Miracle-dz/UniFAR-FTUs huggingface dataset:
Finding motifs from all sequences with and without binding sites

MOTIVATION Finding common patterns, motifs, from a set of promoter regions of coregulated genes is an important problem in molecular biology. Most existing motif-finding algorithms consider a set of sequences bound by the transcription factor as the only input. However, we can get better results by considering sequences that are not bound by the transcription factor as an additional input. RESULTS First, instead of using the simple hyper-geometric analysis, we propose to calculate the likelihood based on a more precise probabilistic analysis which considers motif length, sequence length and number of binding sites as input parameters for testing whether motif is found. Second, we adopt an heuristic algorithm bases on our analysis to find motifs. For the simulated and real datasets, our algorithm ALSE compares favorably against common motif-finding programs such as SeedSearch and MEME in all cases and performs very well, especially when each input sequence contains more than one binding site. AVAILABILITY ALSE is available for download at the homepage http://alse.cs.hku.hk CONTACT cmleung2@cs.hku.hk.
Shear-selected Cluster Cosmology: Tomography and Optimal Filtering

We study the potential of weak-lensing surveys to detect clusters of galaxies, using a fast particle-mesh cosmological N-body simulation algorithm specifically tailored to investigate the statistics of these shear-selected clusters. In particular, we explore the degree to which the radial positions of galaxy clusters can be determined tomographically, by using photometric redshifts of background source galaxies. We quantify the errors in the tomographic redshifts, Δz ≡ ztomography - zreal, and study their dependence on mass, redshift, detection significance, and filtering scheme. For clusters detected with signal-to-noise ratio S/N ≳ 4.5, the fraction of clusters with tomographic redshift errors |Δz| ≤ 0.2 is 45% and the rms deviation from the real redshifts is ⟨(Δz)2⟩1/2 = 0.41, with smaller errors for higher S/N. A tomographic matched filtering (TMF) scheme, which combines tomography and matched filtering, is introduced that optimally detects clusters of galaxies in weak-lensing surveys. The TMF exploits the extra information provided by photometric redshifts of background source galaxies, neglected in previous studies, to optimally weight the sources. The efficacy and reliability of the TMF are investigated using a large ensemble of mock observations from our simulations, and detailed comparisons are made to other filters. Using photometric redshift information with the TMF enhances the number of clusters detected with S/N ≳ 4.5 by as much as 76%, and it increases the dynamic range of weak-lensing searches for clusters, detecting more high-redshift clusters and extending the mass sensitivity down to the scale of large groups. Furthermore, we find that coarse redshift binning of source galaxies with as few as three bins is sufficient to realize the gains of the TMF. Thus, the tomographic filtering techniques presented here can be applied to current ground-based weak-lensing data in as few as three bands, since two colors and magnitude prior are sufficient to bin source galaxies this coarsely. Cosmological applications of shear-selected cluster samples are also discussed.
Acquisition Timing Managing Uncertainty in a Formal Standards-Based Industry : A Real Options Perspective

Scholars have theorized that firms can intervene in the creation of formal technology standards to reduce uncertainty and influence the outcome to their advantage. One approach is through early acquisition: Firms can acquire targets with relevant technology prior to standardization. Using real options logic, the authors show how early acquisitions can be considered a growth option under certain circumstances. They find that acquisitions are more likely to occur before the passage of the standard when (a) acquirers lacked relevant technical knowledge, (b) target firms possessed relevant technical knowledge, and (c) acquirers had a prior equity investment in the target firm. †An earlier version of this article was presented at the 2004 annual meeting of the Southern Management Association in San Antonio, Texas. This article has greatly benefited from the thoughtful and constructive comments of Allen Amason, associate editor, and three anonymous reviewers. This article was accepted under the editorship of Daniel Feldman. When new technologies compete for market space, firms face uncertainty regarding which will prevail and, concurrently, when to enter a technology. Entry timing in technologically intensive industries is strategically significant to managers and investors because it affects subsequent firm performance (Christensen, Suarez, & Utterback, 1998), particularly because firms that enter early might select the wrong technology (Barney, 1986). The downside risks of early entry are particularly evident in " winner-take-all " markets (such as the information and telecommunications [ITC] industry) where initial investments are typically very high (Arthur, 1996). One branch of real options logic suggests that because this uncertainty is outside of managerial control, the ability to defer irreversible investments is strategically valuable firms continue to enter emerging technologies through acquisition (Chaudhuri & Tabrizi, 1999), which would seem to defy the logic of deferral. One reason might be that the way formal technology standards are crafted illustrates that firms might not regard uncertainty as completely exogenous and, if so, might pursue growth rather than deferral options. Formal technology standards assure interconnectivity and interoperability among components from multiple producers (Farrell, Monroe, & Saloner, 1994; Ozsomer & Cavusgil, 2000) and define which technologies will successfully enter the market and which will not. McGrath (1997) noted that uncertainty accompanying such technological change can be decomposed into technical and exogenous market factor components. However, she also argued for a third form of uncertainty: factors outside the firm but subject to strategic action, such that the firm may influence outcomes to its …
VDB: High-resolution sparse volumes with dynamic topology

