Miracle-dz/UniFAR-FTUs huggingface dataset:
The Kinematic Rotating Hinge Prosthesis for Complex Knee Arthroplasty

Fifty-eight patients (69 knees) treated with the Kinematic Rotating Hinged knee prosthesis for complex primary and salvage revision total knee arthroplasty were followed up for an average of 75.2 months (range, 24–199 months). The indications for use of the Kinematic Rotating Hinged knee prosthesis included severe bone loss combined with ligamentous instability (30 knees), nonunion of a periprosthetic fracture (10 knees), an acute periprosthetic fracture (nine knees), severe collateral ligamentous instability (five knees), reimplantation for infection (six knees), nonunion of a supracondylar femoral fracture (four knees), congenital dislocation of the knee (three knees), and treatment of a severely comminuted distal femur (two knees). At the time of surgery, the average patient age was 72 years (range, 46–92 years). Preoperatively, knee extension averaged 4.94° (range, 0°–40°) and flexion averaged 81° (range, 15°–125°). At final followup, knee extension averaged 1.25° (range, −5°–25°) and flexion averaged 94.2° (range, 5°–125°). The preoperative Knee Society Knee score averaged 40.3 points (range, 2–93 points) and improved to 77 points (range, 33–99 points) at final followup. Complications were numerous: 23 (32%) patients experienced at least one complication and 12 (17%) patients had two or more complications. Deep periprosthetic infection was the most common complication (14.5%), followed by patellar complications (13%), and prosthetic component breakage (10%). During the period of this study, there were 15,798 primary and 2673 revision total knee arthroplasties done at the authors’ institution. The patients receiving a Kinematic Rotating Hinged knee prosthesis represent a highly complex and small subset (0.37%) of the overall population having knee arthroplasty. Although the use of the Kinematic Rotating Hinged knee prosthesis for these limited indications has been useful for the authors, the incidence of complications and the poor outcome of these complications is disconcerting. Hinged total knee arthroplasty should be reserved for the final salvage option of the treatment options available when doing complex primary and salvage revision knee arthroplasties.
Alu Sequences in Undifferentiated Human Embryonic Stem Cells Display High Levels of A-to-I RNA Editing

Adenosine to Inosine (A-to-I) RNA editing is a site-specific modification of RNA transcripts, catalyzed by members of the ADAR (Adenosine Deaminase Acting on RNA) protein family. RNA editing occurs in human RNA in thousands of different sites. Some of the sites are located in protein-coding regions but the majority is found in non-coding regions, such as 3′UTRs, 5′UTRs and introns - mainly in Alu elements. While editing is found in all tissues, the highest levels of editing are found in the brain. It was shown that editing levels within protein-coding regions are increased during embryogenesis and after birth and that RNA editing is crucial for organism viability as well as for normal development. In this study we characterized the A-to-I RNA editing phenomenon during neuronal and spontaneous differentiation of human embryonic stem cells (hESCs). We identified high editing levels of Alu repetitive elements in hESCs and demonstrated a global decrease in editing levels of non-coding Alu sites when hESCs are differentiating, particularly into the neural lineage. Using RNA interference, we showed that the elevated editing levels of Alu elements in undifferentiated hESCs are highly dependent on ADAR1. DNA microarray analysis showed that ADAR1 knockdown has a global effect on gene expression in hESCs and leads to a significant increase in RNA expression levels of genes involved in differentiation and development processes, including neurogenesis. Taken together, we speculate that A-to-I editing of Alu sequences plays a role in the regulation of hESC early differentiation decisions.
Genome-Scale Genotype-Phenotype Matching of Two Lactococcus lactis Isolates from Plants Identifies Mechanisms of Adaptation to the Plant Niche

