Miracle-dz/UniFAR-FTUs huggingface dataset:
Lung neuroendocrine tumours: deep sequencing of the four World Health Organization histotypes reveals chromatin‐remodelling genes as major players and a prognostic role for TERT, RB1, MEN1 and KMT2D

Next‐generation sequencing (NGS) was applied to 148 lung neuroendocrine tumours (LNETs) comprising the four World Health Organization classification categories: 53 typical carcinoid (TCs), 35 atypical carcinoid (ACs), 27 large‐cell neuroendocrine carcinomas, and 33 small‐cell lung carcinomas. A discovery screen was conducted on 46 samples by the use of whole‐exome sequencing and high‐coverage targeted sequencing of 418 genes. Eighty‐eight recurrently mutated genes from both the discovery screen and current literature were verified in the 46 cases of the discovery screen, and validated on additional 102 LNETs by targeted NGS; their prevalence was then evaluated on the whole series. Thirteen of these 88 genes were also evaluated for copy number alterations (CNAs). Carcinoids and carcinomas shared most of the altered genes but with different prevalence rates. When mutations and copy number changes were combined, MEN1 alterations were almost exclusive to carcinoids, whereas alterations of TP53 and RB1 cell cycle regulation genes and PI3K/AKT/mTOR pathway genes were significantly enriched in carcinomas. Conversely, mutations in chromatin‐remodelling genes, including those encoding histone modifiers and members of SWI–SNF complexes, were found at similar rates in carcinoids (45.5%) and carcinomas (55.0%), suggesting a major role in LNET pathogenesis. One AC and one TC showed a hypermutated profile associated with a POLQ damaging mutation. There were fewer CNAs in carcinoids than in carcinomas; however ACs showed a hybrid pattern, whereby gains of TERT, SDHA, RICTOR, PIK3CA, MYCL and SRC were found at rates similar to those in carcinomas, whereas the MEN1 loss rate mirrored that of TCs. Multivariate survival analysis revealed RB1 mutation (p = 0.0005) and TERT copy gain (p = 0.016) as independent predictors of poorer prognosis. MEN1 mutation was associated with poor prognosis in AC (p = 0.0045), whereas KMT2D mutation correlated with longer survival in SCLC (p = 0.0022). In conclusion, molecular profiling may complement histology for better diagnostic definition and prognostic stratification of LNETs. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
A 0.015mm2 63fJ/conversion-step 10-bit 220MS/s SAR ADC with 1.5b/step redundancy and digital metastability correction

A low power and very low area 10-bit 220MS/s SAR ADC is presented. The ADC employs a redundancy scheme that relaxes the DAC settling requirement and enables high sample rates, as well as a digital metastability identification and correction algorithm that exploits the redundancy as an error-correction code. The proposed ADC was implemented in CMOS 65nm, and takes up only 0.015mm2. At 220MS/s it consumes 4.3mW and achieves 51.7dB SNDR for a full scale sinusoidal input. For OFDM-like signals (wide-band 13dB Peak-to-RMS) the equivalent ENOB is 9.1 bit at 220MS/s. The figure-of-merit (FOM) is 63fJ/(conversion-step) at 220MS/s and 43fJ/conv-step at 160Ms/s.
Bucket-like space partitioning data structures with applications to ray-tracing

