Miracle-dz/UniFAR-FTUs huggingface dataset:
Data exploration tools for the Gene Ontology database

MOTIVATION To improve the ability of biologists (both researchers and students) to ask biologically interesting questions of the Gene Ontology (GO) database and to explore the ontologies by seeing large portions of the ontology graphs in context, along with details of individual terms in the ontologies. RESULTS GoGet and GoView are two new tools built as part of an extensible web application system based on Java 2 Enterprise Edition technology. GoGet has a user interface that enables users to ask biologically interesting questions, such as (1) What are the DNA binding proteins involved in DNA repair, but not in DNA replication? and (2) Of the terms containing the word triphosphatase, which have associated gene products from mouse, but not fruit fly? The results of such queries can be viewed in a collapsed tabular format that eases the burden of getting through large tables of data. GoView enables users to explore the large directed acyclic graph structure of the ontologies in the GO database. The two tools are coordinated, so that results from queries in GoGet can be visualized in GoView in the ontology in which they appear, and explorations started from GoView can request details of gene product associations to appear in a result table in GoGet. AVAILABILITY Free access to the GoGet query tool and free download of the GoView ontology viewer are provided to all users at http://db.math.macalester.edu/goproject. In addition, source code for the GoView tool is also available from this site, along with a user manual for both tools.
The acute effect of D-tagatose on food intake in human subjects

A double-blind randomized crossover study was performed with nineteen normal-weight men to investigate the effect on subsequent ad libitum food intake of replacing 29 g sucrose with 29 g D-TAGATOSE AS SWEETENER TO A BREAKFAST MEAL. d-Tagatose is a malabsorbed stereoisomer of fructose with potential application as a bulk sweetener. Food intake was measured at lunch offered 4 h after the breakfast meal, during the afternoon with access to abundant snacks, and finally at a supper buffet 9 h after the breakfast. Energy intake at lunch and during the snacking period was similar after ingesting the two sugars, while it was 15 % lower after ingesting d-tagatose than with sucrose at supper (P < 0·05). Gastrointestinal factors such as the osmotic effects of unabsorbed d-tagatose causing distension of the gut might have mediated the acute appetite-suppressing effect. The present paper also refers to data from a preceding study in which we observed an increased self-reported energy intake after ingestion of d-tagatose compared with sucrose which, in fact, suggests a relative hyperphagic effect of d-tagatose. However, self-reported food intake may be biased by selective under-reporting and this subsequent study with a more controlled assessment of food intake was therefore conducted. This present study did not support any hyperphagic effect of d-tagatose, but rather suggests that d-tagatose may contribute to a reduced energy intake.
adaQAC: Adaptive Query Auto-Completion via Implicit Negative Feedback

Query auto-completion (QAC) facilitates user query composition by suggesting queries given query prefix inputs. In 2014, global users of Yahoo! Search saved more than 50% keystrokes when submitting English queries by selecting suggestions of QAC. Users' preference of queries can be inferred during user-QAC interactions, such as dwelling on suggestion lists for a long time without selecting query suggestions ranked at the top. However, the wealth of such implicit negative feedback has not been exploited for designing QAC models. Most existing QAC models rank suggested queries for given prefixes based on certain relevance scores. We take the initiative towards studying implicit negative feed- back during user-QAC interactions. This motivates re-designing QAC in the more general "(static) relevance"(adaptive) implicit negative feedback? framework. We propose a novel adaptive model adaQAC that adapts query auto-completion to users' implicit negative feedback towards unselected query suggestions. We collect user-QAC interaction data and perform large-scale experiments. Empirical results show that implicit negative feedback significantly and consistently boosts the accuracy of the investigated static QAC models that only rely on relevance scores. Our work compellingly makes a key point: QAC should be designed in a more general framework for adapting to implicit negative feedback.
A quantitative analysis of intensity-modulated radiation therapy plans and comparison of homogeneity indices for the treatment of gynecological cancers

