Miracle-dz/UniFAR-FTUs huggingface dataset:
Directions for Optimization of Photosynthetic Carbon Fixation: RuBisCO's Efficiency May Not Be So Constrained After All

The ubiquitous enzyme Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) fixes atmospheric carbon dioxide within the Calvin-Benson cycle that is utilized by most photosynthetic organisms. Despite this central role, RuBisCO's efficiency surprisingly struggles, with both a very slow turnover rate to products and also impaired substrate specificity, features that have long been an enigma as it would be assumed that its efficiency was under strong evolutionary pressure. RuBisCO's substrate specificity is compromised as it catalyzes a side-fixation reaction with atmospheric oxygen; empirical kinetic results show a trend to tradeoff between relative specificity and low catalytic turnover rate. Although the dominant hypothesis has been that the active-site chemistry constrains the enzyme's evolution, a more recent study on RuBisCO stability and adaptability has implicated competing selection pressures. Elucidating these constraints is crucial for directing future research on improving photosynthesis, as the current literature casts doubt on the potential effectiveness of site-directed mutagenesis to improve RuBisCO's efficiency. Here we use regression analysis to quantify the relationships between kinetic parameters obtained from empirical data sets spanning a wide evolutionary range of RuBisCOs. Most significantly we found that the rate constant for dissociation of CO2 from the enzyme complex was much higher than previous estimates and comparable with the corresponding catalytic rate constant. Observed trends between relative specificity and turnover rate can be expressed as the product of negative and positive correlation factors. This provides an explanation in simple kinetic terms of both the natural variation of relative specificity as well as that obtained by reported site-directed mutagenesis results. We demonstrate that the kinetic behaviour shows a lesser rather than more constrained RuBisCO, consistent with growing empirical evidence of higher variability in relative specificity. In summary our analysis supports an explanation for the origin of the tradeoff between specificity and turnover as due to competition between protein stability and activity, rather than constraints between rate constants imposed by the underlying chemistry. Our analysis suggests that simultaneous improvement in both specificity and turnover rate of RuBisCO is possible.
Situating the default-mode network along a principal gradient of macroscale cortical organization

Significance We describe an overarching organization of large-scale connectivity that situates the default-mode network at the opposite end of a spectrum from primary sensory and motor regions. This topography, based on the differentiation of connectivity patterns, is also embedded in the spatial distance along the cortical surface between these respective systems. In addition, this connectivity gradient accounts for the respective positions of canonical networks and captures a functional spectrum from perception and action to more abstract cognitive functions. These results suggest that the default-mode network consists of regions at the top of a representational hierarchy that describe the current cognitive landscape in the most abstract terms. Understanding how the structure of cognition arises from the topographical organization of the cortex is a primary goal in neuroscience. Previous work has described local functional gradients extending from perceptual and motor regions to cortical areas representing more abstract functions, but an overarching framework for the association between structure and function is still lacking. Here, we show that the principal gradient revealed by the decomposition of connectivity data in humans and the macaque monkey is anchored by, at one end, regions serving primary sensory/motor functions and at the other end, transmodal regions that, in humans, are known as the default-mode network (DMN). These DMN regions exhibit the greatest geodesic distance along the cortical surface—and are precisely equidistant—from primary sensory/motor morphological landmarks. The principal gradient also provides an organizing spatial framework for multiple large-scale networks and characterizes a spectrum from unimodal to heteromodal activity in a functional metaanalysis. Together, these observations provide a characterization of the topographical organization of cortex and indicate that the role of the DMN in cognition might arise from its position at one extreme of a hierarchy, allowing it to process transmodal information that is unrelated to immediate sensory input.
The sage handbook of grounded theory

