Removing orientation-induced localization biases in single-molecule microscopy using a broadband metasurface mask

Nanoscale localization of single molecules is a crucial function in several advanced microscopy techniques, including single-molecule tracking and wide-field super-resolution imaging. Until now, a central consideration of such techniques is how to optimize the precision of molecular localization. However, as these methods continue to push towards the nanometre size scale, an increasingly important concern is the localization accuracy. In particular, single fluorescent molecules emit with an anisotropic radiation pattern of an oscillating electric dipole, which can cause significant localization biases using common estimators. Here we present the theory and experimental demonstration of a solution to this problem based on azimuthal filtering in the Fourier plane of the microscope. We do so using a high-efficiency dielectric metasurface polarization/phase device composed of nanoposts with subwavelength spacing. The method is demonstrated both on fluorophores embedded in a polymer matrix and in dL5 protein complexes that bind malachite green

Factors Influencing Physicians’ Screening Behavior for Liver Cancer Among High-risk Patients

BACKGROUND: Little is known about physicians’ screening patterns for liver cancer despite its rising incidence. OBJECTIVE: Describe physician factors associated with liver cancer screening. DESIGN: Mailed survey. PARTICIPANTS: Physicians practicing in family practice, internal medicine, gastroenterology, or nephrology in 3 northern California counties in 2004. MEASUREMENTS: Sociodemographic and practice measures, liver cancer knowledge, attitudes, and self-reported screening behaviors. RESULTS: The response rate was 61.8% (N = 459). Gastroenterologists (100%) were more likely than Internists (88.4%), family practitioners (84.2%), or nephrologists (75.0%) to screen for liver cancer in high-risk patients (p = 0.016). In multivariate analysis, screeners were more likely than nonscreeners to think that screening for liver cancer reduced mortality (odds ratio [OR] 1.60, CI 1.09–2.34) and that not screening was a malpractice risk (OR 1.88, CI 1.29–2.75). Screeners were more likely than nonscreeners to order any screening test if it was a quality of care measure (OR 4.39, CI 1.79–10.81). CONCLUSIONS: Despite debate about screening efficacy, many physicians screen for liver cancer. Their screening behavior is influenced by malpractice and quality control concerns. More research is needed to develop better screening tests for liver cancer, to evaluate their effectiveness, and to understand how physicians behave when there is insufficient evidence

Combining Path Integration and Remembered Landmarks When Navigating without Vision

This study investigated the interaction between remembered landmark and path integration strategies for estimating current location when walking in an environment without vision. We asked whether observers navigating without vision only rely on path integration information to judge their location, or whether remembered landmarks also influence judgments. Participants estimated their location in a hallway after viewing a target (remembered landmark cue) and then walking blindfolded to the same or a conflicting location (path integration cue). We found that participants averaged remembered landmark and path integration information when they judged that both sources provided congruent information about location, which resulted in more precise estimates compared to estimates made with only path integration. In conclusion, humans integrate remembered landmarks and path integration in a gated fashion, dependent on the congruency of the information. Humans can flexibly combine information about remembered landmarks with path integration cues while navigating without visual information.National Institutes of Health (U.S.) (Grant T32 HD007151)National Institutes of Health (U.S.) (Grant T32 EY07133)National Institutes of Health (U.S.) (Grant F32EY019622)National Institutes of Health (U.S.) (Grant EY02857)National Institutes of Health (U.S.) (Grant EY017835-01)National Institutes of Health (U.S.) (Grant EY015616-03)United States. Department of Education (H133A011903

Budding Yeast Dma Proteins Control Septin Dynamics and the Spindle Position Checkpoint by Promoting the Recruitment of the Elm1 Kinase to the Bud Neck

The first step towards cytokinesis in budding yeast is the assembly of a septin ring at the future site of bud emergence. Integrity of this ring is crucial for cytokinesis, proper spindle positioning, and the spindle position checkpoint (SPOC). This checkpoint delays mitotic exit and cytokinesis as long as the anaphase spindle does not properly align with the division axis. SPOC signalling requires the Kin4 protein kinase and the Kin4-regulating Elm1 kinase, which also controls septin dynamics. Here, we show that the two redundant ubiquitin-ligases Dma1 and Dma2 control septin dynamics and the SPOC by promoting the efficient recruitment of Elm1 to the bud neck. Indeed, dma1 dma2 mutant cells show reduced levels of Elm1 at the bud neck and Elm1-dependent activation of Kin4. Artificial recruitment of Elm1 to the bud neck of the same cells is sufficient to re-establish a normal septin ring, proper spindle positioning, and a proficient SPOC response in dma1 dma2 cells. Altogether, our data indicate that septin dynamics and SPOC function are intimately linked and support the idea that integrity of the bud neck is crucial for SPOC signalling

A quantitative analysis of complexity of human pathogen-specific CD4 T cell responses in healthy M. tuberculosis infected South Africans

Author Summary: Human pathogen-specific immune responses are tremendously complex and the techniques to study them ever expanding. There is an urgent need for a quantitative analysis and better understanding of pathogen-specific immune responses. Mycobacterium tuberculosis (Mtb) is one of the leading causes of mortality due to an infectious agent worldwide. Here, we were able to quantify the Mtb-specific response in healthy individuals with Mtb infection from South Africa. The response is highly diverse and 66 epitopes are required to capture 80% of the total reactivity. Our study also show that the majority of the identified epitopes are restricted by multiple HLA alleles. Thus, technical advances are required to capture and characterize the complete pathogen-specific response. This study demonstrates further that the approach combining identified epitopes into "megapools" allows capturing a large fraction of the total reactivity. This suggests that this technique is generally applicable to the characterization of immunity to other complex pathogens. Together, our data provide for the first time a quantitative analysis of the complex pathogen-specific T cell response and provide a new understanding of human infections in a natural infection setting

Obesity and renal cell cancer – a quantitative review

Obesity has been associated with an increased risk of renal cell cancer among women, while the evidence for men is considered weaker. We conducted a quantitative summary analysis to evaluate the existing evidence that obesity increases the risk of renal cell cancer both among men and women. We identified all studies examining body weight in relation to kidney cancer, available in MEDLINE from 1966 to 1998. The quantitative summary analysis was limited to studies assessing obesity as body mass index (BMI, kg m−2), or equivalent. The risk estimates and the confidence intervals were extracted from the individual studies, and a mixed effect weighted regression model was used. We identified 22 unique studies on each sex, and the quantitative analysis included 14 studies on men and women, respectively. The summary relative risk estimate was 1.07 (95% CI 1.05–1.09) per unit of increase in BMI (corresponding to 3 kg body weight increase for a subject of average height). We found no evidence of effect modification by sex. Our quantitative summary shows that increased BMI is equally strongly associated with an increased risk of renal cell cancer among men and women. © 2001 Cancer Research Campaignhttp://www.bjcancer.co

Clinical evaluation of marketed orthodontic products: are researchers behind the times? A meta-epidemiological study.

BACKGROUND: The role of marketing and industry in the treatment decisions of orthodontists has received increasing attention in recent years with clinical research typically undertaken subsequent to established use of these devices and often failing to confirm the promise of manufacturers' claims. This meta-epidemiological study was undertaken to assess the proportion of clinical trials in orthodontics evaluating commercially marketed products and to evaluate the direction of the results of these studies. METHODS: Electronic searching was undertaken to identify randomized controlled trials (RCTs) published over a 5-year period (1 January 2012 to 31 December 2016). Data obtained included the type of marketed intervention, direction of effect and declaration of both industry sponsorship and conflict of interest. RESULTS: Eighty-four RCTs published in 23 scientific journals were included with the highest percentage in the American Journal of Dentofacial Orthopedics (AJO-DO) (23.8%), followed by the European Journal of Orthodontics (EJO) (14.3%), Journal of Orthodontics (JO) (10.7%) and Angle Orthodontist (AO) (10.7%). Overall, 45% (38/84) of clinical trials assessed involved analysis of marketed products after their introduction. Interventions to improve oral health or circumvent the risk of iatrogenic damage, such as white spot lesions, were most commonly assessed (15.8%), with the relative merits of non-surgical adjuncts (14.1%) and other orthodontic auxiliaries (13.1%) also frequently evaluated. In 44% of RCTs, a positive effect of the marketed intervention was not reported. Industry sponsorship of the research was declared in 9.5% RCTs. No significant associations between the direction of the effect and both declaration of industry sponsorship (p = 0.56) and conflict of interest (p = 0.96) were detected. Moreover, for marketed and non-marketed products, no significant associations for both declaration of industry sponsorship (p = 0.44) and conflict of interest (p = 0.28) were found. CONCLUSIONS: Almost half of orthodontic clinical trials over the past 5 years involve analysis of marketed products after their introduction. The results highlight a potential source of waste in orthodontic research emanating from existing approaches to licensing and marketing of orthodontic products

Structural Annotation of Mycobacterium tuberculosis Proteome

Of the ∼4000 ORFs identified through the genome sequence of Mycobacterium tuberculosis (TB) H37Rv, experimentally determined structures are available for 312. Since knowledge of protein structures is essential to obtain a high-resolution understanding of the underlying biology, we seek to obtain a structural annotation for the genome, using computational methods. Structural models were obtained and validated for ∼2877 ORFs, covering ∼70% of the genome. Functional annotation of each protein was based on fold-based functional assignments and a novel binding site based ligand association. New algorithms for binding site detection and genome scale binding site comparison at the structural level, recently reported from the laboratory, were utilized. Besides these, the annotation covers detection of various sequence and sub-structural motifs and quaternary structure predictions based on the corresponding templates. The study provides an opportunity to obtain a global perspective of the fold distribution in the genome. The annotation indicates that cellular metabolism can be achieved with only 219 folds. New insights about the folds that predominate in the genome, as well as the fold-combinations that make up multi-domain proteins are also obtained. 1728 binding pockets have been associated with ligands through binding site identification and sub-structure similarity analyses. The resource (http://proline.physics.iisc.ernet.in/Tbstructuralannotation), being one of the first to be based on structure-derived functional annotations at a genome scale, is expected to be useful for better understanding of TB and for application in drug discovery. The reported annotation pipeline is fairly generic and can be applied to other genomes as well