The aim of present study was to evaluate the intensity-modulated radiation therapy (IMRT) plans using different homogeneity and conformity indices in gynecological cancers, as well as to compare and find out the most reliable and accurate measure of the dose homogeneity among the available indices. In this study, a cohort of 12 patients were registered for evaluation, those receiving dynamic IMRT treatment on Clinac-2300C/D linear accelerator with 15-Mega Voltage (MV) photon beam. Dynamic IMRT plans were created on Eclipse treatment planning system with Helios dose volume optimization software. Homogeneity indices (HI) such as H index, modified H index, HI index, modified HI index, and S-index (sigma-index) proposed by M Yoon et al. (2007) were calculated and compared. The values of S-index vary from 1.63 to 2.99. The results indicate that the H and HI indices and their modified versions may not provide the correct dose homogeneity information, but the S-index provides accurate information about the dose homogeneity in the Planning Target Volume (PTV). Each plan was compared with 6-MV photon energy on the basis of S-index and conformity index (CI). Organs at risk (OAR) doses with 6-MV and 15-MV beams were also reported.
Normal Cardiac Magnetic Resonance Measurements and Interobserver Discrepancies in Volumes and Mass Using the Papillary Muscle Inclusion Method

Background: The potential of cardiac magnetic resonance (CMR) imaging to provide precise and reproducible measurements might not be realized currently. Methods: We acquired CMR images on 30 healthy adults and compared readings of 2 experienced physicians to determine sources of measurement variability. Results: Simultaneous review of tracings revealed 3 major sources of interobserver variability: 1) choice of end- diastolic/end-systolic frames; 2) choice of the most basal left and right ventricular short-axis slices; and, 3) approach to endocardial edge selection. Study Plan. These objectives were to be achieved through a prospective study in an adequate number of healthy subjects. Qualifying subjects were to undergo a stan- dardized functional CMR evaluation. Predefined cardiovas- cular measurements were made using workstation-specific methods. Key volume and mass measurements were to be performed independently by 2 observers to improve accu- racy, to determine reproducibility, and to develop consensus methods. Results were to be used for clinical and research
Binding of purified, soluble major histocompatibility complex polypeptide chains onto isolated T-cell receptors. I. Reactivity against allo- and self-determinants

In this study, we tried to get information about the fine antigen- binding ability of purified, soluble, idiotype-positive T-cell receptor molecules. Lewis anti-DA T-cell receptors were purified from normal Lewis serum by the use of anti-idiotypic immunosorbent and sodium dodecyl sulfate-polyacrylamide gel, and were coupled to cyanogen bromide-activated Sepharose 4B. In parallel, Lewis anti-DA, Lewis anti- BN, and DA anti-Lewis alloantibody immunosorbents were prepared. The major Ag-B chain (44,000 daltons) and the two polypeptide chains (34,000 and 27,000 daltons) of Ia were purified from Lewis, DA, and BN lymphocytes and absorbent on the above-mentioned immunosorbents. We found that the major Ag-B chain as well as the two Ia chains were bound to the alloantibody columns if they were derived from the corresponding allogeneic strain. No retaining ability for self-major histocompatibility complex (MHC) or third-party MHC chains was noted with the alloantibody immunosorbents. When using immunosorbents made up of idiotypic T-cell receptors, only two MHC polypeptides of the relevant allo-MHC type were retained, namely, the Ag-B and the heavy Ia chains. No detectable activity was observed when testing the same column for reactivity against third-party MHC polypeptide chains. However, the Lewis anti-DA T-cell receptors could be shown to display weak, but significant, reactivity toward one Lewis MHC polypeptide chain, that is, the heavy chain of Ia type.
Overview of the TREC 2013 Session Track

The TREC Session track ran for the fourth time in 2013. The track has the primary goal of providing test collections and evaluation measures for studying information retrieval over user sessions rather than one-time queries. These test collections are meant to be portable, reusable, statistically powerful, and open to anyone that wishes to work on the problem of retrieval over sessions. The experimental design of the track was similar to that of the previous two years [4, 5]:
Optimal admission control policy for mobile cloud computing hotspot with cloudlet

We consider an admission control problem and adaptive resource allocation for running mobile applications on a cloudlet. We formulate an optimization problem for dynamic resource sharing of mobile users in mobile cloud computing (MCC) hotspot with a cloudlet as a semi-Markov decision process (SMDP). SMDP is transformed into a linear programming (LP) model and it is solved to obtain an optimal solution. In the optimization model, the quality of service (QoS) for different classes of mobile user is taken into account under resource constraints (i.e., bandwidth and server). The numerical results are presented to illustrate that the proposed admission control scheme can achieve a desirable performance and improve throughput of an MCC hotspot significantly.
Catheter-Related Infections , a Diagnostic Problem