Data structures based on uniform subdivisions of the space —also known as bucketing— have the nice properties that they can be walked through very easily and can provide neighborhood relations at low cost. For data sets which are uniformly scattered in 2D or 3D space, this makes the imple- mentation of algorithms such as ray tracing, nearest neigh- bors computation or Delaunay triangulation almost trivial. But should the processed data set admit dense clusters, the spatial partitioning does not result in data partitioning so that the performances are collapsing. Although it has been known for a long time in dimension one that recursive bucket-sort admits a linear complexity for a wide range of probability densities, recursive bucket- like data structures have not received any attention in the computational geometry community. It has been observed in computer graphics that these were the fastest to ray-trace, but the question of understanding why they are not just another space partitioning data structure but rather the only data structure that succeeds in capturing the probabilistic properties of data distribution remains open. This paper is a first step in this direction and investi- gates hierarchical recursive and non recursive data struc- tures for ray-tracing. First, we show that precisely analyz- ing an optimized ray-tracer is a difficult task due to the context sensitivity of the calls costs of the functions called most often. Second, we exhibit statistics showing that if uniform grids are definitely not the right data structure to use for non-uniform distributions, recursive grids are very good at handling such distributions. Third, we present sev- eral improvements of the Hierarchy of Uniform Grids data structure, which result for the best cases in running times improved by up to a factor three with reference to the pre- viously best known solution.
Alterations to the expression level of mitochondrial transcription factor A, TFAM, modify the mode of mitochondrial DNA replication in cultured human cells

Mitochondrial transcription factor A (TFAM) is an abundant mitochondrial protein of the HMG superfamily, with various putative roles in mitochondrial DNA (mtDNA) metabolism. In this study we have investigated the effects on mtDNA replication of manipulating TFAM expression in cultured human cells. Mammalian mtDNA replication intermediates (RIs) fall into two classes, whose mechanistic relationship is not properly understood. One class is characterized by extensive RNA incorporation on the lagging strand, whereas the other has the structure of products of conventional, strand-coupled replication. TFAM overexpression increased the overall abundance of RIs and shifted them substantially towards those of the conventional, strand-coupled type. The shift was most pronounced in the rDNA region and at various replication pause sites and was accompanied by a drop in the relative amount of replication-termination intermediates, a substantial reduction in mitochondrial transcripts, mtDNA decatenation and progressive copy number depletion. TFAM overexpression could be partially phenocopied by treatment of cells with dideoxycytidine, suggesting that its effects are partially attributable to a decreased rate of fork progression. TFAM knockdown also resulted in mtDNA depletion, but RIs remained mainly of the ribosubstituted type, although termination intermediates were enhanced. We propose that TFAM influences the mode of mtDNA replication via its combined effects on different aspects of mtDNA metabolism.
Shim6: Level 3 Multihoming Shim Protocol for IPv6

This document defines the Shim6 protocol, a layer 3 shim for providing locator agility below the transport protocols, so that multihoming can be provided for IPv6 with failover and load sharing properties, without assuming that a multihomed site will have a provider independent IPv6 address prefix which is announced in the global IPv6 routing table. The hosts in a site which has multiple provider allocated IPv6 address prefixes, will use the Shim6 protocol specified in this document to setup state with peer hosts, so that the state can later be used to failover to a different locator pair, should the original one stop working.
Servo-constraint generalized inverse dynamics for robot manipulator control design

Novel concept of inverse dynamics for robot manipulator control is developed. The concept is based on generalized inversion, and therefore it avoids limitations and shortcomings of square inversion that are frequently encountered in conventional inverse dynamics. A servo-constraint on the manipulator is defined, the satisfaction of which implies that the desired robot kinematics is satisfied. A prescribed stable linear second-order dynamics in a servo-constraint deviation norm measure variable is evaluated along trajectory solutions of the manipulator, resulting in a linear algebraic relation in the control vector. Generalized inversion of the relation via the Greville formula yields a control law that is linearly parameterized in a free null-control vector. The null-control vector is projected onto nullspace of the controls coefficient in the linear algebraic relation, and therefore it does not affect servo-constraint dynamics. The design freedom offered by the null-control vector is utilized to stabilize manipulator's internal dynamics, and to provide a perturbed feedback linearizing transformation of the global closed loop system dynamics. Generalized inversion singularity avoidance is made by replacing the Moore-Penrose generalized inverse in the Greville formula by a damped generalized inverse, resulting in uniformly ultimately bounded robot manipulator trajectory tracking.
Exploiting Omissive Faults in Synchronous Approximate Agreement