ABSTRACT Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various nondairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL-1403, SK11, and MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two L. lactis plant isolates. Diagnostic sequencing of their genomes resulted in over 2.5 Mb of sequence for each strain. A high synteny was found with the genome of L. lactis IL-1403, which was used as a template for contig mapping and locating deletions and insertions in the plant L. lactis genomes. Numerous genes were identified that do not have homologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the degradation of complex plant polymers such as xylan, arabinan, glucans, and fructans but also for the uptake and conversion of typical plant cell wall degradation products such as α-galactosides, β-glucosides, arabinose, xylose, galacturonate, glucuronate, and gluconate. Further niche-specific differences are found in genes for defense (nisin biosynthesis), stress response (nonribosomal peptide synthesis and various transporters), and exopolysaccharide biosynthesis, as well as the expected differences in various mobile elements such as prophages, plasmids, restriction-modification systems, and insertion sequence elements. Many of these genes were identified for the first time in Lactococcus lactis. In most cases good correspondence was found with the phenotypic characteristics of these two strains.
Quantitative Cartilage Imaging in Knee Osteoarthritis

Quantitative measures of cartilage morphology (i.e., thickness) represent potentially powerful surrogate endpoints in osteoarthritis (OA). These can be used to identify risk factors of structural disease progression and can facilitate the clinical efficacy testing of structure modifying drugs in OA. This paper focuses on quantitative imaging of articular cartilage morphology in the knee, and will specifically deal with different cartilage morphology outcome variables and regions of interest, the relative performance and relationship between cartilage morphology measures, reference values for MRI-based knee cartilage morphometry, imaging protocols for measurement of cartilage morphology (including those used in the Osteoarthritis Initiative), sensitivity to change observed in knee OA, spatial patterns of cartilage loss as derived by subregional analysis, comparison of MRI changes with radiographic changes, risk factors of MRI-based cartilage loss in knee OA, the correlation of MRI-based cartilage loss with clinical outcomes, treatment response in knee OA, and future directions of the field.
Overview of Male Reproductive Pathology

An understanding of form and function is important for examination of the male reproductive tract. A basic understanding of spermatogenesis and hormonal function in the reproductive tract is essential for the pathologists in this evaluation. Gross and histologic reproductive changes need to be distinguished from normal variation and correlated with the reproductive status of the animal. This is especially important when correlating histologic changes with organ weight and other reproductive parameters, such as seminal analysis data. Sexual maturity of animals and tissue handing can impact interpretation. Sexual immaturity of preclinical safety animals can present challenges for accurate identification of compound-related changes. Likewise, proper handling of unfixed reproductive tissues and appropriate selection of a fi xation protocol are important in avoiding artifacts that may interfere with the microscopic evaluation. The histopathology technician needs to recognize testicular landmarks that allow for correct orientation at trimming so the pathologist can assess not only the morphology of seminiferous tubules but also the outfl ow tract. For the most effective evaluation of the male reproductive tract, the testes and epididymides should be examined concurrently. Although the term ``staging'' is often used inappropriately, the pathologist should review testicular tissues in a ``stage-aware'' manner. This article reviews gross and histologic changes of the male reproductive tract as well as tissue orientation and fixation to assist in accurate interpretation of potential treatment-related changes in male reproduction.
A model-prover for constrained dynamic conversations

In a service-oriented architecture, systems communicate by exchanging messages. In this work, we propose a formal model based on OCL-constrained UML Class diagrams and a methodology based on Alloy Analyzer respectively for describing and verifying any first-order constrained client-server conversations. This framework allows us to verify conversation protocol designs at a fairly detailed level and to check first-order logic constraints on both message flows and message contents.
Adjustable iterative soft-output detection for massive MIMO uplink