In critically ill patients, catheter-related bloodstream infections (CRBSIs) are associated with increased mortality, length of stay in the ICU and extra costs. The relative risk of infection can be best determined by analyzing rates of catheter-related bloodstream infections per 1000 catheter-days. Coagulase-negative staphylococci, Staphylococcus aureus and Candida spp are the pathogens found most commonly both on catheter tips and in blood. The commonly used definitions of intravascular catheterrelated infections are summarized in this review. Clinical signs of catheter-related infections are unreliable because of their poor sensitivity and specificity. Therefore diagnosis is mainly dependent on microbiological techniques. The available diagnostic tests can be classified as methods requiring removal of the central venous catheter and methods not requiring removal of the catheter. The reliability of the various methods is described; none of the described methods has a 100% sensitivity and specificity, and therefore diagnosing CRBSI is still problematic. Finally a diagnostic approach to catheter-related infection is proposed. Catheter-Related Infections, a Diagnostic Problem r e v i e w 2007 NJCC_05 bwerk v1.indd 260 12-10-2007 15:19:21 netherlands journal of critical care 261 neth j crit care • volume 11 • no 5 • october 2007 Table 1. Organisms isolated from catheter tip samples and blood [10,11] Total N = 168 Total N = 105 Organism Catheter tip % CRBSI* % CNS** S. aureus Candida spp Enterococcus spp Pseudomonas spp Acinetobacter spp Enterobacter spp Klebsiella spp Proteus spp Corynebacterium spp E. coli Others 49.1 11.9 7.2 5.9 4.9 4.2 4.2 3.6 2.4 2.4 1.8 3.6 34 17 9 6 6
Cellubrevin-targeted Fluorescence Uncovers Heterogeneity in the Recycling Endosomes*

The pH and trafficking of recycling endosomes have previously been studied using transferrin. We have used another approach, one in which the vesicle transport protein cellubrevin was appended with a luminal IgG epitope to allow targeting of fluorescein-5′-isothiocyanate (FITC)-labeled anti-IgG F(ab) antibodies to the recycling endosomes in living cells. FITC-F(ab) was specifically internalized by COS cells transfected with cellubrevin-Ig, which at steady state accumulated in a pericentriolar region similar to rhodamine-transferrin. Confocal microscopic analysis showed that endosome labeling by these two markers was heterogeneous. This differential distribution was not induced by the IgG tag, since endogenous Cb and Tf were also partitioned into separate endosomal populations. We used fluorescence ratio imaging of internalized FITC-F(ab) to measure the pH of cellubrevin-enriched recycling endosomes (pHCb) and FITC-transferrin to measure the pH of transferrin-enriched recycling endosomes (pHTf). In COS cells, cellubrevin endosomes (mean pHCb 6.1 ± 0.05; range, 5.2–6.6) were more acidic than transferrin endosomes (mean pHTf 6.5 ± 0.05; range, 5.6–7.2). Similar results were obtained in Chinese hamster ovary cells. Treatment with the vacuolar H+-ATPase inhibitor bafilomycin A1caused pHTf to increase (ΔpHTf = 1.2 pH units) to a greater extent than pHCb (ΔpHCb = 0.5 pH units). Furthermore, inhibition of the Na+/K+-ATPase by ouabain or acetylstrophanthidin caused pHTf to decrease by 0.6 pH units but had no effect on pHCb. Based on the combination of these morphological and functional data, we suggest that the recycling endosomes are heterogeneous in their biochemical compositions, ion transport properties, and pH values.
Over-loaded DS-CDMA system waveform design using doubly orthogonal wavelet packets

One significant difference between CDMA systems and FDMA/TDMA systems is that the number of users supported in a CDMA system is not hard-limited by the number of frequency bands or time slots. Whenever a new user is added to a CDMA system, the existing users will suffer a slightly higher interference level. The interference level highly depends on the orthogonality of user waveforms. We present an algorithm to construct a set of wavelet packet based user waveforms for CDMA systems. This algorithm provides more signature waveforms than previously proposed wavelet packet based waveform division systems. The basic waveform set is constructed utilizing double orthogonality based on wavelet packets and binary Walsh codes. This double orthogonality produces auto- and cross-correlations that are much better than the conventional wavelet packet sets and are comparable to the pseudo random binary codes. Under system overload, the waveforms introduce a tolerable interference level to the users.
Influence of Molecular Noise on the Growth of Single Cells and Bacterial Populations

During the last decades experimental studies have revealed that single cells of a growing bacterial population are significantly exposed to molecular noise. Important sources for noise are low levels of metabolites and enzymes that cause significant statistical variations in the outcome of biochemical reactions. In this way molecular noise affects biological processes such as nutrient uptake, chemotactic tumbling behavior, or gene expression of genetically identical cells. These processes give rise to significant cell-to-cell variations of many directly observable quantities such as protein levels, cell sizes or individual doubling times. In this study we theoretically explore if there are evolutionary benefits of noise for a growing population of bacteria. We analyze different situations where noise is either suppressed or where it affects single cell behavior. We consider two specific examples that have been experimentally observed in wild-type Escherichia coli cells: (i) the precision of division site placement (at which molecular noise is highly suppressed) and (ii) the occurrence of noise-induced phenotypic variations in fluctuating environments. Surprisingly, our analysis reveals that in these specific situations both regulatory schemes [i.e. suppression of noise in example (i) and allowance of noise in example (ii)] do not lead to an increased growth rate of the population. Assuming that the observed regulatory schemes are indeed caused by the presence of noise our findings indicate that the evolutionary benefits of noise are more subtle than a simple growth advantage for a bacterial population in nutrient rich conditions.
OF GEOMETRIC AND RADIOMETRIC ANALYSES OF PAINTINGS

This paper presents an overview of a number of diagnostic campaigns carried out to assess the conservation state of paintings. The specific characteristics required in cultural heritage applications have been investigated and are reported, where two main fields are considered: radiometric analyses using multispectral images and 3D surveying for geometric deformation analysis by means of photogrammetry and laser scanning. The activities described were accomplished in interdisciplinary teams, composed of photogrammetrists, art-historians, restorers and experts of nondestructive diagnostic techniques.
Parallel coordinates metrics for classification visualization

The high dimensionality of data presents a major issue in understanding and interpreting the results of classification learning. Among the various approaches that address this issue, parallel coordinates visualization has proven its capabilities to enhance investigation and comprehension of data dimension features especially when the number of dimensions is high and there are numerous output classes. We propose several parallel coordinates metrics, namely entropy, class ordering, and edge crossing, to further facilitate inspection of data features and their relevance to output class. Experiments on real world datasets are presented to show the effectiveness of the proposed approach.
DLL based test solution for interposers in 2.5-D ICs

Silicon interposer is the enabling technology for 2.5D IC integration which supports higher levels of integration and improved electrical performance. An interposer can suffer from various physical defects affecting the overall performance of 2.5D ICs. This paper presents a new method to perform manufacturing tests for interposers utilizing a Delay Locked Loop (DLL). In the proposed method short-time intervals are first amplified through a time-amplifier and then measured. Simulation results using ADS software with 65 nm TSMC CMOS technology indicates that proposed method can detect minor structural defects affecting the propagation delay of interconnect by more than 1.5ps resolution.
Consumer Sentiment and Economic Activity: A Cross Country Comparison

The objective of this article is to reassess the validity of the consumer confidence (or sentiment) indices in anticipating the evolution of economic activity by considering a fairly high number of countries across the world (i.e. France, Germany, Italy, UK, USA, Japan, Canada and Australia) over a period of about thirty years, from the beginning of the seventies till the end of 2002 (quarterly data). To our knowledge this is the first attempt to analyse the consumer confidence index for several countries over such a long period of time. We model the CSIoutput relationship in a cointegrated vector autoregression (VAR) framework, by considering a common set of variables for all countries. Our findings suggest that: (a) what appears to be the main driving forces of consumer confidence cannot be simply summarised on the basis of .
Human Pose as Context for Object Detection