In a fault-tolerant distributed system, it is often necessary for nonfaulty processes to agree on the value of a shared data item. The criterion of Approximate Agreement does not require processes to achieve exact agreement on a value; rather, they need only agree to within a predefined numerical tolerance. Approximate Agreement can be achieved through convergent voting algorithms. Previous research has studied convergent voting algorithms under mixed-mode or hybrid fault models, such as the Thambidurai and Park Hybrid fault model, comprised of three fault modes: asymmetric, symmetric, and benign. This paper makes three major contributions to the state of the art in fault-tolerant convergent voting. (1) We partition both the asymmetric and symmetric fault modes into disjoint omissive and transmissive submodes. The resulting five-mode hybrid fault model is a superset of previous hybrid fault models. (2) We present a new family of voting algorithms, called Omission Mean Subsequence Reduced (OMSR), which implicitly recognize and exploit omissive behavior in malicious faults while still maintaining full Byzantine fault tolerance; (3) We show that OMSR voting algorithms are more fault-tolerant than previous voting algorithms if any of the currently active faults is omissive.
Most patients regain prefracture basic mobility after hip fracture surgery in a fast-track programme.

INTRODUCTION Treatment of patients with hip fracture has improved over the past decade. Still, some patients do not regain independent mobility within their primary hospital stay even if they follow a multimodal fast-track surgical programme. The aim of the present article was to examine the validity of the preliminary prefracture New Mobility Score (NMS), age and fracture type as independent predictors of in-hospital outcome after hip fracture surgery. MATERIAL AND METHODS The study comprised a total of 213 consecutive patients with a median age of 82 years who were admitted from their own home to a special hip fracture unit. Outcome variables were the regain of independency in basic mobility as evaluated by the Cumulated Ambulation Score, and discharge destination in the community. RESULTS Multiple logistic regression analysis revealed that patients with a low prefracture NMS and/or an intertrochanteric fracture were 6.5 and four times more likely to not regain independency in basic mobility during admittance than patients with a high prefracture NMS level and a cervical fracture, respectively. In addition, the odds of not regaining independent mobility increased with age by 5% per year. The same three variables significantly increased the odds of patients not being discharged to their own home. CONCLUSION Prefracture NMS, age and fracture type were confirmed as independent predictors of in-hospital outcome in patients with hip fracture who followed a multimodal rehabilitation concept.
Stimulating somatosensory psychophysics: a double-blind, sham-controlled study of the neurobiological mechanisms of tDCS

The neuromodulation technique transcranial direct current stimulation (tDCS) is thought to produce its effects on behavior by altering cortical excitability. Although the mechanisms underlying the observed effects are thought to rely on the balance of excitatory and inhibitory neurotransmission, the physiological principles of the technique are not completely understood. In this study, we examine the influence of tDCS on vibrotactile adaptation, using a simple amplitude discrimination paradigm that has been shown to exhibit modifications in performance due to changes in inhibitory neurotransmission. Double-blind tDCS (Anodal/Sham) of 1 mA was delivered for 600 s to electrodes positioned in a somatosensory/contralateral orbit montage. Stimulation was applied as part of a pre/post design, between blocks of the behavioral tasks. In accordance with previous work, results obtained before the application of tDCS indicated that amplitude discrimination thresholds were significantly worsened during adaptation trials, compared to those achieved at baseline. However, tDCS failed to modify amplitude discrimination performance. Using a Bayesian approach, this finding was revealed to constitute substantial evidence for the null hypothesis. The failure of DC stimulation to alter vibrotactile adaptation thresholds is discussed in the context of several factors that may have confounded the induction of changes in cortical plasticity.
Tracking of fixed shape moving objects based on modified particle filters