Minimum mean square error (MMSE) detection algorithms in massive multiple-input multiple-output (MIMO) uplink suffer from prohibitively high complexity of exact matrix inversion. Conventional detection algorithms based on Neumann series expansion (NSE), which approximates the matrix inversion, can only be efficient with small number of NSE terms. Worse still, conventional NSE-based approaches are facing convergence problems in poor propagation environments. In this paper, we introduce an adjustable iterative detection algorithm based on NSE to solve the complexity and convergence problems. Furthermore, we propose an efficient approach to approximately compute the log-likelihood ratios (LLRs) with low-complexity. Both the analytical and numerical results have shown that the proposed approach has benefits in terms of computational complexity and convergence rate, especially in the case of poor propagation environments.
Rapid Serial Visual Presentation in dynamic graph visualization

Rapid Serial Visual Presentation is an effective approach for browsing and searching large amounts of data. By presenting subsequent images at high frequency, we utilize the perceptual abilities of the human visual system to rapidly process certain visual features. While this concept is successfully used in video and image browsing, we demonstrate how it can be applied to dynamic graph visualization. In this paper, we introduce a visualization technique for time-varying graphs that is scalable with respect to the number of time steps. The graph visualization is based on the Parallel Edge Splatting technique, which employs a space-efficient display of a sequence of dynamically changing graphs. To illustrate the usefulness of our approach we analyzed method call graphs recorded during the execution of the open source software system JHotDraw. Furthermore, we studied a time-varying social network representing researchers and their dynamic communication structure while attending the ACM Hypertext 2009 conference.
A Decentralized and Cooperative Workflow Scheduling Algorithm

In the current approaches to workflow scheduling, there is no cooperation between the distributed workflow brokers and as a result, the problem of conflicting schedules occur. To overcome this problem, in this paper, we propose a decentralized and cooperative workflow scheduling algorithm. The proposed approach utilizes a peer-to-peer (P2P) coordination space with respect to coordinating the application schedules among the Grid wide distributed workflow brokers. The proposed algorithm is completely decentralized in the sense that there is no central point of contact in the system, the responsibility of the key functionalities such as resource discovery and scheduling coordination are delegated to the P2P coordination space. With the implementation of our approach, not only the performance bottlenecks are likely to be eliminated but also efficient scheduling with enhanced scalability and better autonomy for the users are likely to be achieved. We prove the feasibility of our approach through an extensive trace driven simulation study.
Computational Morphometry for Detecting Changes in Brain Structure Due to Development, Aging, Learning, Disease and Evolution

The brain, like any living tissue, is constantly changing in response to genetic and environmental cues and their interaction, leading to changes in brain function and structure, many of which are now in reach of neuroimaging techniques. Computational morphometry on the basis of Magnetic Resonance (MR) images has become the method of choice for studying macroscopic changes of brain structure across time scales. Thanks to computational advances and sophisticated study designs, both the minimal extent of change necessary for detection and, consequently, the minimal periods over which such changes can be detected have been reduced considerably during the last few years. On the other hand, the growing availability of MR images of more and more diverse brain populations also allows more detailed inferences about brain changes that occur over larger time scales, way beyond the duration of an average research project. On this basis, a whole range of issues concerning the structures and functions of the brain are now becoming addressable, thereby providing ample challenges and opportunities for further contributions from neuroinformatics to our understanding of the brain and how it changes over a lifetime and in the course of evolution.
Using overlap volume histogram and IMRT plan data to guide and automate VMAT planning: a head-and-neck case study.