We have developed a novel hierarchical data structure for the efficient representation of sparse, time-varying volumetric data discretized on a 3D grid. Our “VDB”, so named because it is a Volumetric, Dynamic grid that shares several characteristics with B+trees, exploits spatial coherency of time-varying data to separately and compactly encode data values and grid topology. VDB models a virtually infinite 3D index space that allows for cache-coherent and fast data access into sparse volumes of high resolution. It imposes no topology restrictions on the sparsity of the volumetric data, and it supports fast (average O(1)) random access patterns when the data are inserted, retrieved, or deleted. This is in contrast to most existing sparse volumetric data structures, which assume either static or manifold topology and require specific data access patterns to compensate for slow random access. Since the VDB data structure is fundamentally hierarchical, it also facilitates adaptive grid sampling, and the inherent acceleration structure leads to fast algorithms that are well-suited for simulations. As such, VDB has proven useful for several applications that call for large, sparse, animated volumes, for example, level set dynamics and cloud modeling. In this article, we showcase some of these algorithms and compare VDB with existing, state-of-the-art data structures.
SYMMETRIES IN LÉVY TERM STRUCTURE MODELS

Symmetry results between call and put options have been widely studied in equity markets. We provide similar symmetry results between caps and floors in a Heath–Jarrow–Morton, a LIBOR and a forward price model, driven by time-inhomogeneous Levy processes. On the way, we review the basic properties of these models.
Hsp90 Governs Echinocandin Resistance in the Pathogenic Yeast Candida albicans via Calcineurin

Candida albicans is the leading fungal pathogen of humans, causing life-threatening disease in immunocompromised individuals. Treatment of candidiasis is hampered by the limited number of antifungal drugs whose efficacy is compromised by host toxicity, fungistatic activity, and the emergence of drug resistance. We previously established that the molecular chaperone Hsp90, which regulates the form and function of diverse client proteins, potentiates resistance to the azoles in C. albicans and in the model yeast Saccharomyces cerevisiae. Genetic studies in S. cerevisiae revealed that Hsp90's role in azole resistance is to enable crucial cellular responses to the membrane stress exerted by azoles via the client protein calcineurin. Here, we demonstrate that Hsp90 governs cellular circuitry required for resistance to the only new class of antifungals to reach the clinic in decades, the echinocandins, which inhibit biosynthesis of a critical component of the fungal cell wall. Pharmacological or genetic impairment of Hsp90 function reduced tolerance of C. albicans laboratory strains and resistance of clinical isolates to the echinocandins and created a fungicidal combination. Compromising calcineurin function phenocopied compromising Hsp90 function. We established that calcineurin is an Hsp90 client protein in C. albicans: reciprocal co-immunoprecipitation validated physical interaction; Hsp90 inhibition blocked calcineurin activation; and calcineurin levels were depleted upon genetic reduction of Hsp90. The downstream effector of calcineurin, Crz1, played a partial role in mediating calcineurin-dependent stress responses activated by echinocandins. Hsp90's role in echinocandin resistance has therapeutic potential given that genetic compromise of C. albicans HSP90 expression enhanced the efficacy of an echinocandin in a murine model of disseminated candidiasis. Our results identify the first Hsp90 client protein in C. albicans, establish an entirely new role for Hsp90 in mediating resistance to echinocandins, and demonstrate that targeting Hsp90 provides a promising therapeutic strategy for the treatment of life-threatening fungal disease.
Consideration of Immediate and Future Consequences in Accepting and Responding to Anthropogenic Climate Change

Decreasing greenhouse gas emissions (climate change mitigation) is one of the most important types of pro-environmental behavior. Greenhouse gases have been repeatedly cited as a leading cause of climate change (CC). However, before engaging in CC mitigation behaviors, individuals must accept the reality of CC. Few studies addressing the influence of individual time perspective on climate change mitigation have been found. No study investigating the relationship between time perspectives and acceptance of the reality of CC exists. This study was aimed at filling that research gap. The study examines the impact of consideration of immediate and distant consequences of behavior on individual acceptance of the reality of CC and commitment to engage in CC mitigation behaviors. Two-hundred-and-forty-five undergraduate students responded to an instrument investigating those variables. A structural-equation model revealed that consideration of distant consequences affects acceptance of CC, but considering immediate consequences do not influence that acceptance. Accepting that CC is real affects the commitment to act pro-environmentally, which in turn influences CC mitigation commitment. Consideration of distant consequences also positively affects willingness to engage in CC mitigation; yet, consideration of immediate consequences produced no effect on that commitment.
160-270-GHz InP HEMT MMIC Low-Noise Amplifiers

