Miracle-dz/UniFAR-FTUs huggingface dataset:
Autologous resurfacing

Background: There is a discrepancy between the interest in joint‐reconstructions and the current knowledge about the healing‐processes involved. Major reconstructions are performed with osteosynthesized allografts and fresh allografts for cartilage. Objectives: The main question to be answered is: what do we know about metaphyseal and epiphyseal cancellous bone healing, contact healing of the subchondral bone and its influence on cartilage healing? Can we achieve healing of all four compartments in contact? Purpose: The purpose is to systematically investigate through animal testing the healing processes of metaphyseal and epiphyseal bone, including the subchondral bone and the healing of cartilage of press‐fit‐inserted grafts, considering nondemineralized high‐resolution histology. Material and Methods: Primary cancellous‐bone healing of osteosynthesized hemi‐osteotomies was studied in 13 canine tibial heads, the contact healing was investigated in 7 dogs and 18 giant‐rabbits comparing contact‐healing of press‐fit‐inserted autologs cylindrical grafts with empty defects applying the wet‐grinding diamond‐technology. Bench‐experiments on the epiphyseal bones of swine including pullout‐tests of cylindrical grafts formed the basis for validation of that press‐fit diamond technology. Results: Primary metaphyseal and epiphyseal contact healing, including hyaline cartilage, was found in all compartments of the meta‐and epiphysis in the precisely performed experiments. The press‐fit principle, which employs cylindrical grafts and diamond instrumentation featuring a difference of 15/100 mm between graft and recipient bed, achieved high loads between 73.48 and 178.95 N (mean value 118.16 and standard deviation 32.79) in the pullout tests. Conclusion: Autologous press‐fit grafting with alignment of the bony baseplate using wet‐grinding precision has attained promising histo‐morphological results. Microsc. Res. Tech., 78:40–51, 2015. © 2014 Wiley Periodicals, Inc.
Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors

The α9 subunit of nicotinic acetylcholine receptors (nAChRs) exists mainly in heteropentameric assemblies with α10. Accumulating data indicate the presence of three different binding sites in α9α10 nAChRs: the α9(+)/α9(−), the α9(+)/α10(−), and the α10(+)/α9(−). The major role of the principal (+) side of the extracellular domain (ECD) of α9 subunit in binding of the antagonists methyllylcaconitine and α-bungarotoxin was shown previously by the crystal structures of the monomeric α9-ECD with these molecules. Here we present the 2.26-Å resolution crystal structure of α9-ECD in complex with α-conotoxin (α-Ctx) RgIA, a potential drug for chronic pain, the first structure reported for a complex between an nAChR domain and an α-Ctx. Superposition of this structure with those of other α-Ctxs bound to the homologous pentameric acetylcholine binding proteins revealed significant similarities in the orientation of bound conotoxins, despite the monomeric state of the α9-ECD. In addition, ligand-binding studies calculated a binding affinity of RgIA to the α9-ECD at the low micromolar range. Given the high identity between α9 and α10 ECDs, particularly at their (+) sides, the presented structure was used as template for molecular dynamics simulations of the ECDs of the human α9α10 nAChR in pentameric assemblies. Our results support a favorable binding of RgIA at α9(+)/α9(−) or α10(+)/α9(−) rather than the α9(+)/α10(−) interface, in accordance with previous mutational and functional data.
Constrained Orthogonal Segment Stabbing

Let $S$ and $D$ each be a set of orthogonal line segments in the plane. A line segment $s\in S$ \emph{stabs} a line segment $s'\in D$ if $s\cap s'\neq\emptyset$. It is known that the problem of stabbing the line segments in $D$ with the minimum number of line segments of $S$ is NP-hard. However, no better than $O(\log |S\cup D|)$-approximation is known for the problem. In this paper, we introduce a constrained version of this problem in which every horizontal line segment of $S\cup D$ intersects a common vertical line. We study several versions of the problem, depending on which line segments are used for stabbing and which line segments must be stabbed. We obtain several NP-hardness and constant approximation results for these versions. Our finding implies, the problem remains NP-hard even under the extra assumption on input, but small constant approximation algorithms can be designed.
Bayesian approach for three-dimensional aquifer characterization at the Hanford 300 Area

