Miracle-dz/UniFAR-FTUs huggingface dataset:
Electron microscopy characterisation of in vivo collagen and mineral ultra-structures, their development and pathologies

The investigation of the nanostructure of mineralised tissues is challenging due to the intrinsic complexity of the hierarchical biocomposites and heterogeneity of biological samples. Despite numerous transmission electron microscopy (TEM) studies investigating a variety of mineralised tissues, details of the collagen-mineral ultrastructure and the origins of collagen and mineral formation are not fully understood. Analytical scanning transmission electron microscopy (STEM), combined with electron energy-loss spectroscopy (EELS), has the potential of identifying bone composition at a very high spatial resolution. We used these techniques to investigate the in vivo mineralisation process, and to probe the structural/compositional origins of bone-related pathologies at high spatial resolution. High-pressure freezing/freeze substitution (HPS/FS) methods were employed to preserve features of mineralisation process, specifically the structure and chemistry of the mineral and collagen phases and the distribution of diffusible mineral ions. The application of STEMEELS in the biomineralisation studies is, however, limited, partially due to the absence of an EELS library of mineral and collagen standards. We developed an EELS spectra collection of biominerals (hydroxyapatite, carbonated hydroxyapatite, beta-tricalcium phosphate and calcite) so that biominerals can be identified by composition and coordination environment. For the first time, an extensive collection of all major elemental edges (phosphorus, carbon, calcium, oxygen) is presented and compared. We then used this library to characterise in vivo mineralisation processes. We examined turkey tendon, which calcifies with age, in order to understand the mineralisation process. We identified chemical and structural signatures representative of the non-, poorly and well mineralised tissues. In particular, a chemical signature of pyridinebased compounds was identified and a protocol was developed to assess changes in the nanoscale chemistry of the collagen-mineral matrix in disrupted tissues. We observed a change in the oxidation state of pyridine-based compounds in the collagen fibrils, which most likely occurs pror to nucleation. Mineral ions (calcium, phosphate) were delivered into the collagen matrix, either in the form of amorphous calcium phosphate vesicles or by diffusion from the
Inequality , Costly Redistribution and Welfare in an Open Economy

This paper studies the welfare implications of trade liberalization in a world in which trade increases income inequality, and in which redistribution needs to occur via a distortionary income tax-transfer system. We provide tools to characterize and quantify the actual amount of compensation that will take place following trade opening, as well as the efficiency costs of undertaking such redistribution. We propose two types of adjustments to standard measures of the welfare gains from trade: a ‘welfarist’ correction inspired by the Atkinson (1970) index of inequality, and a ‘costly-redistribution’ correction capturing the efficiency costs associated with the behavioral responses of agents to trade-induced shifts across marginal tax rates. We calibrate our model to the United States over the period 1979-2007 using data on the distribution of adjusted gross income in public samples of IRS tax returns, as well as CBO information on the tax liabilities and transfers received by agents at different percentiles of the U.S. income distribution. Our preliminary quantitative results suggest that these corrections are nonnegligible and erode about one-fifth of the gains from trade. ∗We thank Nathan Hendren and Esteban Rossi-Hansberg for fruitful conversations during the early stages of this project. We are also grateful to seminar audiences at LSE, Barcelona and Geneva for their suggestions.
Maximizing Symmetric Submodular Functions