We present two low-noise amplifiers for the frequency range of 160 to 270 GHz. The amplifiers were fabricated using a 35-nm InP HEMT technology and designed for room temperature and cryogenic operation. A four-stage amplifier in a common-source topology and a three-stage amplifier utilizing a cascode stage at the output achieve 15 to 25-dB on-wafer measured gain from 160 to 270 GHz. When packaged in WR5 waveguide housings the amplifiers exhibit room temperature measured noise of 600 to 760 K from 160 to 220 GHz. When cryogenically cooled the three-stage amplifier shows a noise of 80 to 115 K over the range of 164 to 220 GHz. Furthermore, our initial room temperature measurements show a noise figure of 7-8 dB over the 220 to 252 GHz range for a four-stage amplifier packaged in a WR3 waveguide housing.
Generation of Uniform Colloidal Assemblies in Soft Microfluidic Devices

Experimental LEDs were fabricated in the following manner. Indium tin oxide (ITO) sub-strates were cleaned by ultrasonication in detergent, acetone, and isopropanol. Cleaning was followed by a 5 min oxygen plasma etch at 100 W at 300 Torr of oxygen. After etching, poly(3,4-ethylenedioxythiophene) (PEDOT, Baytron P8000 from Bayer) was spin-cast at 3800 RPM in air. The substrates were baked at 110 C in a nitrogen atmosphere to remove the water. The organic blends were spin-cast to get 100 nm thick films. The substrates were baked at 80 C for 2 h after spin-casting the organic layer. Metalization of the cathodes was carried out at 7  10 ±7 Torr to deposit 80 nm of calcium and 130 nm of silver. All LED testing was done under nitrogen atmosphere. LIV (LIV = lumi-nance, current, voltage) data were acquired by inserting the substrate into a barium sulfate-coated integrating sphere with a radiometricaly calibrated detector and sweeping the voltage while the current and radiant flux was measured. The exitance was calculated by dividing the radiant flux by the emitting area. The electroluminescence spectra were acquired using an Ocean Optics S2000 fiber optic spectrometer. Cyclic voltammetric measurements were performed on an EG&G Princeton Applied Research model 273A potentiostat/galvanostat system using a standard three-electrode cell configuration. Electrolyte solutions utilized n-Bu 4 NPF 6 (0.10 M) in acetonitrile. The polymer or porphyrin films were coated on Pt or glassy carbon disk working electrodes by dipping the electrode into the corresponding solution and then drying in air. Pt wire and saturated calomel electrodes (SCE) were used respectively as counter and reference electrodes, while the ferrocene/ferricinium redox couple was utilized as an internal potentio-metric standard. Scan rates in these experiments were 100 mV s ±1. Assuming the energy level of the ferrocene/ferrocinium redox couple is 4.8 eV below the vacuum level, the potentiometrically derived HOMO and LUMO energy levels of the guests and hosts used in these experiments were plotted relative to vacuum. For polymers for which only reduction or oxidation potentials were obtained, their HOMO or LUMO levels were estimated from the combination of the cyclic voltammetric data and the optical bandgap (onset energy of the absorption spectrum); this method for estimating the valence and conduction band energies of conducting polymers has been discussed previously [21]. The absolute emission energy of DD and DDD in the solid state vary as a function of the host matrix and …
Heat-Passing Framework for Robust Interpretation of Data in Networks

Researchers are regularly interested in interpreting the multipartite structure of data entities according to their functional relationships. Data is often heterogeneous with intricately hidden inner structure. With limited prior knowledge, researchers are likely to confront the problem of transforming this data into knowledge. We develop a new framework, called heat-passing, which exploits intrinsic similarity relationships within noisy and incomplete raw data, and constructs a meaningful map of the data. The proposed framework is able to rank, cluster, and visualize the data all at once. The novelty of this framework is derived from an analogy between the process of data interpretation and that of heat transfer, in which all data points contribute simultaneously and globally to reveal intrinsic similarities between regions of data, meaningful coordinates for embedding the data, and exemplar data points that lie at optimal positions for heat transfer. We demonstrate the effectiveness of the heat-passing framework for robustly partitioning the complex networks, analyzing the globin family of proteins and determining conformational states of macromolecules in the presence of high levels of noise. The results indicate that the methodology is able to reveal functionally consistent relationships in a robust fashion with no reference to prior knowledge. The heat-passing framework is very general and has the potential for applications to a broad range of research fields, for example, biological networks, social networks and semantic analysis of documents.
A capabilities approach to higher education: geocapabilities and implications for geography curricula