This study presents a stochastic, three- dimensional characterization of a heterogeneous hydraulic conductivity field within the Hanford 300 Area, Washing- ton, USA, by assimilating large-scale, constant-rate injec- tion test data with small-scale, three-dimensional electro- magnetic borehole flowmeter (EBF) measurement data. We first inverted the injection test data to estimate the transmis- sivity field, using zeroth-order temporal moments of pres- sure buildup curves. We applied a newly developed Bayesian geostatistical inversion framework, the method of anchored distributions (MAD), to obtain a joint posterior distribution of geostatistical parameters and local log-transmissivities at multiple locations. The unique aspects of MAD that make it suitable for this purpose are its ability to integrate multi- scale, multi-type data within a Bayesian framework and to compute a nonparametric posterior distribution. After we combined the distribution of transmissivities with depth- discrete relative-conductivity profile from the EBF data, we inferred the three-dimensional geostatistical parameters of the log-conductivity field, using the Bayesian model-based geostatistics. Such consistent use of the Bayesian approach throughout the procedure enabled us to systematically incor- porate data uncertainty into the final posterior distribution. The method was tested in a synthetic study and validated us- ing the actual data that was not part of the estimation. Results showed broader and skewed posterior distributions of geosta- tistical parameters except for the mean, which suggests the importance of inferring the entire distribution to quantify the parameter uncertainty.
Differences in myoelectric manifestations of fatigue in sprinters and long distance runners

The aim of this study was to determine whether the rate of change of surface EMG variables during a constant force isometric fatiguing contraction (80% MVC, 30 s of duration) of vastus medialis obliquus (VMO) and vastus lateralis (VL) muscles is able to distinguish between nine sprinters and nine long distance runners. Signals were recorded with linear arrays of eight electrodes. Muscle fiber conduction velocity (CV), mean frequency (MNF) of EMG signal power spectrum and average rectified value (ARV) of the EMG signal were calculated both from the whole signal (global approach) and from motor unit action potentials (MUAP distribution approach) extracted from the signal. Results showed significant differences only in the MUAP distribution approach. For this approach, the rates of change of conduction velocity (CV) (both absolute and normalized with respect to the initial value) were found to be always greater in the sprinter (VMO: −0.012 ± 0.011 m s−2 and −0.25 ± 0.21%/s; VL: −0.014 ± 0.009 m s−2 and −0.27 ± 0.17%/s) than in the long distance runner group (VMO: −0.004 ± 0.006 m s−2 and −0.08 ± 0.14%/s; VL: 0.003 ± 0.012 m s−2 and 0.08 ± 0.26%/s) (VL: p = 0.016, VMO: p = 0.034). No differences were observed in the CV initial values and in rates of change of MNF, while MNF initial values recorded from the VMO were found to be greater (119.6 ± 25.1 Hz) in the sprinter group than in the long distance runner group (99.2 ± 12.1 Hz, p = 0.016). A correlation was found between initial values and rates of change of CV in the VMO (r = 0.61, p < 0.01, N = 18, Spearman correlation coefficient). The consistency of these findings with the expected fiber type composition between sprinters and long distance runners and the identification of a set of candidated variables for the assessment of muscle adaptation during training and/or rehabilitation programs represent the main results of the study.
Metering for Exposure Stacks

When creating a High‐Dynamic‐Range (HDR) image from a sequence of differently exposed Low‐Dynamic‐Range (LDR) images, the set of LDR images is usually generated by sampling the space of exposure times with a geometric progression and without explicitly accounting for the distribution of irradiance values of the scene. We argue that this choice can produce sub‐optimal results both in terms of the number of acquired pictures and the quality of the resulting HDR image.
Comparative evaluation of 2D feature correspondence selection algorithms

