Miracle-dz/UniFAR-FTUs huggingface dataset:
Financing a future for public biological data

MOTIVATION The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available; database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions. METHODS This study examines the finances and use statistics of a few of these organizations in more depth, and reviews several economic models that may help sustain them. RESULTS Six organizations were studied. Their administrative overhead is fairly low; non-administrative personnel and computer-related costs account for 77% of expenses. One smaller, more specialized US database, in 1997, had 60% of total access from US domains; a majority (56%) of its US accesses came from commercial domains, although only 2% of the 153 databases originally studied received any industrial support. The most popular model used to gain industrial support is asymmetric pricing: preferentially charging the commercial users of a database. At least five biological databases have recently begun using this model. Advertising is another model which may be useful for the more general, more heavily used sites. Microcommerce has promise, especially for databases that do not attract advertisers, but needs further testing. The least income reported for any of the databases studied was $50,000/year; applying this rate to 400 biological databases (a lower limit of the number of such databases, many of which require far larger resources) would mean annual support need of at least $20 million. To obtain this level of support is challenging, yet failure to accept the challenge could be catastrophic. CONTACT lynda@tc.umn. edu
Mining topic-specific concepts and definitions on the web

Traditionally, when one wants to learn about a particular topic, one reads a book or a survey paper. With the rapid expansion of the Web, learning in-depth knowledge about a topic from the Web is becoming increasingly important and popular. This is also due to the Web's convenience and its richness of information. In many cases, learning from the Web may even be essential because in our fast changing world, emerging topics appear constantly and rapidly. There is often not enough time for someone to write a book on such topics. To learn such emerging topics, one can resort to research papers. However, research papers are often hard to understand by non-researchers, and few research papers cover every aspect of the topic. In contrast, many Web pages often contain intuitive descriptions of the topic. To find such Web pages, one typically uses a search engine. However, current search techniques are not designed for in-depth learning. Top ranking pages from a search engine may not contain any description of the topic. Even if they do, the description is usually incomplete since it is unlikely that the owner of the page has good knowledge of every aspect of the topic. In this paper, we attempt a novel and challenging task, mining topic-specific knowledge on the Web. Our goal is to help people learn in-depth knowledge of a topic systematically on the Web. The proposed techniques first identify those sub-topics or salient concepts of the topic, and then find and organize those informative pages, containing definitions and descriptions of the topic and sub-topics, just like those in a book. Experimental results using 28 topics show that the proposed techniques are highly effective.
X-ray computed tomography reconstruction on non-standard trajectories for robotized inspection

X-ray computed tomography (CT) is a powerful tool to characterize or localize inner flaws and to verify the geometric conformity of an object. In contrast to medical applications, the scanned object in non-destructive testing (NDT) might be very large and composed of high-attenuation materials and consequently the use of a standard circular trajectory for data acquisition would be impossible due to constraints in space. For this reason, the use of robotic arms is one of the acknowledged new trends in NDT since it allows more flexibility in acquisition trajectories and therefore could be used for 3D reconstruction of hardly accessible regions that might be a major limitation of classical CT systems. A robotic X-ray inspection platform has been installed at CEA LIST. The considered system integrates two robots that move the X-ray generator and detector. Among the new challenges brought by robotic CT, we focus in this thesis more particularly on the limited access viewpoint imposed by the setup where important constraints control the mechanical motion of the platform. The second major challenge is the truncation of projections that occur when only a field-of-view (FOV) of the object is viewed by the detector. Before performing real robotic inspections, we highly rely on CT simulations to evaluate the capability of the reconstruction algorithm corresponding to a defined scanning trajectory and data acquisition configuration. For this purpose, we use CIVA which is an advanced NDT simulation platform developed at CEA and that can provide a realistic model for radiographic acquisitions and is capable of simulating the projection data corresponding to a specific CT scene defined by the user. Thus, the main objective of this thesis is to develop analytical and iterative reconstruction algorithms adapted to nonstandard trajectories and to integrate these algorithms in CIVA software as plugins of reconstruction.
Effects-Based Air Operations Planning Framework: A Knowledge-Based Simulation Approach