High resolution imaging and its processing is one of the most researched areas now-a-days. Recognition of moving object in a remote scene is a challenging task because of presence of multiple objects present there. Similarly, to track an object after the recognition part is also difficult task because of constant change in not only the coordinates of the target object but also the objects that are cause of occlusion for it. To simplify the task, a constant updating of the algorithms have been carried out in this area pertaining to main two tasks in task. One being is how to reduce the time to recognize the object and other is to efficiently track it, possibly in real time. In this paper, a unified approach is presented which efficiently tracks an object using Particle filter. First step is to identify the coordinates of the object and then a bounding box is placed on it. Then tracking algorithm uses particle filter to efficiently track the moving object in successive frames using probabilistic estimation. The particle filter uses posterior distribution of random variables related to Markov chain for estimation.
SimPoint 3.0: Faster and More Flexible Program Analysis

This paper describes the new features available in the Sim-Point 3.0 release. The release provides two techniques for drastically reducing the run-time of SimPoint: faster searching to ﬁnd the best clustering, and efﬁciently clustering large numbers of intervals. SimPoint 3.0 also provides an option to output only the simulation points that represent the majority of execution, which can reduce simulation time without much increase in error. Finally, this release provides support for correctly clustering variable length intervals, taking into consideration the weight of each interval during clustering. This paper describes SimPoint 3.0’s new features, how to use them, and points out some common pitfalls.
Effects of Structured Versus Usual Care on Renal Endpoint in Type 2 Diabetes: The SURE Study

OBJECTIVE Multifaceted care has been shown to reduce mortality and complications in type 2 diabetes. We hypothesized that structured care would reduce renal complications in type 2 diabetes. RESEARCH DESIGN AND METHODS A total of 205 Chinese type 2 diabetic patients from nine public hospitals who had plasma creatinine levels of 150–350 μmol/l were randomly assigned to receive structured care (n = 104) or usual care (n = 101) for 2 years. The structured care group was managed according to a prespecified protocol with the following treatment goals: blood pressure <130/80 mmHg, A1C <7%, LDL cholesterol <2.6 mmol/l, triglyceride <2 mmol/l, and persistent treatment with renin-angiotensin blockers. The primary end point was death and/or renal end point (creatinine >500 μmol/l or dialysis). RESULTS Of these 205 patients (mean ± SD age 65 ± 7.2 years; disease duration 14 ± 7.9 years), the structured care group achieved better control than the usual care group (diastolic blood pressure 68 ± 12 vs. 71 ± 12 mmHg, respectively, P = 0.02; A1C 7.3 ± 1.3 vs. 8.0 ± 1.6%, P < 0.01). After adjustment for age, sex, and study sites, the structured care (23.1%, n = 24) and usual care (23.8%, n = 24; NS) groups had similar end points, but more patients in the structured care group attained ≥3 treatment goals (61%, n = 63, vs. 28%, n = 28; P < 0.001). Patients who attained ≥3 treatment targets (n = 91) had reduced risk of the primary end point (14 vs. 34; relative risk 0.43 [95% CI 0.21–0.86] compared with that of those who attained ≤2 targets (n = 114). CONCLUSIONS Attainment of multiple treatment targets reduced the renal end point and death in type 2 diabetes. In addition to protocol, audits and feedback are needed to improve outcomes.
International Journal of Information Management Understanding the Role of Consistency during Web–mobile Service Transition: Dimensions and Boundary Conditions

With the advancement of mobile technologies, numerous web service providers have begun to extend their web services to the mobile context. To understand users' mobile service adoption behaviour in the context of the web–mobile service transition, this study investigates the role of consistency between web and mobile services by proposing a typology of consistency and examining the extent to which and the boundary conditions under which consistency works. Specifically, consistency is classified into behavioural consistency (e.g., operational consistency) and object-based consistency, which includes consistency in information, system and service in terms of the information systems success model. We also contend the mediating effect of operational consistency and the interaction effect of trust in web services and operational consistency. A field survey with 235 mobile service users confirms our mediating and moderating hypotheses. The implications for theory and practice are also discussed.
Tour into the picture with water surface reflection and object movements