Correspondence selection aiming at seeking correct feature correspondences from raw feature matches is pivotal for a number of feature-matching-based tasks. Various 2D (image) correspondence selection algorithms have been presented with decades of progress. Unfortunately, the lack of an in-depth evaluation makes it difficult for developers to choose a proper algorithm given a specific application. This paper fills this gap by evaluating eight 2D correspondence selection algorithms ranging from classical methods to the most recent ones on four standard datasets. The diversity of experimental datasets brings various nuisances including zoom, rotation, blur, viewpoint change, JPEG compression, light change, different rendering styles and multi-structures for comprehensive test. To further create different distributions of initial matches, a set of combinations of detector and descriptor is also taken into consideration. We measure the quality of a correspondence selection algorithm from four perspectives, i.e., precision, recall, F-measure and efficiency. According to evaluation results, the current advantages and limitations of all considered algorithms are aggregately summarized which could be treated as a "user guide" for the following developers.
TIM1 is an endogenous ligand for LMIR5/CD300b: LMIR5 deficiency ameliorates mouse kidney ischemia/reperfusion injury

Leukocyte mono-immunoglobulin (Ig)–like receptor 5 (LMIR5)/CD300b is a DAP12-coupled activating receptor predominantly expressed in myeloid cells. The ligands for LMIR have not been reported. We have identified T cell Ig mucin 1 (TIM1) as a possible ligand for LMIR5 by retrovirus-mediated expression cloning. TIM1 interacted only with LMIR5 among the LMIR family, whereas LMIR5 interacted with TIM4 as well as TIM1. The Ig-like domain of LMIR5 bound to TIM1 in the vicinity of the phosphatidylserine (PS)-binding site within the Ig-like domain of TIM1. Unlike its binding to TIM1 or TIM4, LMIR5 failed to bind to PS. LMIR5 binding did not affect TIM1- or TIM4-mediated phagocytosis of apoptotic cells, and stimulation with TIM1 or TIM4 induced LMIR5-mediated activation of mast cells. Notably, LMIR5 deficiency suppressed TIM1-Fc–induced recruitment of neutrophils in the dorsal air pouch, and LMIR5 deficiency attenuated neutrophil accumulation in a model of ischemia/reperfusion injury in the kidneys in which TIM1 expression is up-regulated. In that model, LMIR5 deficiency resulted in ameliorated tubular necrosis and cast formation in the acute phase. Collectively, our results indicate that TIM1 is an endogenous ligand for LMIR5 and that the TIM1–LMIR5 interaction plays a physiological role in immune regulation by myeloid cells.
FFPred 2.0: Improved Homology-Independent Prediction of Gene Ontology Terms for Eukaryotic Protein Sequences

To understand fully cell behaviour, biologists are making progress towards cataloguing the functional elements in the human genome and characterising their roles across a variety of tissues and conditions. Yet, functional information – either experimentally validated or computationally inferred by similarity – remains completely missing for approximately 30% of human proteins. FFPred was initially developed to bridge this gap by targeting sequences with distant or no homologues of known function and by exploiting clear patterns of intrinsic disorder associated with particular molecular activities and biological processes. Here, we present an updated and improved version, which builds on larger datasets of protein sequences and annotations, and uses updated component feature predictors as well as revised training procedures. FFPred 2.0 includes support vector regression models for the prediction of 442 Gene Ontology (GO) terms, which largely expand the coverage of the ontology and of the biological process category in particular. The GO term list mainly revolves around macromolecular interactions and their role in regulatory, signalling, developmental and metabolic processes. Benchmarking experiments on newly annotated proteins show that FFPred 2.0 provides more accurate functional assignments than its predecessor and the ProtFun server do; also, its assignments can complement information obtained using BLAST-based transfer of annotations, improving especially prediction in the biological process category. Furthermore, FFPred 2.0 can be used to annotate proteins belonging to several eukaryotic organisms with a limited decrease in prediction quality. We illustrate all these points through the use of both precision-recall plots and of the COGIC scores, which we recently proposed as an alternative numerical evaluation measure of function prediction accuracy.
Understanding and Enhancing Patient Compliance with Diabetic Regimens