PART ONE: ORIGINS AND HISTORY GT in Historical Perspective - Antony Bryant and Kathy Charmaz An Epistemological Account Discovery of GT in Practice - Eleanor Krassner Covan Legacy of Multiple Mentors Living GT - Susan Leigh Star Cognitive amd Emotional Forms of Pragmatism PART TWO: GTM AND FORMAL GT Doing Formal Theory - Barney Glaser Essential Properties for Growing GT - Phyllis Stern Evolution of Formal GT - Margaret Kearney Orthodoxy versus Power - Jane Hood PART THREE: GT IN PRACTICE Grounding Categories - Ian Dey Development of Categories - Udo Kelle Abduction - Jo Reichertz Sampling in GT - Janice Morse Memo-Writing in GT - Lora Lempert Coding - Judith Holton PART FOUR: PRACTICALITIES Making Teams Work in Conducting GT - Carolyn Wiener Teaching GT - Sharlene Hesse-Biber GT as a Tool for IS Research - Cathy Urquhart PART FIVE: GT IN THE RESEACRH METHODS CONTEXT GT and Situational Analysis - Adele Clarke and Carrie Friese GT and Action Research - Bob Dick Integrating GT and Feminist Methods - Virginia Olesen Accommodating Critical Theory - Barry Gibson GT and the Politics of Interpretation - Norman Denzin GT and Diversity - Denise O'Neil Green et al Ethnography - Stefan Timmermans and Iddo Tavory PART SIX: GT IN THE CONTEXT OF THE SOCIAL SCIENCES GT and Reflexivity - Katja Mruck and Guenter Mey Mediating Structure and Interaction - Bruno Hildenbrand Tensions in Using GT - Karen Locke GT and Pragmatism - Joerg Struebing
The Syk-binding Ubiquitin Ligase c-Cbl Mediates Signaling-dependent B Cell Receptor Ubiquitination and B Cell Receptor-mediated Antigen Processing and Presentation*

Background: c-Cbl associates with various signaling molecules to regulate diverse signaling networks via ubiquitination of receptors and/or protein tyrosine kinases. Results: c-Cbl drives ubiquitin-dependent Ag·BCR trafficking to MIIC and BCR-mediated antigen processing and presentation. Conclusion: c-Cbl directs BCR-mediated antigen processing and presentation. Significance: c-Cbl coordinates antigen-induced BCR signaling and rapid BCR-mediated antigen processing and presentation to drive a strong humoral immune response. B cell receptor (BCR)-mediated antigen (Ag) processing and presentation lead to B cell-T cell interactions, which support affinity maturation and immunoglobulin class switching. These interactions are supported by generation of peptide-MHC class II complexes in multivesicular body-like MIIC compartments of B cells. Previous studies have shown that trafficking of Ag·BCR complexes to MVB-like MIIC occurs via an ubiquitin-dependent pathway and that ubiquitination of Ag·BCR complexes occurs by an Src family kinase signaling-dependent mechanism that is restricted to lipid raft-resident Ag·BCR complexes. This study establishes that downstream Syk-dependent BCR signaling is also required for BCR ubiquitination and BCR-mediated antigen processing and presentation. Knockdown studies reveal that of the two known Syk-binding E3 ubiquitin ligases c-Cbl and Cbl-b, only c-Cbl appears to have a central role in BCR ubiquitination, trafficking to MIIC, and ubiquitin-dependent BCR-mediated antigen processing and presentation. These results establish the novel role for Syk signaling and the Syk-binding ubiquitin ligase c-Cbl in the BCR-mediated processing and presentation of cognate antigen and define one mechanism by which antigen-induced BCR ubiquitination is modulated to impact the initiation and maturation of the humoral immune response.
Causal inference in epidemiological research

Traditionally, statistics has been viewed as the branch of science which deals with association. Many epidemiological research questions, however, are concerned with causation, not association. In this thesis we develop novel statistical methodology to address four epidemiological problems properly, from a causal inference point of view. We show, that for these four problems, our methods offer an attractive alternative to the ‘standard’ methodology, which may not yield the desired (causal) inference. List of publications This thesis is based on the following papers, which will be referred to in the text by their Roman numerals. I. Sjolander A, Humphreys K, Palmgren J. (2008). On informative detection bias in screening studies. Statistics in Medicine 27, 2635-2650. II. Sjolander A, Humphreys K, Vansteelandt S, Bellocco R, Palmgren J. (2008). Sensitivity analysis for principal stratum direct effects, with an application to a study of physical activity and coronary heart disease. Biometrics DOI: 10.1111/j.1541-0420.2008. 01108.x. III. Sjolander A. (2008). Bounds on natural direct effects in the presence of confounded intermediate variables. Statistics in Medicine DOI: 10.1002/sim.3493. IV. Sjolander A, Humphreys K, Vansteelandt S. (2008). A principal stratification approach to assess the differences in prognosis between cancers caused by hormone replacement therapy and by other factors. Submitted.
Of borders and homes: the imaginary community of (trans)sexual citizenship 1

Abstract This essay maps the connections between transgender/transsexual rights and nationalism in Australia. Comparing Jay Prosser’s idea of a transsexual ‘politics of home’ with the recent legalisation of transsexual marriage in Australia, it argues that marriage rights are granted by the state on the ability of particular bodies to maintain and reproduce a series of demarcated zones: between male and female, but also between ‘Australian’ and ‘un‐Australian’, ‘white’ and ‘non‐white. ’ This has been most evident in a successful Australian transsexual marriage case, Re Kevin, where the success of the respondents relied on arguing that transsexuality is a biological condition. Establishing the gender of the transsexual respondent involved ‘proving’ biology through reference to his social performance of normative masculinity. But the norms of masculinity used to ‘prove’ such a thing are socially constructed and, as such, racialised: home maintenance, proficiency with power‐tools, enjoying the white Australian tradition of barbeques and sport. Exploring the Australian political context of the court case, where ‘Australian‐ness’ has a particular meaning and a particular value, I critique the liberal‐democratic capitalist structure of rights claims in which gender variant subjects must present ‘whiteness’ as a form of cultural capital in exchange for rights. The cost of this exchange falls overwhelmingly on gender variant subjects who don’t present a racially/culturally normative performance of masculinity.
Political Scandal: Power and Visibility in the Media Age

List of Illustrations. Preface. Acknowledgements. Introduction. 1. What is Scandal? 2. The Rise of Mediated Scandal. 3. Scandal as a Mediated Event. 4. The Nature of Political Scandal. 5. Sex Scandals in the Political Field. 6. Financial Scandals in the Political Field. 7. Power Scandals. 8. The Consequences of Scandal. Conclusion. Notes. Index.
The semantics of human facial expressions

This paper points out that a major shift of paradigm is currently going on in the study of the human face and it seeks to articulate and to develop the fundamental assumptions underlying this shift. The main theses of the paper are: 1) Facial expressions can convey meanings comparable to the meanings of verbal utterances. 2) Semantic analysis (whether of verbal utterances or of facial expressions) must distinguish between the context-independent invariant and its contextual interpretations. 3) Certain components of facial behavior (? facial gestures? ) do have constant context-independent meanings. 4) The meanings of facial components and configurations of components have an inherent first-person and present tense orientation. 5) The basis for the interpretation of facial gestures is, above all, experiential. 6) The meanings of some facial expressions are universally intelligible and can be interpreted without reference to any local conventions. 7) To be fruitful, the semantic analysis of facial expressions needs a methodology. This can be derived from the methodological experience of linguistic semantics. The author illustrates and supports these theses by analyzing a range of universally interpretable facial expressions such as the following ones: ? brow furrowed? (i.e. eyebrows drawn together); eyebrows raised; eyes wide open; corners of the mouth raised; corners of the mouth lowered; mouth open (while not speaking); lips pressed together; upper lip and nose ? raised? (and, consequently, nose wrinkled).
Leader Election in Sparse Dynamic Networks with Churn

We investigate the problem of electing a leader in a sparse but well-connected synchronous dynamic network in which up to a fraction of the nodes chosen adversarially can leave/join the network per time step. At this churn rate, all nodes in the network can be replaced by new nodes in a constant number of rounds. Moreover, the adversary can shield a fraction of the nodes (which may include the leader) by repeatedly churning their neighbourhood and thus hinder their communication with the rest of the network. However, empirical studies in peer-to-peer networks have shown that a significant fraction of the nodes are usually stable and well connected. It is, therefore, natural to take advantage of such stability and well-connectedness to establish a leader that can maintain good communication with rest of the nodes. Since the dynamics could change eventually, it is also essential to re-elect a new leader whenever the current leader has either left the network or is not well-connected with rest of the nodes. In such re-elections, care must be taken to avoid premature and spurious leader election resulting in more than one leader present in the network at the same time. We assume a broadcast based communication model in which each node can send up to O(log3n) bits per round and is unaware of its receivers a priori. We present a randomized algorithm that can, in O(log n) rounds, detect and reach consensus about the health of the leader (i.e., whether it is able to maintain good communication with rest of the network). In the event that the network decides that the leader's ability to communicate is unhealthy, a new leader is re-elected in a further O(log2n) rounds. Our running times hold with high probability, and, furthermore, we are guaranteed with high probability that there is at most one leader at any time.
8: An Evolving Logic of Participant Observation, Educational Ethnography, and Other Case Studies

The aspiration of the author in this chapter is straightforward but wide ranging: to provide a context and logic for the discussion of the genre of research that is coming to be known by such varied labels as educational ethnography, participant observation, qualitative observation, case study, or field study. For the most part, I will use these terms as synonyms. Such an aspiration is warranted for several reasons. First, the method seems very simple, and some methodologists perceive it this way. Biddle (1967) called it "the broadest and simplest methodology used in classroom studies. " The researcher goes into an educational setting with a pencil and pad, makes a few observations, takes some notes, and writes a report, a dissertation, or a book. For some it seems almost this easy; others stumble about and have incredible difficulty. Second, a growing group of researchers, evaluators, and policymakers (e.g., NIE's Experimental Schools, NIE's School Capacity for Problem Solving, Nuffield Humanities Evaluation, OECD's Center for Educational Research and Innovation, and NSF's Case Studies in Science Education) have been urging inquiry and evaluation using these techniques. Third, several major methodologists have disparaged the use of such procedures: the two most significant statements are Scriven's (1967) classic paper on evaluation and Campbell and Stanley's (1963) classic chapter on experimental research in education. The former attacked "process studies" and "noncomparative evalua-
Keeping focus: a study of Attention Problems in the GWAS era

of oral presentation 21st World Congress of Psychiatric Genetics; October 17-21, 2013; Boston, USA. 7. Cross-Disorder Group of the Psychiatric Genomics Consortium, Lee SH, Ripke S, et al. Genetic relationship between five psychiatric disorders estimated from genomewide SNPs. Nat Genet. 2013;45:984-994. 8. van der Sluis S, Posthuma D, Nivard MG, Verhage M, Dolan CV. Power in GWAS: lifting the curse of the clinical cut-off. Mol Psychiatry. 2013;18:2-3. 9. Lubke GH, Hudziak JJ, Derks EM, van Bijsterveldt TC, Boomsma DI. Maternal ratings of attention problems in ADHD: evidence for the existence of a continuum. J Am Acad Child Adolesc Psychiatry. 2009;48:1085-1093. 10. Levy F, Hay DA, McStephen M, Wood C, Waldman I. Attention-deficit hyperactivity disorder: a category or a continuum? Genetic analysis of a large-scale twin study. J Am Acad Child Adolesc Psychiatry. 1997;36:737-744. 11. Larsson H, Anckarsater H, Rastam M, Chang Z, Lichtenstein P. Childhood attentiondeficit hyperactivity disorder as an extreme of a continuous trait: a quantitative genetic study of 8,500 twin pairs. J Child Psychol Psychiatry. 2012;53:73-80. 12. Groen-Blokhuis MM, Middeldorp CM, Abdellaoui A, et al. Attention Deficit Hyperactivity Disorder polygenic risk scores predict Attention Problems in a
Perceptions of a Statewide Mentor Program for New Itinerant Vision Professionals