Abstract A geographical education offers more than skills, subject knowledge and generic attributes. It also develops a set of discipline-specific capabilities that contribute to a graduate’s future learning and experience, granting them special ways of thinking for lifelong development and for contributing to the welfare of themselves, their community and their world. This paper considers the broader purposes and values of disciplinary teaching in contributing to individual human development. Set in the context of recent debates concerning the role of the university and the neo-liberalisation of higher education this paper explores approaches to developing the geography curriculum in ways that re-assert the educational value of geographical thinking for students. Using international examples of teaching and learning practice in geography, we recognise five geocapabilities: use of the geographical imagination; ethical subject-hood with respect to the impacts of geographical processes; integrative thinking about society–environment relationships; spatial thinking; and the structured exploration of places. A capabilities approach offers a productive and resilient response to the threats of pedagogic frailty and increasingly generic learning in higher education. Finally, a framework to stimulate dialogue about curriculum development and the role of geocapabilities in the higher education curriculum is suggested.
Protein characterisation by synchrotron radiation circular dichroism spectroscopy

Abstract Circular dichroism (CD) spectroscopy is a well-established technique for the study of proteins. Synchrotron radiation circular dichroism (SRCD) spectroscopy extends the utility of conventional CD spectroscopy (i.e. using laboratory-based instruments) because the high light flux from a synchrotron enables collection of data to lower wavelengths, detection of spectra with higher signal-to-noise levels and measurements in the presence of strongly absorbing non-chiral components such as salts, buffers, lipids and detergents. This review describes developments in instrumentation, methodologies and bioinformatics that have enabled new applications of the SRCD technique for the study of proteins. It includes examples of the use of SRCD spectroscopy for providing static and dynamic structural information on molecules, including determinations of secondary structures of intact proteins and domains, assessment of protein stability, detection of conformational changes associated with ligand and drug binding, monitoring of environmental effects, examination of the processes of protein folding and membrane insertion, comparisons of mutant and modified proteins, identification of intermolecular interactions and complex formation, determination of the dispositions of proteins in membranes, identification of natively disordered proteins and their binding partners and examination of the carbohydrate components of glycoproteins. It also discusses how SRCD can be used in conjunction with macromolecular crystallography and other biophysical techniques to provide a more complete picture of protein structures and functions, including how proteins interact with other macromolecules and ligands. This review also includes a discussion of potential new applications in structural and functional genomics using SRCD spectroscopy and future instrumentation and bioinformatics developments that will enable such studies. Finally, the appendix describes a number of computational/bioinformatics resources for secondary structure analyses that take advantage of the improved data quality available from SRCD. In summary, this review discusses how SRCD can be used for a wide range of structural and functional studies of proteins.
An analysis of a circadian model using the small-gain approach to monotone systems

In this note, we show how certain properties of Goldbeter's 1995 model for circadian oscillations can be proved mathematically, using techniques from the recently developed theory of monotone systems with inputs and outputs. The theory establishes global asymptotic stability, and in particular no oscillations, if the rate of transcription is somewhat smaller than that assumed by Goldbeter. This stability persists even under arbitrary delays in the feedback loop.
Legislated Multiculturalism & Second-Generation Hybrid Identities: A Phenomenological Study of Canadian Ismaili Muslim Men in Montreal, Quebec

The recent controversy over the 2014 proposed Quebec Charter of Values suggests the integration of minorities is, at present, a fundamental social and political debate in such a multicultural nation as Canada. Yet, minimal consideration has been given to secondgeneration citizens who find themselves living between various dimensions of culture. This study examines the impact of legislated multiculturalism and how it has evolved to influence second-generation Canadians in this country. This qualitative research explores the contemporary challenges of multiculturalism by examining the phenomenological analysis of second-generation Canadian Ismaili Muslim men in Montreal, Quebec. In-depth interviews were conducted to expand their perspective of identity negotiation in Canada. Research findings suggest that a symbolic sense of identity is created by simultaneously being part of the cultures found in Quebec, Canada and the global Ismaili Muslim diaspora community. This study argues that research participants challenge fixed conceptions of cultural identity markers; that their sense of diaspora community is indispensable to their perception of home and belonging in Canada; and that the legislation of multiculturalism is a practical and positive influence for second-generation Canadians. This discussion of the second-generation identity, along with the literature review and findings, provides further insight into the Canadian approach of multiculturalism.