Behavioral research on patient compliance with regimens to manage diabetes has suffered from lack of conceptual rigor, although a handful of recent studies and reviews are more theoretically oriented. The present review proposes a comprehensive conceptual framework in the context of learning theory to explain patient compliance and to derive approaches for enhancing compliance. The conceptual framework is the health belief model (HBM) expanded to include the concept of perceived self-efficacy. This expanded model may both serve as an agenda for future research as well as a set of guidelines for the education of patients with diabetes. A variety of educational interventions is recommended for use in patient education provided they succeed in reinforcing relevant health beliefs, behavioral skills, and the sense of self-efficacy. The problem of long-term maintenance, of particular significance in chronic disease management, is addressed by the relapse prevention model derived from social learning theory and emphasizing self-efficacy and the learning of coping skills.
[A user-friendly scale for the short and long term outcome of bipolar disorder: the CGI-BP-M].

UNLABELLED Bipolar disorder is a cyclic and polymorphic disease. Patients may show manic, hipomanic, depressive or mixed symptoms, and they may be in partial or complete remission. For this reason, the assessment of the course, severity and outcome of the disorder is very complex. Most of the available psychometric instruments have been designed for the assessment of acute episodes of specific polarity. METHODS We present the modified version of the Clinical Global Impression for Bipolar Disorder (CGI-BP-M) a condensed version of the CGI-BP, which is also an adaptation of the CGI for bipolar patients. RESULTS The CGI-BP-M takes only a few minutes to complete, and it has proved to be useful in the assessment of the short and long-term efficacy of several treatments such as olanzapine and quetiapine. Significant improvements in several subescales of the CGI-BP-M after treatment with these compounds are shown. CONCLUSIONS The CGI-BP-M, a user-friendly scale for the assessment of manic, hypomanic, depressive or mixed symptoms, and long-term outcome of bipolar disorder, is a useful tool for the assessment of the efficacy of several treatments.
Using Virtualization to Improve Software Rejuvenation

In this paper, we present an approach for software rejuvenation based on automated self-healing techniques that can be easily applied to off-the-shelf Application Servers and Internet sites. Software aging and transient failures are detected through continuous monitoring of system data and performability metrics of the application server. If some anomalous behavior is identified the system triggers an automatic rejuvenation action. This self-healing scheme is meant to be the less disruptive as possible for the running service and to get a zero downtime for most of the cases. In our scheme, we exploit the usage of virtualization to optimize the self-recovery actions. The techniques described in this paper have been tested with a set of open-source Linux tools and the XEN virtualization middleware. We conducted an experimental study with two applications benchmarks (Tomcat/Axis and TPC-W). Our results demonstrate that virtualization can be extremely helpful for software rejuvenation and fail-over in the occurrence of transient application failures and software aging.
Low phase noise and linear gain VCO using self-switched biasing

A low power and low phase noise LC-tank VCO with linear gain for 2.4 GHz ISM band is presented. Self-switched biasing technology is adopted to reduce flicker noise. Low power consumption is achieved by reducing supply voltage for the character of this structure. To extend the linear range of VCO gain (Kvco) in low supply voltage condition, distributed varactor biasing is used. The proposed VCO is implemented in 0. 18μm CMOS process. The measured phase noise is −122.9 dBc/Hz at 1MHz offset from 2.5 GHz oscillation frequency, while consuming 2.6 mA current with 1.2 V supply voltage, and the FOM is 186 dBc/Hz.
Optimal Controlled Variable Selection with Structural Constraints Using MIQP Formulations

Abstract Optimal control structure selection is vital to operate the process plants optimally in the presence of disturbances. In this paper we review the controlled variable selection, c = Hy, where y includes all the measurements. The objective is to find the matrix H such that steady-state operation is optimized while controlled variables c ' s are kept constant using inputs, when there are disturbances. Several cases are studied such as the optimal individual measurements, the optimal combinations of fewer/all measurements and the optimal combinations with structural constraints. The proposed methods are evaluated on a distillation column case study with 41 trays.
A Quantum-Inspired Similarity Measure for the Analysis of Complete Weighted Graphs