Symmetric submodular functions are an important family of submodular functions capturing many interesting cases, including cut functions of graphs and hypergraphs. Maximization of such functions subject to various constraints receives little attention by current research, unlike similar minimization problems that have been widely studied. In this work, we identify a few submodular maximization problems for which one can get a better approximation for symmetric objectives than the state-of-the-art approximation for general submodular functions. We first consider the problem of maximizing a non-negative symmetric submodular function f:2N → R+ subject to a down-monotone solvable polytope P ⊆ [0, 1]N. For this problem, we describe an algorithm producing a fractional solution of value at least 0.432 ċ f(OPT), where OPT is the optimal integral solution. Our second result considers the problem max{f(S): |S| = k} for a non-negative symmetric submodular function f:2N → R+. For this problem, we give an approximation ratio that depends on the value k/|N| and is always at least 0.432. Our method can also be applied to non-negative non-symmetric submodular functions, in which case it produces 1/e − o(1) approximation, improving over the best-known result for this problem. For unconstrained maximization of a non-negative symmetric submodular function, we describe a deterministic linear-time 1/2-approximation algorithm. Finally, we give a [1 − (1 − 1/k)k − 1]-approximation algorithm for Submodular Welfare with k players having identical non-negative submodular utility functions and show that this is the best possible approximation ratio for the problem.
RDML: structured language and reporting guidelines for real-time quantitative PCR data

The XML-based Real-Time PCR Data Markup Language (RDML) has been developed by the RDML consortium (http://www.rdml.org) to enable straightforward exchange of qPCR data and related information between qPCR instruments and third party data analysis software, between colleagues and collaborators and between experimenters and journals or public repositories. We here also propose data related guidelines as a subset of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to guarantee inclusion of key data information when reporting experimental results.
Polyhydroxyalkanoate (PHA) Accumulation in Sulfate-Reducing Bacteria and Identification of a Class III PHA Synthase (PhaEC) in Desulfococcus multivorans

ABSTRACT Seven strains of sulfate-reducing bacteria (SRB) were tested for the accumulation of polyhydroxyalkanoates (PHAs). During growth with benzoate Desulfonema magnum accumulated large amounts of poly(3-hydroxybutyrate) [poly(3HB)]. Desulfosarcina variabilis (during growth with benzoate), Desulfobotulus sapovorans (during growth with caproate), and Desulfobacterium autotrophicum (during growth with caproate) accumulated poly(3HB) that accounted for 20 to 43% of cell dry matter. Desulfobotulus sapovorans and Desulfobacterium autotrophicum also synthesized copolyesters consisting of 3-hydroxybutyrate and 3-hydroxyvalerate when valerate was used as the growth substrate. Desulfovibrio vulgaris and Desulfotalea psychrophila were the only SRB tested in which PHAs were not detected. When total DNA isolated from Desulfococcus multivorans and specific primers deduced from highly conserved regions of known PHA synthases (PhaC) were used, a PCR product homologous to the central region of class III PHA synthases was obtained. The complete pha locus of Desulfococcus multivorans was subsequently obtained by inverse PCR, and it contained adjacent phaEDm and phaCDm genes. PhaCDm and PhaEDm were composed of 371 and 306 amino acid residues and showed up to 49 or 23% amino acid identity to the corresponding subunits of other class III PHA synthases. Constructs of phaCDm alone (pBBRMCS-2::phaCDm) and of phaEDmCDm (pBBRMCS-2::phaEDmCDm) in various vectors were obtained and transferred to several strains of Escherichia coli, as well as to the PHA-negative mutants PHB−4 and GPp104 of Ralstonia eutropha and Pseudomonas putida, respectively. In cells of the recombinant strains harboring phaEDmCDm small but significant amounts (up to 1.7% of cell dry matter) of poly(3HB) and of PHA synthase activity (up to 1.5 U/mg protein) were detected. This indicated that the cloned genes encode functionally active proteins. Hybrid synthases consisting of PhaCDm and PhaE of Thiococcus pfennigii or Synechocystis sp. strain PCC 6308 were also constructed and were shown to be functionally active.
Segmented shape memory alloy actuators using hysteresis loop control

A new approach to the design and control of shape memory alloy (SMA) actuators is presented. SMA wires are divided into many segments and their thermal states are controlled individually as a group of finite state machines. Instead of driving a current to the entire SMA wire and controlling the wire length based on the analog strain–temperature characteristics, the new method controls the binary state (hot or cold) of individual segments and thereby the total displacement is proportional to the length of the heated segments, i.e. austenite phase. Although the thermomechanical properties of SMA are highly nonlinear and uncertain with a prominent hysteresis, segmented binary control is robust and stable, providing characteristics similar to a stepping motor. However, the heating and cooling of each segment to its bi-stable states entail longer time and larger energy for transition. In this paper, an efficient method for improving the speed of response and power consumption is developed by exploiting the inherent hysteresis of SMA. Instead of keeping the extreme temperatures continuously, the temperatures return to intermediate ‘hold’ temperatures closer to room temperature but sufficient to keep constant phase. Coordination of the multitude of segments having independent thermal states allows for faster response with little latency time even for thick SMA wires. Based on stress dependent thermomechanical characteristics, the hold temperature satisfying a given stress margin is obtained. The new control method is implemented using the Peltier effect thermoelectric devices for selective segment-by-segment heating and cooling. Experiments demonstrate the effectiveness of the proposed method.
Improving the Quality of Random Number Generators by Applying a Simple Ratio Transformation

It is well-known that the quality of random number generators can often be improved by combining several generators, e.g. by summing or subtracting their results. In this paper we investigate the ratio of two random number generators as an alternative approach: the smaller of two input random numbers is divided by the larger, resulting in a rational number from $[0,1]$. We investigate theoretical properties of this approach and show that it yields a good approximation to the ideal uniform distribution. To evaluate the empirical properties we use the well-known test suite \textsc{TestU01}. We apply the ratio transformation to moderately bad generators, i.e. those that failed up to 40\% of the tests from the test battery \textsc{Crush} of \textsc{TestU01}. We show that more than half of them turn into very good generators that pass all tests of \textsc{Crush} and \textsc{BigCrush} from \textsc{TestU01} when the ratio transformation is applied. In particular, generators based on linear operations seem to benefit from the ratio, as this breaks up some of the unwanted regularities in the input sequences. Thus the additional effort to produce a second random number and to calculate the ratio allows to increase the quality of available random number generators.
Haplotype synthesis analysis in public reference data reveals functional variants underlying known genome-wide associated susceptibility loci

The functional mechanisms underlying disease association identified by Genome-wide Association Studies remain unknown for susceptibility loci located outside gene coding regions. In addition to the regulation of gene expression, synthesis of effects from multiple surrounding functional variants has been suggested as an explanation of hard-to-interpret associations. Here, we define filter criteria based on linkage disequilibrium measures and allele frequencies which reflect expected properties of synthesizing variant sets. For eligible candidate sets we search for those haplotypes that are highly correlated with the risk alleles of a genome-wide associated variant. We applied our methods to 1,000 Genomes reference data and confirmed Crohn’s Disease and Type 2 Diabetes susceptibility loci. Of these, a proportion of 32% allowed explanation by three-variant-haplotypes carrying at least two functional variants, as compared to a proportion of 16% for random variants (P = 2.92 · 10−6). More importantly, we detected examples of known loci whose association can fully be explained by surrounding missense variants: three missense variants from MUC19 synthesize rs11564258 (L0C105369736/MUC19, intron; Crohn’s Disease). Next, rs2797685 (PER3, intron; Crohn’s Disease) is synthesized by a 57 kilobase haplotype defined by five missense variants from PER3 and three missense variants from UTS2. Finally, the association of rs7178572 (HMG20A, intron; Type 2 Diabetes) can be explained by the synthesis of eight haplotypes, each carrying at least one missense variant in either PEAK1, TBC1D2B, CHRNA5 or ADAMTS7. In summary, application of our new methods highlights the potential of synthesis analysis to guide functional follow-up investigation of findings from association studies.
Sensing the environment through SpiderSense

Recent scientific advances allow the use of technology to expand the number of forms of energy that can be perceived by humans. Smart sensors can detect hazards that human sensors are unable to perceive, for example radiation. This fusing of technology to human s forms of perception enables exciting new ways of perceiving the world around us. In this paper we describe the design of SpiderSense, a wearable device that projects the wearer s near environment on the skin and allows for directional awareness of objects around him. The millions of sensory receptors that cover the skin presents opportunities for conveying alerts and messages. We discuss the challenges and considerations of designing similar wearable devices.
Wireless MIMO switching with MMSE relaying

A wireless relay which forms a one-to-one mapping from the inputs (uplinks) to the outputs (downlinks) is called a multiple-input-multiple-output (MIMO) switch. The MIMO switch carries out precode-and-forward, where all users send their signals in the uplink and then the MIMO switch precodes the received vector signal for broadcasting in the downlink. Ideally, each user employs a receive filter to recover its desired signal from one other user with no or little interference from other users. We propose a joint design of the precoder and the receive filters to achieve the minimum-mean-square-error (MMSE), assuming full channel state information is available at the relay. Our results indicate that the proposed MMSE relaying scheme outperforms the existing ZF/MMSE schemes.
Triple-Parity RAID and Beyond

How much longer will current RAID techniques persevere? The RAID levels were codified in the late 1980s; double-parity RAID, known as RAID-6, is the current standard for high-availability, space-efficient storage. The incredible growth of hard-drive capacities, however, could impose serious limitations on the reliability even of RAID-6 systems. Recent trends in hard drives show that triple-parity RAID must soon become pervasive. In 2005, Scientific American reported on Kryder’s law, which predicts that hard-drive density will double annually. While the rate of doubling has not quite maintained that pace, it has been close.
Fibroblast Behavior on PMMAEA and PMMAEA-Collagen Films and Nanofibers

Fibroblast Behavior on PMMAEA and PMMAEA-Collagen Films and Nanofibers The influence of different physical forms of substrates on fibroblast behavior was examined by comparing the following experimental and control groups: 1) glass coverslips, 2) poly(methyl methacrylateco- ethyl acrylate) (PMMAEA) cast films, 3) electrospun PMMAEA nanofibers, 4) electrospun PMMAEA/collagen nanofibers, and 5) electrospun collagen. Cell adhesion, spreading and proliferation were compared on the different substrates. It was observed that fibroblasts on electrospun PMMAEA, PMMAEA-collagen, and collagen substrates spread more slowly after plating, and did not spread out to the extent observed for glass or PMMAEA films. Cells on electrospun fibers exhibited more filopodial-like structures and fewer stress fibers than the glass and PMMAEA film surfaces. Cell viability studies showed that although cells remained viable on all substrates, proliferation was faster on glass and PMMAEA films than on electrospun substrates. Overall, fibroblast behavior appeared to more closely resemble in vivo behavior on the electrospun nanofibers than on films or glass substrates.
Note identification in Carnatic Music from Frequency Spectrum

Raga refers to melodic modes used in Indian Classical Music. It's a series of five or more musical notes upon which a melody is made. Note identification forms the basis for Raga Identification in Music. Characterisation of a note in Carnatic Music is challenging due to the extensive use of Gamakas. In this paper, we propose a System that takes a wav file as input, analyses the frequency characteristics and performs note mapping. The prominent notes in the Raga are selected by a Statistical T Test based on the duration of occurrence of a note. A Test data of around 15 raga alapanas was used. The renditions ranged from 3 – 8 minute clips of various artistes, both male and female. The System performs with an accuracy of 90%.
Coated Tongue Region Extraction using the Fluorescence Response of the Tongue Coating by Ultraviolet Light Source

An effective extraction method for extracting a coated tongue is proposed in this paper, which is used as the diagnostic criteria in the tongue diagnosis. Proposed method uses the fluorescence response characteristics of the coated tongue that is occurred by using the ultraviolet light. Specially, this method can solved the previous problems including the issue in the limits of the diagnosis environment and in the objectivity of the diagnosis results. In our method, original tongue image is acquired by using the ultraviolet light, and binarization is performed by thresholding a valley-points in the histogram that corresponds to the color difference of tongue body and tongue coating. Final view image is presented to the oriental doctor, after applying the canny-edge algorithm to the binary image, and edge image is added to the original image. In order to evaluate the performance of the our proposed method, after building a various tongue image, we compared the true region of coated tongue by the oriental doctor`s hand with the extracted region by the our method. As a result, the proposed method showed the average 87.87% extraction ratio. The shape of the extracted coated tongue region showed also significantly higher similarity.
Sequential estimation of shape parameters in multivariate dynamic models Dante Amengual

Sequential maximum likelihood and GMM estimators of distributional parameters obtained from the standardised innovations of multivariate conditionally heteroskedastic dynamic regression models evaluated at Gaussian PML estimators preserve the consistency of mean and variance parameters while allowing for realistic distributions. We assess the e¢ ciency of those estimators, and obtain moment conditions leading to sequential estimators as e¢ cient as their joint maximum likelihood counterparts. We also obtain standard errors for the quantiles required in VaR and CoVaR calculations, and analyse the e¤ects on these measures of distributional misspeci cation. Finally, we illustrate the small sample performance of these procedures through Monte Carlo simulations. Keywords: Elliptical Distributions, E¢ cient Estimation, Systemic Risk, Value at Risk. JEL: C13, C32, G11 We would like to thank Manuel Arellano, Christian Bontemps, Olivier Faugeras, Javier Mencía, Francisco Peñaranda, Marcos Sanso and David Veredas, as well as audiences at CEMFI, CREST, Princeton, Rimini, Toulouse, the Finance Forum (Granada, 2011) the Symposium of the Spanish Economic Association and the Conference in honour of M. Hashem Pesaran (Cambridge, 2011) for useful comments and suggestions. Of course, the usual caveat applies. Amengual and Sentana gratefully acknowledge. nancial support from the Spanish Ministry of Science and Innovation through grants ECO 2008-00280 and 2011-26342.
You, Me … and Drugs – A Love Triangle: Important Considerations When Both Members of a Couple Are Abusing Substances

Concordant couples can be defined as couples in which both partners have issues with “substance abuse. ” Studies demonstrate that couples display similar patterns of “substance abuse” that cannot be explained by sociodemographic factors alone. Unfortunately, few studies have focused on the unique relationship dynamics and needs of concordant couples. “Substance abuse” by a client's partner can profoundly affect their recovery and treatment. It is therefore important to understand how clients are influenced by their partners’ use. This article attempts to define the needs and issues of concordant couples within a broader psychosocial context. In addition, an overview on the concordant couple literature is provided, along with a discussion of effective treatment and potential barriers to treatment.
A Generic Transformation to Enable Optimal Repair in MDS Codes for Distributed Storage Systems

We propose a generic transformation that can convert any nonbinary <inline-formula> <tex-math notation="LaTeX">$(n=k{+}r,k)$ </tex-math></inline-formula> maximum distance separable (MDS) code into another <inline-formula> <tex-math notation="LaTeX">$(n,k)$ </tex-math></inline-formula> MDS code over the same field such that: 1) some arbitrarily chosen <inline-formula> <tex-math notation="LaTeX">$r$ </tex-math></inline-formula> nodes have the optimal repair bandwidth and the optimal rebuilding access; 2) for the remaining <inline-formula> <tex-math notation="LaTeX">$k$ </tex-math></inline-formula> nodes, the normalized repair bandwidth and the normalized rebuilding access (over the file size) are preserved; and 3) the sub-packetization level is increased only by a factor of <inline-formula> <tex-math notation="LaTeX">$r$ </tex-math></inline-formula>. Two immediate applications of this generic transformation are then presented. The first application is that we can transform any nonbinary MDS code with the optimal repair bandwidth or the optimal rebuilding access for the systematic nodes only, into a new MDS code which possesses the corresponding repair optimality for all nodes. The second application is that by applying the transformation multiple times, any nonbinary <inline-formula> <tex-math notation="LaTeX">$(n,k)$ </tex-math></inline-formula> scalar MDS code can be converted into an <inline-formula> <tex-math notation="LaTeX">$(n,k)$ </tex-math></inline-formula> MDS code with the optimal repair bandwidth and the optimal rebuilding access for all nodes, or only a subset of nodes, whose sub-packetization level is also optimal.