Introduction Mentoring is valuable for the retention of new teachers. This article describes a model statewide mentor program for new itinerant vision professionals who work with students from birth to age 22. The results of a recent survey of satisfaction are reported, along with implications for the field. Methods The protégés who participated in the statewide mentor program completed an electronic satisfaction survey. Of the 76 participants who had been assigned a mentor during the 2011–12 academic year, 56 responded (74%). Both quantitative and qualitative questions were included in the survey. The quantitative questions were analyzed using percentages, and the qualitative data was analyzed and put into themes using the data analysis process of triangulation. Results Seventy-one percent of the participants reported having had more than 10 interactions with their mentors over the previous year. The topics most frequently addressed with their mentors were performing evaluations (89%), locating resources (84%), and writing goals and objectives (79%). The most helpful mentoring techniques that were used included guided problem-solving techniques (70%), effective listening (68%), and the provision of teaching materials (57%). The majority of the protégés (82%) thought that their mentors had definitely contributed to the quality of their teaching. The top stressors for new vision professionals were related to organization and time management, evaluations, and collaboration with others. Discussion The results of the survey demonstrate that the mentor program had a positive outcome for the participants as new educators. It also provided information on the stressors faced by these new vision professionals. Implications for practitioners This article can serve as a model for other states that are interested in developing a mentor program for new itinerant vision professionals, and can serve as a guide for personnel preparation programs to address further the areas that the protégés identified as those in which they felt the least competent.
Author ' s personal copy Dynamic simulation of locally inextensible vesicles suspended in an arbitrary two-dimensional domain , a boundary integral method

We consider numerical algorithms for the simulation of hydrodynamics of two-dimensional vesicles suspended in a viscous Stokesian fluid. The motion of vesicles is governed by the interplay between hydrodynamic and elastic forces. Continuum models of vesicles use a two-phase fluid system with interfacial forces that include tension (to maintain local ‘‘surface” inextensibility) and bending. Vesicle flows are challenging to simulate. On the one hand, explicit time-stepping schemes suffer from a severe stability constraint due to the stiffness related to high-order spatial derivatives in the bending term. On the other hand, implicit time-stepping schemes can be expensive because they require the solution of a set of nonlinear equations at each time step. Our method is an extension of the work of Veerapaneni et al. [S.K. Veerapaneni, D. Gueyffier, D. Zorin, G. Biros, A boundary integral method for simulating the dynamics of inextensible vesicles suspended in a viscous fluid in 2D, Journal of Computational Physics 228(7) (2009) 2334–2353], in which a semi-implicit time-marching scheme based on a boundary integral formulation of the Stokes problem for vesicles in an unbounded medium was proposed. In this paper, we consider two important generalizations: (i) confined flows within arbitrary-shaped stationary/moving geometries; and (ii) flows in which the interior (to the vesicle) and exterior fluids have different viscosity. In the rest of the paper, we will refer to this as the ‘‘viscosity contrast”. These two problems require solving additional integral equations and cause nontrivial modifications to the previous numerical scheme. Our method does not have severe time-step stability constraints and its computational cost-per-time-step is comparable to that of an explicit scheme. The discretization is pseudo-spectral in space, and multistep BDF in time. We conduct numerical experiments to investigate the stability, accuracy and the computational cost of the algorithm. Overall, our method achieves several orders of magnitude speed-up compared to standard explicit schemes. As a preliminary validation of our scheme, we study the dependence of the inclination angle of a single vesicle in shear flow on the viscosity contrast and the reduced area of the vesicle, the lateral migration of vesicles in shear flow, the dispersion of two vesicles, and the effective viscosity of a dilute suspension of vesicles. 2010 Elsevier Inc. All rights reserved. 0021-9991/$ see front matter 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.jcp. 2010.05. 006 * Corresponding author. E-mail addresses: rahimian@gatech.edu (A. Rahimian), shravan@ims.nyu. edu (S.K. Veerapaneni), gbiros@acm.org, biros@seas.upenn. edu (G. Biros). Journal of Computational Physics 229 (2010) 6466–6484
Corporate Cash Holdings , Board Structure , and Ownership Concentration : Evidence from Singapore

Corporations hold cash balances for a variety of reasons. We document that board size and nonmanagement blockholder ownership are significantly related to the ratio of cash to net assets for a sample of publicly listed firms in Singapore. While the relationship between board size and cash holdings is positive and significant, non-management blockholder ownership is inversely related to cash holdings. Our findings are consistent with the agency cost hypothesis. Since firms with large boards and low non-management blockholder ownership are normally poorly governed, shareholders of such firms do not have much power in forcing the managers to distribute the excess cash to them. As a result, those firms hold higher cash balances than firms who have better control mechanisms (ie: small board and large non-management blockholder ownership).