A Look at the Attrition of Women in STEM

The underrepresentation of women in leadership positions in Science, Technology, Engineering, and Mathematics (STEM) is usually attributed to the ‘leaky pipeline phenomenon’, according to which an increasing proportion of women leave their occupational fields at each stage along their career paths. This attrition is most pronounced for the academic biological sciences, in which the most significant attrition occurs at the postgraduate-to-group leader transition. To illustrate: in the UK in 2014/15, 66% of bioscience postgraduate students, but only 18% of professors, were female. A huge gender difference in leadership positions is evident across all STEM fields: overall, 82% of all professors are men, as of 2014. This attrition of women in the STEM workforce raises questions over specific barriers faced by women in this field for career advancement. These barriers can be multi-faceted; thus, accurately identifying the main barriers and designing policies to address them will be essential to resolving gender disparity in the field of STEM

Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens.

Intercellular communication mediated by direct interactions between membrane-embedded cell surface receptors is crucial for the normal development and functioning of multicellular organisms. Detecting these interactions remains technically challenging, however. This manuscript describes a systematic genome-scale CRISPR/Cas9 knockout genetic screening approach that reveals cellular pathways required for specific cell surface recognition events. This assay utilizes recombinant proteins produced in a mammalian protein expression system as avid binding probes to identify interaction partners in a cell-based genetic screen. This method can be used to identify the genes necessary for cell surface interactions detected by recombinant binding probes corresponding to the ectodomains of membrane-embedded receptors. Importantly, given the genome-scale nature of this approach, it also has the advantage of not only identifying the direct receptor but also the cellular components that are required for the presentation of the receptor at the cell surface, thereby providing valuable insights into the biology of the receptor

Genome-scale identification of cellular pathways required for cell surface recognition

A range of biochemically diverse molecules located in the plasma membrane - such as proteins, glycans, and lipids - mediate cellular recognition events, initiation of signalling pathways, and the regulation of processes important for the normal development and function of multicellular organisms. Interactions mediated by cell surface receptors can be challenging to detect in biochemical assays, because they are often highly transient, and membrane-embedded receptors are difficult to solubilise in their native conformation. The biochemical features of low-affinity extracellular protein interactions have therefore necessitated the development of bespoke methods to detect them. Here, I develop a genome-scale cell-based genetic screening approach using CRISPR-Cas9 knockout technology that reveals cellular pathways required for specific cell surface recognition events. Using a panel of high-affinity monoclonal antibodies, I first establish a method from which I identify not only the direct receptor but also other required gene products, such as co-receptors, post-translational modifications, and transcription factors contributing to antigen expression and subsequent antibody-antigen recognition on the surface of cells. I next adapt this method to identify cellular factors required for receptor interactions for a panel of recombinant proteins corresponding to the ectodomains of cell surface proteins to the endogenous surface receptors present on a range of cell lines. In addition to finding general cellular features recognised by many ectodomains, I also identify direct interaction partners of recombinant protein probes on cell surfaces together with intracellular genes required for such associations. Using this method, I identify IGF2R as a binding partner for the R2 subunit of GABAB receptors, providing a mechanism for the internalisation and regulation of GABAB receptor signalling. The results here demonstrate that this single approach can identify the molecular nature and cell biology of surface receptors without the need to make any prior assumptions regarding their biochemical properties

An Integrated Knowledge Discovery and Data Mining Process Model

Enterprise decision making is continuously transforming in the wake of ever increasing amounts of data. Organizations are collecting massive amounts of data in their quest for knowledge nuggets in form of novel, interesting, understandable patterns that underlie these data. The search for knowledge is a multi-step process comprising of various phases including development of domain (business) understanding, data understanding, data preparation, modeling, evaluation and ultimately, the deployment of the discovered knowledge. These phases are represented in form of Knowledge Discovery and Data Mining (KDDM) Process Models that are meant to provide explicit support towards execution of the complex and iterative knowledge discovery process. Review of existing KDDM process models reveals that they have certain limitations (fragmented design, only a checklist-type description of tasks, lack of support towards execution of tasks, especially those of the business understanding phase etc) which are likely to affect the efficiency and effectiveness with which KDDM projects are currently carried out. This dissertation addresses the various identified limitations of existing KDDM process models through an improved model (named the Integrated Knowledge Discovery and Data Mining Process Model) which presents an integrated view of the KDDM process and provides explicit support towards execution of each one of the tasks outlined in the model. We also evaluate the effectiveness and efficiency offered by the IKDDM model against CRISP-DM, a leading KDDM process model, in aiding data mining users to execute various tasks of the KDDM process. Results of statistical tests indicate that the IKDDM model outperforms the CRISP model in terms of efficiency and effectiveness; the IKDDM model also outperforms CRISP in terms of quality of the process model itself

Effect of prenatal species-specific and music stimulation on the postnatal auditory preference of domestic chick

Perinatal sensory experience plays an important role in the development of perceptual preferences. In the present study prenatal enrichment with sound stimulus was given to see its effect on the development of postnatal auditory preference. Auditory stimulation with either species-specific (chicken maternal and hatching calls) or music (slow and fast sitar music) sounds was provided to two separate sets of fertilized eggs from the day 10 of incubation. The postnatal auditory preference of the chicks to either species-specific or music sounds was then tested at different time periods after hatching. All the chicks, irrespective of the type of prenatal exposure, showed preference for species-specific maternal calls. Notably, the music stimulated chicks did not show preference for either slow or fast music. In both the experimental groups, the number of chicks responding to the species-specific maternal calls was significantly (P<0.001) more at 24 h and 48 h post hatch, when compared with the unstimulated control group. Comparison of the species-specific stimulated group with the music stimulated group, for auditory preference to the maternal calls, did not show any significant difference. Further, in the species-specific sound stimulated groups, there was a significant (P<0.001) increase in the number of chicks responding to maternal calls at 60 h of age with repeated testing. However, there was no effect of peer imprinting on the auditory preference of the chicks, in both the experimental groups. The results indicate that prenatal auditory experience with either speciesspecific or non-specific music enhances the postnatal auditory preference of chicks for the species-specific sounds

Investigating cellular recognition using crispr/cas9 genetic screening.

Neighbouring cells can recognise and communicate with each other by direct binding between cell surface receptor and ligand pairs. Examples of cellular recognition events include pathogen entry into a host cell, sperm-egg fusion, and self/nonself discrimination by the immune system. Despite growing appreciation of cell surface recognition molecules as potential therapeutic targets, identifying key factors contributing to cellular recognition remains technically challenging to perform on a genome-wide scale. Recently, genome-scale clustered regularly interspaced short palindromic repeats (CRISPR) knockout or activation (CRISPR-KO/CRISPRa) screens have been applied to identify the molecular determinants of cellular recognition. In this review, we discuss how CRISPR-KO/CRISPRa screening has contributed to our understanding of cellular recognition processes, and how it can be applied to investigate these important interactions in a range of biological contexts. Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved

Numerical analysis of stresses on layer-by-layer basis in FML composite cylinder subjected to external hydrostatic loading.

The aim of the research work was to numerically investigate the residual stresses induced between the layers of fiber metal laminate (FML) cylinder (glass/epoxy reinforced aluminum laminates) under buckling hydrostatic loading. For the analysis of buckling behavior of FML cylinders, various fiber orientations such as 0/90˚, 60/30˚, ±45˚ and ±55˚ and different FRP thickness of 1, 2, and 3 mm were considered. The aluminum cylinder of inner diameter 80 mm, length 800 mm and wall thickness 1 mm was modeled with SHELL281 element type and a total of 1033 elements were used for computing the induced residual stresses between the layers. The results show that magnitude of residual stresses between the layers decreased along the thickness from outer layer towards the inner layer in sine wave form. The maximum residual Von-Mises stress was at inner aluminum layer while the maximum residual radial stress was at the outermost layer of FML cylinder due to the inward pressure. Among all types of FML cylinder 0/90˚ fiber oriented FML cylinder exhibited the least radial stress and a maximum Von-Mises stress along the FRP thickness

Hypothesis-driven science in large-scale studies: the case of GWAS

It is now well-appreciated by philosophers that contemporary large-scale `-omics' studies in biology stand in non-trivial relationships to more orthodox hypothesis-driven approaches. These relationships have been clarified substantially by Ratti (2015); however, there remains much more to be said regarding how an important field of genomics cited in that work---`genome-wide association studies' (GWAS)---fits into this framework. In the present article, we propose a revision to Ratti's framework more suited to studies such as GWAS. In the process of doing so, we introduce to the philosophical literature novel exploratory experiments in (phospho)proteomics, and demonstrate how these experiments interplay with the above considerations

Numerical analysis of the effect of fiber orientation on hydrostatic buckling behavior of fiber metal composite cylinder

The external hydrostatic buckling behavior of fiber metal laminate (FML) composite cylinders was investigated numerically. The critical buckling pressure predicted by eigenvalue analysis was compared with experimental results. The numerical results showed different modes of buckling and buckling deformation for cylinders of different fiber orientation when subjected to external hydrostatic loading. FML cylinder with 0/90 fiber orientation exhibited higher buckling strength and lower buckling deformation as compared to FML cylinders of 60/30, 45, and 55 fiber orientations. The orientation of fiber has significant influence on the performance of FML composite cylinder as compared to fiberreinforced plastic thickness. The correlation between numerical and experimental results is discussed in terms of buckling strength, circumferential stiffness, and buckling deformations. It was observed that the cylinders were less sensitive to initial imperfections irrespective of fiber-reinforced plastic thickness. In addition, the results of finite element analysis and experimental results indicate good matches

Genome-scale identification of cellular pathways required for cell surface recognition.

Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challenges by using a genome-scale, cell-based genetic screening approach using CRISPR gene knockout technology to identify cellular pathways required for specific cell surface recognition events. By using high-affinity monoclonal antibodies and low-affinity ligands, we determined the necessary screening parameters, including the importance of establishing binding contributions from the glycocalyx, that permitted the unequivocal identification of genes encoding directly interacting membrane-embedded receptors with high statistical confidence. Importantly, we show that this genome-wide screening approach additionally identified receptor-specific pathways that are required for functional display of receptors on the cell surface that included chaperones, enzymes that add post-translational modifications, trafficking proteins, and transcription factors. Finally, we demonstrate the utility of the approach by identifying IGF2R (insulin like growth factor 2 receptor) as a binding partner for the R2 subunit of GABAB receptors. We show that this interaction is direct and is critically dependent on mannose-6-phosphate, providing a mechanism for the internalization and regulation of GABAB receptor signaling. We conclude that this single approach can reveal both the molecular nature and the genetic pathways required for functional cell surface display of receptors recognized by antibodies, secreted proteins, and membrane-embedded ligands without the need to make any prior assumptions regarding their biochemical properties. © 2018 Sharma et al.; Published by Cold Spring Harbor Laboratory Press