Detecting small objects in images is a challenging problem particularly when they are often occluded by hands or other body parts. Recently, joint modelling of human pose and objects has been proposed to improve both pose estimation as well as object detection. These approaches, however, focus on explicit interaction with an object and lack the flexibility to combine both modalities when interaction is not obvious. We therefore propose to use human pose as an additional context information for object detection. To this end, we represent an object category by a binary star model and train regression forests that localize parts of an object for each modality separately. Predictions of the two modalities are then combined to detect the bounding box of the object. We evaluate our approach on three challenging datasets which vary in the amount of object interactions and the quality of automatically extracted human poses.
Diffuse Ionized Gas in Three Sculptor Group Galaxies

We present a study of the diffuse ionized gas (DIG) in three Sculptor group galaxies: NGC 55, NGC 253, and NGC 300. The study is based on narrow band imagery in H-alpha+[NII](6548+6583A) and [SII] (6717+6731A). We find that DIG contributes 33 to 58% of the total H-alpha luminosity in these galaxies, or 30 to 54% after correcting for scattered light. We find that NGC 300 has a higher fractional DIG luminosity than the other galaxies in our sample, but it is not clear whether this is a significant difference or an effect of the high inclination of the other galaxies. The diffuse emission, averaged over the optical extent of the disk, has a face-on emission measure of 5 to 10 pc cm^{-6}. The DIG is concentrated near HII regions, although significant emission is seen at large distances from HII regions, up to 0.5 to 1 kpc. The [SII]/(H-alpha+[NII]) ratio is enhanced in the DIG, typically around 0.3 to 0.5, compared to 0.2 for the HII regions in these galaxies. These properties are similar to those measured for the DIG in the Milky Way and in other nearby spirals. The line ratios, large-scale distribution, and energy requirement suggest that photoionization is the dominant ionization mechanism.
In‐patient rehabilitation in haemophilic subjects with total knee arthroplasty

Summary. Total knee arthroplasty (TKA) is a major orthopaedic surgery intervention, indicated for severe haemophilic arthropathy. The aim of our study was to analyse rehabilitation outcome in haemophilic patients after TKA. A consecutive series of 21 patients (23 knees) was retrospectively evaluated. The mean age was 37 ± 8 years (range 22–55). Physiotherapy treatment was performed twice a day for 5 days week−1, for 3 h day−1. Assessment included knee range of motion (ROM), Visual Analogue Scale (VAS) for pain evaluation, Western Ontario and McMaster University (WOMAC) Score for functional outcome, Medical Research Council Scale (MRC) for quadriceps muscle strength evaluation, incidence of adverse events and a self‐reported questionnaire. The patients’data were recorded before surgery (t0), at Rehabilitation Unit admission (t1), before discharge (t2) and at follow‐up (t3), 11–48 months after rehabilitation. Western Ontario and McMaster University Score (ref. score: 0–96) was 56.7 ± 12 at t0 and 6.2 ± 6 at t3 (t3 vs. t0: P < 0.001). Visual Analogue Scale (ref. score: 0–10) decreased from 5.0 ± 2 at t1 to 2.1 ± 2 at t2 (t2 vs. t1: P < 0.05) and to 0.1 ± 0 at t3 (t3 vs. t2: P < 0.05). Flexion degrees increased from 43.4 ± 21° at t1 to 80.2 ± 15° at t2 (t2 vs. t1: P < 0.001) and to 95.0 ± 15° at t3 (t3 vs t2: P < 0.05). According to MRC (ref. score: 0–5), quadriceps muscle strength increased from 2.3 ± 0.6 at t1 to 3.6 ± 0.5 at t2 (t2 vs. t1: P < 0.05). Adverse events were found in four patients. Patients’ satisfaction on their outcome at follow‐up was referred as good by 72% of patients or excellent by 28% of patients. Postsurgical intensive rehabilitation in haemophilic patients resulted effective, safe and feasible.
Solving the Top-K Problem with Fixed-Memory Heuristic Search

The Top-K problem is defined as follows. Given L lists of real numbers, find the top K scoring L-tuples. A tuple is scored by the sum of its components. Rare event modeling is often reduced to the Top-K problem. In this paper, we present the application of a fixedmemory heuristic search algorithm (namely, SMA*) and its distributed-memory extension to the Top-K problem. Our approach has efficient runtime complexity and super-linear speedup in distributed-memory setting. Experimental studies on both synthetic and real-world data sets show the effectiveness of our approach.