PURPOSE To investigate whether an overlap volume histogram (OVH)-driven planning application using an intensity-modulated radiation therapy (IMRT) database can guide and automate volumetric-modulated arc therapy (VMAT) planning for head-and-neck cancer. METHODS Based on comparable head-and-neck dosimetric results between planner-generated VMAT and IMRT plans, an inhouse developed, OVH-driven automated planning application containing a database of prior clinical head-and-neck IMRT plans is built into Pinnacle(3) SmartArc for VMAT planning. Double-arc VMAT plans of four oropharynx, four nasopharynx, and four larynx patients are generated and compared with corresponding clinical IMRT plans. RESULTS Each VMAT plan is automatically generated in two optimization rounds, while the average number of optimization rounds in generating a clinical IMRT plan is 43. In VMAT plans, statistical superiority (p < 0.01) in sparing of the cord+4 mm, brainstem, brachial plexus, larynx, and inner ear is observed with a slight degradation in low-dose-level planning target volume (PTV) coverage. On average, D(0.1 cc) to the cord+4 mm, brainstem and brachial plexus is reduced by 3.7, 4.9, and 1.6 Gy, respectively; V(50 Gy) to the larynx is reduced by 5.3%; mean dose to the inner ear is reduced by 4.4 Gy; V(95) of low-dose-level PTV coverage is reduced by 0.3% with p = 0.25. CONCLUSIONS IMRT-data-driven VMAT planning offers a potential method for generating VMAT plans that are comparable to IMRT plans in terms of dosimetric quality.
Region-Based Spatial Sampling for Image Classification

Local descriptors with Bag-of-Words representation were widely used for image classification. Especially, local descriptors of dense spatial sampling were demonstrated to be able to further improve performances of image classification. However, denser spatial sampling is impractical due to huge computation cost. To handle this issue, we propose a new region-based sampling strategy in this paper. We first perform an over-segmentation to get image regions, and then we extract local descriptors around the region boundaries and inside the regions respectively with a popular sampling strategy. Thus, almost at the same computation cost, the proposed method can capture more salient points and obtain much better classification performance. Extensive experiments are conducted on two widely-used datasets (UIUC Sports and Caltech-101). The experimental results demonstrate the effectiveness of the proposed method. Specifically, the proposed method updates the state-of-the-art on UIUC Sports dataset with a classification accuracy of 89.38%.
Gain-of-function Mutations Reveal Expanded Intermediate States and a Sequential Action of Two Gates in MscL

The tension-driven gating transition in the large mechanosensitive channel MscL proceeds through detectable states of intermediate conductance. Gain-of-function (GOF) mutants with polar or charged substitutions in the main hydrophobic gate display altered patterns of subconducting states, providing valuable information about gating intermediates. Here we present thermodynamic analysis of several GOF mutants to clarify the nature and position of low-conducting conformations in the transition pathway. Unlike wild-type (WT) MscL, which predominantly occupies the closed and fully open states with very brief substates, the mild V23T GOF mutant frequently visits a multitude of short-lived subconducting states. Severe mutants V23D and G22N open in sequence: closed (C) → low-conducting substate (S) → open (O), with the first subtransition occurring at lower tensions. Analyses of equilibrium state occupancies as functions of membrane tension show that the C→S subtransition in WT MscL is associated with only a minor conductance increment, but the largest in-plane expansion and free energy change. The GOF substitutions strongly affect the first subtransition by reducing area (ΔA) and energy (ΔE) changes between C and S states commensurably with the severity of mutation. GOF mutants also exhibited a considerably larger ΔE associated with the second (S→O) subtransition, but a ΔA similar to WT. The area changes indicate that closed conformations of GOF mutants are physically preexpanded. The tension dependencies of rate constants for channel closure (k off) predict different positions of rate-limiting barriers on the energy-area profiles for WT and GOF MscL. The data support the two-gate mechanism in which the first subtransition (C→S) can be viewed as opening of the central (M1) gate, resulting in an expanded water-filled “leaky” conformation. Strong facilitation of this step by polar GOF substitutions suggests that separation of M1 helices associated with hydration of the pore in WT MscL is the major energetic barrier for opening. Mutants with a stabilized S1 gate demonstrate impeded transitions from low-conducting substates to the fully open state, whereas extensions of S1–M1 linkers result in a much higher probability of reverse O→S transitions. These data strongly suggest that the bulk of conductance gain in the second subtransition (S→O) occurs through the opening of the NH2-terminal (S1) gate and the linkers are coupling elements between the M1 and S1 gates.
Teleseismic Traveltime Tomography of Northern Sumatra

We imaged the mantle structure beneath northern Sumatra by inverting high‐quality seismic arrival time data and using a newly developed eikonal equation‐based teleseismic tomography method. Traveltime differences between neighboring stations were reliably extracted by cross‐correlating teleseismic waveforms, which were recorded by 26 stations from January 2009 to January 2018. Both P and S wave tomographic results show the oblique subduction of the Indo‐Australian oceanic lithosphere beneath the Sunda plate. The maximum penetration depth of the subducted slab into the mantle varies roughly from 400 km in the north to 800 km in the south. The plunging fold of the subducted slab, which mimics the shape of the trench and the volcanic arc, has less curvature than that reported in the literature; additionally, our results suggest that the gentle slab fold can be traced to a depth of about 500 km. Furthermore, a slab tear may exist beneath northern Sumatra.
Extending Contract theory with Safety Integrity Levels

In functional safety standards such as ISO 26262 and IEC 61508, Safety Integrity Levels (SILs) are assigned to top-level safety requirements on a system. The SILs are then either inherited or decomposed down to safety requirements on sub-systems, such that if the sub-systems are sufficiently reliable in fulfilling their respective safety requirements, as specified by the SILs, then it follows that the system is sufficiently reliable in fulfilling the top-level safety requirement. Present contract theory has previously been shown to provide a suitable foundation to structure safety requirements, but does not include support for the use of SILs. An extension of contract theory with the notion of SILs is therefore presented. As a basis for structuring the breakdown of safety requirements, a graph, called a contract structure, is introduced that provides a necessary foundation to capture the notions of SIL inheritance and decomposition in the context of contract theory.
Depth Classification of Wildlife Footage

This paper discuss our work in automatically detecting ‘close-up’ versus ‘long’ shots in a large video database, using natural image statistics. The database in question is the Granada (Bristol) wildlife archive which has over 20 Tbytes (several thousand hours) of digitized footage and associated meta data on-line. We extract a number of features from each image and use a Neural Network to classify the images in the feature space spanned by these features. The features are of two different types, the first type extracts spectral information from the Power Spectrum of the Fourier Transform of the image. The second type of features we extract are different complexity measurements of the images. Our method is able to correctly discriminate between different shots with an accuracy of over 96% .
Adolf Meyer and the development of American psychiatry.

Adolf Meyer was a major force in molding psychiatry into its current form; his teachings are so solidly incorporated into American psychiatric theory and practice that the extent of his influence is often over-looked. He brought American psychiatry its pluralistic and instrumental orientation, its holistic approach, its psychobiological understanding that human behavior is integrated at a symbolic level, its conceptualization of psychiatric disorders as maladaptive reaction patterns rather than as discrete disease entities, its interest in the psychotherapy of the psychoses. He provided psychiatry with a fundamental scientific orientation that fitted into the remainder of science and also opened the way for the inclusion of data concerning human experience and biography in biological thinking.
Bounding the Search Space for Global Optimization of Neural Networks Learning Error: An Interval Analysis Approach

Training a multilayer perceptron (MLP) with algorithms employing global search strategies has been an important research direction in the field of neural networks. Despite a number of signifcant results, an important matter concerning the bounds of the search region| typically defined as a box--where a global optimization method has to search for a potential global minimizer seems to be unresolved. The approach presented in this paper builds on interval analysis and attempts to define guaranteed bounds in the search space prior to applying a global search algorithm for training an MLP. These bounds depend on the machine precision and the term "guaranteed" denotes that the region defined surely encloses weight sets that are global minimizers of the neural network's error function. Although the solution set to the bounding problem for an MLP is in general non-convex, the paper presents the theoretical results that help deriving a box which is a convex set. This box is an outer approximation of the algebraic solutions to the interval equations resulting from the function implemented by the network nodes. An experimental study using well known benchmarks is presented in accordance with the theoretical results.