We develop a novel method for measuring the similarity between complete weighted graphs, which are probed by means of the discrete-time quantum walks. Directly probing complete graphs using discrete-time quantum walks is intractable due to the cost of simulating the quantum walk. We overcome this problem by extracting a commute time minimum spanning tree from the complete weighted graph. The spanning tree is probed by a discrete-time quantum walk which is initialized using a weighted version of the Perron–Frobenius operator. This naturally encapsulates the edge weight information for the spanning tree extracted from the original graph. For each pair of complete weighted graphs to be compared, we simulate a discrete-time quantum walk on each of the corresponding commute time minimum spanning trees and, then, compute the associated density matrices for the quantum walks. The probability of the walk visiting each edge of the spanning tree is given by the diagonal elements of the density matrices. The similarity between each pair of graphs is then computed using either: 1) the inner product or 2) the negative exponential of the Jensen–Shannon divergence between the probability distributions. We show that in both cases the resulting similarity measure is positive definite and, therefore, corresponds to a kernel on the graphs. We perform a series of experiments on publicly available graph datasets from a variety of different domains, together with time-varying financial networks extracted from data for the New York Stock Exchange. Our experiments demonstrate the effectiveness of the proposed similarity measures.
The Homogeneity of Interstellar Oxygen in the Galactic Disk

We present an analysis of high-resolution Hubble Space Telescope (HST) Space Telescope Imaging Spectrograph (STIS) observations of O I λ1356 and H I Lyα absorption in 36 sight lines that probe a variety of Galactic disk environments and include paths that range over nearly 4 orders of magnitude in f(H2), over 2 orders of magnitude in ⟨nH⟩, and that extend up to 6.5 kpc in length. Since the majority of these sight lines have also been observed by the Far Ultraviolet Spectroscopic Explorer (FUSE), we have undertaken the study of gas-phase O/H abundance ratio homogeneity using the current sample and previously published Goddard High Resolution Spectrograph (GHRS) results. Two distinct trends are identified in the 56 sight line sample: an apparent decrease in gas-phase oxygen abundance with increasing mean sight-line density (⟨nH⟩) and a gap between the mean O/H ratio for sight lines shorter and longer than about 800 pc. The first effect is a smooth transition between two depletion levels associated with large mean density intervals; it is centered near ⟨nH⟩ = 1.5 cm-3 and is similar to trends evident in gas-phase abundances of other elements. Paths less dense than the central value exhibit a mean O/H ratio of (O/H) = -3.41 ± 0.01 (or 390 ± 10 ppm), which is consistent with averages determined for several long low-density paths observed by STIS (André et al. 2003) and short low-density paths observed by FUSE (Moos et al. 2002). Sight lines of higher mean density exhibit an average O/H value of (O/H) = -3.55 ± 0.02 (284 ± 12 ppm). The data points for low-⟨nH⟩ paths are scattered more widely than those for denser sight lines, because O/H ratios for such paths shorter than 800 pc are generally about 0.10 dex lower than the values for longer ones. Scenarios that would be consistent with these results include a recent infall of metal-poor gas onto the local Galactic disk and an interstellar environment toward Orion that is conducive to reducing the apparent gas-phase oxygen abundance.
Presentation to the National Academy of Sciences Expert Panel, "Surface Temperature Reconstructions for the Past 1,000-2,000 Years." : Supplementary Comments

1 Introduction Thank you for the invitation to speak to you today. We are flattered to be included among so many distinguished presenters and to have the opportunity to be heard by such an eminent panel. We have expressed our concern to the NAS that a couple of panel members have close associations to people who strongly oppose our views. We reiterate the need for the Panel to undertake a thorough and unbiased examination of the evidence we present, and we have prepared our submission on the assumption that this will be done. We are not here to argue for or against the Medieval Warm Period, or to present an alternative interpretation of climate history, but to report on our efforts to evaluate the quality, robustness and statistical significance of multiproxy evidence behind the claim that 20 th century climate change is unprecedented in a millennial context. In this regard we will primarily focus on the following questions put to this panel by Representative Boehlert: