrieved by the gravity cores were shorter than the core barrel penetration (as measured by mud streaks on the outside of the coring system), indicating that the system can likely be improved. This manuscript describes the design, implementation, successes, and lessons learned while coring sediments in a subglacial lake

Negative parental responses to coming out and family functioning in a sample of lesbian and gay young adults

Parental responses to youths' coming out (CO) are crucial to the subsequent adjustment of children and family. The present study investigated the negative parental reaction to the disclosure of same-sex attraction and the differences between maternal and paternal responses, as reported by their homosexual daughters and sons. Participants' perceptions of their parents' reactions (evaluated through the Perceived Parental Reactions Scale, PPRS), age at coming out, gender, parental political orientation, and religiosity involvement, the family functioning (assessed through the Family Adaptability and Cohesion Evaluation Scales, FACES IV), were assessed in 164 Italian gay and lesbian young adults. Pearson correlation coefficients were calculated to assess the relation between family functioning and parental reaction to CO. The paired sample t-test was used to compare mothers and fathers' scores on the PPRS. Hierarchical multiple regression was conducted to analyze the relevance of each variable. No differences were found between mothers and fathers in their reaction to the disclosure. The analysis showed that a negative reaction to coming out was predicted by parents' right-wing political conservatism, strong religious beliefs, and higher scores in the scales Rigid and Enmeshed. Findings confirm that a negative parental reaction is the result of poor family resources to face a stressful situation and a strong belief in traditional values. These results have important implications in both clinical and social fields