Given a still picture, tour into the picture (TIP) generates a walk‐through animation of a 3D scene constructed from the picture. In this paper, we generalize TIP to deal with water surface reflection while allowing foreground objects to move. We formulate a non‐linear optimization problem to find the 3D scene parameters with respect to the camera position, to automatically construct a reasonable 3D scene model, provided with a set of points and their corresponding points on the water surface. To synthesize a stream of reflected images on the water surface in accordance with the camera movement, we propose a novel image‐based approach, which makes the best of the limited information available in the input picture. Furthermore, we incorporate water surface movement data acquired from water simulation on top of stochastic motion textures for objects such as trees and plants, to create a dynamic scene. Copyright © 2006 John Wiley & Sons, Ltd.
Efficient algorithms for combinatorial auctions with volume discounts arising in web service composition

Web services are now a key ingredient of software services offered by software enterprises. Many standardized web services are now available as commodity offerings from web service providers. An important problem for a web service requester is the web service composition problem which involves selecting the right mix of web service offerings to execute an end-to-end business process. Web service offerings are now available in bundled form as composite web services and more recently, volume discounts are also on offer, based on the number of executions of web services requested. In this paper, we develop efficient algorithms for the web service composition problem in the presence of composite web service offerings and volume discounts. We model this problem as a combinatorial auction with volume discounts. We first develop efficient polynomial time algorithms when the end-to-end service involves a linear workflow of web services. Next we develop efficient polynomial time algorithms when the end-to-end service involves a tree workflow of web services.
Development and validation of a screening tool to predict the risk of chronic low back pain in patients presenting with acute low back pain: a study protocol

Introduction Around 40% of people presenting to primary care with an episode of acute low back pain develop chronic low back pain. In order to reduce the risk of developing chronic low back pain, effective secondary prevention strategies are needed. Early identification of at-risk patients allows clinicians to make informed decisions based on prognostic profile, and researchers to select appropriate participants for secondary prevention trials. The aim of this study is to develop and validate a prognostic screening tool that identifies patients with acute low back pain in primary care who are at risk of developing chronic low back pain. This paper describes the methods and analysis plan for the development and validation of the tool. Methods/analysis The prognostic screening tool will be developed using methods recommended by the Prognosis Research Strategy (PROGRESS) Group and reported using the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) statement. In the development stage, we will use data from 1248 patients recruited for a prospective cohort study of acute low back pain in primary care. We will construct 3 logistic regression models to predict chronic low back pain according to 3 definitions: any pain, high pain and disability at 3 months. In the validation stage, we will use data from a separate sample of 1643 patients with acute low back pain to assess the performance of each prognostic model. We will produce validation plots showing Nagelkerke R2 and Brier score (overall performance), area under the curve statistic (discrimination) and the calibration slope and intercept (calibration). Ethics and dissemination Ethical approval from the University of Sydney Ethics Committee was obtained for both of the original studies that we plan to analyse using the methods outlined in this protocol (Henschke et al, ref 11-2002/3/3144; Williams et al, ref 11638).
Discovering Hot Topics in the Blogosphere

Over the last few years, blogs (web logs) have gained massive popularity and have become one of the most influential web social media in our times. Every blog post in the blogosphere has a well defined timestamp, which is not taken into account by search engines. By conducting research regarding this feature of the Blogosphere, we could attempt to discover hot topics during a time interval. We present Kleinberg’s algorithm about finding bursty and hierarchical streams; we apply it on titles of blog posts to discover bursty terms and compare the results to that produced by Blogscope, an online system for the analysis of the Blogosphere. Finally we present some ideas for future research in the field that could help designing a more sophisticated blog search engine than the existing ones.
Software architecture reconstruction: An approach based on combining graph clustering and partitioning

This article proposes an approach of improving the accuracy of automatic software architecture reconstruction. Many research uses clustering for the purpose of architectural reconstruction. Our work improves the results of coupling/cohesion driven clustering by combining it with a partitioning preprocessing that establishes a layering of the classes of the system. Two simple and not really efficient algorithms for software clustering are improved by applying this approach, as it is shown in the validation section.