Planning air warfare operations has always been a complex endeavor. However, as technology evolves at an increasingly fast pace, so does the complexity of managing its resources. In modern air operations, planners have to deal with a highly changing environment influenced by enemy air defenses, weather forecasts, among many other factors, demanding much effort to handle the great number of constraints and uncertainties presented by them. As a result, a number of decision-support systems have emerged attempting to facilitate the planning of air warfare operations. These systems usually rely on a wide variety of methodologies, which sometimes present a challenge in themselves when it comes to assessing the feasibility and effectiveness of the produced plans. Computer simulations are a practical way of providing this assessment, usually by running the resulting plans multiple times and checking the results against key criteria. Yet, establishing the right criteria, properly accounting for the “fog of war,” and avoiding impractical simulation run times and costs are still major challenges. This paper addresses such challenges by proposing the development of a decisionsupport framework that combines ontology-based agile knowledge and a simulation-based mission planning methodology that accounts for the inherent uncertainties that air operations face. We avoid costly computation times required by simulationintensive course-of-action analyzers by initially pruning the solution space through ontological reasoning. Moreover, the approach complies with the Effects-Based Approach to Operations, having a clear correspondence of processes with it. The explanations are focused on a specific scenario concerning intelligence, surveillance, and reconnaissance operations. Keywords—ontologies; effects-based planning; modeling and simulation; semantic matchmaking
F TURNOFF DISTRIBUTION IN THE GALACTIC HALO USING GLOBULAR CLUSTERS AS PROXIES

F turnoff stars are important tools for studying Galactic halo substructure because they are plentiful, luminous, and can be easily selected by their photometric colors from large surveys such as the Sloan Digital Sky Survey (SDSS). We describe the absolute magnitude distribution of color-selected F turnoff stars, as measured from SDSS data, for 11 globular clusters in the Milky Way halo. We find that the Mg distribution of turnoff stars is intrinsically the same for all clusters studied, and is well fit by two half-Gaussian functions, centered at μ = 4.18, with a bright-side σ = 0.36, and with a faint-side σ = 0.76. However, the color errors and detection efficiencies cause the observed σ of the faint-side Gaussian to change with magnitude due to contamination from redder main-sequence stars (40% at 21st magnitude). We present a function that will correct for this magnitude-dependent change in selected stellar populations, when calculating stellar density from color-selected turnoff stars. We also present a consistent set of distances, ages, and metallicities for 11 clusters in the SDSS Data Release 7. We calculate a linear correction function to Padova isochrones so that they are consistent with SDSS globular cluster data from previous papers. We show that our cluster population falls along the Milky Way age–metallicity relationship (AMR), and further find that isochrones for stellar populations on the AMR have very similar turnoffs; increasing metallicity and decreasing age conspire to produce similar turnoff magnitudes and colors for all old clusters that lie on the AMR.
Elucidating the Interacting Domains of Chandipura Virus Nucleocapsid Protein

The nucleocapsid (N) protein of Chandipura virus (CHPV) plays a crucial role in viral life cycle, besides being an important structural component of the virion through proper organization of its interactions with other viral proteins. In a recent study, the authors had mapped the associations among CHPV proteins and shown that N protein interacts with four of the viral proteins: N, phosphoprotein (P), matrix protein (M), and glycoprotein (G). The present study aimed to distinguish the regions of CHPV N protein responsible for its interactions with other viral proteins. In this direction, we have generated the structure of CHPV N protein by homology modeling using SWISS-MODEL workspace and Accelrys Discovery Studio client 2.55 and mapped the domains of N protein using PiSQRD. The interactions of N protein fragments with other proteins were determined by ZDOCK rigid-body docking method and validated by yeast two-hybrid and ELISA. The study revealed a unique binding site, comprising of amino acids 1–30 at the N terminus of the nucleocapsid protein (N1) that is instrumental in its interactions with N, P, M, and G proteins. It was also observed that N2 associates with N and G proteins while N3 interacts with N, P, and M proteins.
Robust nonlinear speed control of PM synchronous motor using boundary layer integral sliding mode control technique

A digital signal processor (DSP)-based robust nonlinear speed control of a permanent magnet synchronous motor (PMSM) is presented. A quasi-linearized and decoupled model including the influence of parameter variations and speed measurement error on the input-output feedback linearization of a PMSM is derived. Based on this model, a boundary layer integral sliding mode controller is designed and compared to a feedback linearization-based controller that uses proportional plus derivative (PD) controller in the outer loop. To show the validity of the proposed control scheme, DSP-based experimental works are carried out and compared with the conventional control scheme.
Automatic Semantic Causal Map Integration

Causal map integration is helpful to broaden group member’s eyesight and sheds insight on the detection of overall group’s cognition tendencies. However the existing causal map integration approaches are either based on human intervention mechanism that is criticized with researcher bias, or based on syntactic mechanism that lacks of semantic. In order to improve the current causal map integration methodology and practice, this study proposes the conceptualization and formalization of an innovative causal map integration approach, automatic semantic causal map integration, grounded on the Sowa’s Conceptual Graph Theory and Kosko’s Fuzzy Knowledge Combination Theory. The system prototype with an example is also illustrated.
BUILDING USER TASK SPACE BY MINING TEMPORALLY PROXIMATE DESKTOP ACTIONS

Awareness of the user's current context, that is, the task the user resides in, can allow for various ways of supporting their work. In this article we present a novel approach for mining user's regular tasks on the basis of temporal proximity of users’ desktop actions without user intervention in a completely automatic, unobtrusive, and unsupervised manner. The proposed method is based on time-based clustering of a user's desktop actions and, in contrast to previous approaches, it does not enforce fixed time constraints on the mined actions, and typical transition times, when they exist, emerge from the logged activity data for that specific user. The performance of our technique was evaluated on a large data set of 724 days of desktop work by five knowledge workers. The results showed that our approach performed very well and was able to cluster those temporally proximate user actions that commonly used fix time window techniques fail to deal with. Notably, the main improvement is in the recall of the tasks, where our approach recalled 10.18% more actions than the predefined time window technique.
A Bayesian Approach for One-Shot Device Testing With Exponential Lifetimes Under Competing Risks

This paper considers a competing risk model for a one-shot device testing analysis under an accelerated life test setting. Due to the consideration of competing risks, the joint posterior distribution becomes quite complicated. The Metropolis-Hastings sampling method is used for the estimation of the posterior means of the variables of interest. A simulation study is carried out to assess the Bayesian approach with different priors, and also to compare it with the EM algorithm for maximum likelihood estimation. Finally, an example from a tumorigenicity experiment is presented.
CaRuby-Nano: a novel high affinity calcium probe for dual color imaging

The great demand for long-wavelength and high signal-to-noise Ca2+ indicators has led us to develop CaRuby-Nano, a new functionalizable red calcium indicator with nanomolar affinity for use in cell biology and neuroscience research. In addition, we generated CaRuby-Nano dextran conjugates and an AM-ester variant for bulk loading of tissue. We tested the new indicator using in vitro and in vivo experiments demonstrating the high sensitivity of CaRuby-Nano as well as its power in dual color imaging experiments. DOI: http://dx.doi. org/10.7554/eLife.05808. 001
Content-based image retrieval by interest-point matching and geometric hashing

This paper presents a content-based image retrieval technique based on interest points matching and geometric hashing. We estimate points with significant luminance variations as interest points. A small region around the interest point is located as an image patch. Low-level features are extracted to describe each image patch. To provide geometric invariant image matching, we index the image patches into a 2-D hash table by geometric hashing technique. Thus, the matching is invariant to global and local geometric transforms. In addition, since we use the image patch to capture the local information, the indexing can effectively handle partial matching. We formulate a matching criterion by weighted voting technique to incorporate the spatial interrelationship into consideration. We have performed a series of experiments to confirm the effectiveness of our method. Images are globally transformed and locally manipulated to examine the efficiency of our indexing scheme. Experimental results indicate satisfactory retrieval in the case of partial matching and geometric transformation.
Recent Advances in Synthetic Methods to Prepare Graphene Oxide

: This article reviews most essential ongoing advances in engineered strategies to create graphene oxide through wet science. In such methods, graphene sheets functionalized with various oxide gatherings: hydroxyl, carboxyl, epoxide, peroxide and ketone. Brodie-Staudenmaier-Tours-Hummers, Modified Hummers and Improved Hummers methods are discussed. The influence of synthesis on the graphene oxide structure is discussed. Physical - Chemical characterization such as Raman Spectroscopy and Fourier-transform infrared spectroscopy (FTIR) is additionally examined toward the end of article.
Deletion of the p66Shc longevity gene reduces systemic and tissue oxidative stress, vascular cell apoptosis, and early atherogenesis in mice fed a high-fat diet

Several experimental and clinical studies have shown that oxidized low-density lipoprotein and oxidation-sensitive mechanisms are central in the pathogenesis of vascular dysfunction and atherogenesis. Here, we have used p66Shc−/− and WT mice to investigate the effects of high-fat diet on both systemic and tissue oxidative stress and the development of early vascular lesions. To date, the p66Shc−/− mouse is the unique genetic model of increased resistance to oxidative stress and prolonged life span in mammals. Computer-assisted image analysis revealed that chronic 21% high-fat treatment increased the aortic cumulative early lesion area by ≈21% in WT mice and only by 3% in p66Shc−/− mice. Early lesions from p66Shc−/− mice had less content of macrophage-derived foam cells and apoptotic vascular cells, in comparison to the WT. Furthermore, in p66Shc−/− mice, but not WT mice, we found a significant reduction of systemic and tissue oxidative stress (assessed by isoprostanes, plasma low-density lipoprotein oxidizability, and the formation of arterial oxidation-specific epitopes). These results support the concept that p66Shc−/− may play a pivotal role in controlling systemic oxidative stress and vascular diseases. Therefore, p66Shc might represent a molecular target for therapies against vascular diseases.
Tumour markers in breast carcinoma correlate with grade rather than with invasiveness

Ductal breast carcinoma in situ (DCIS) is regarded as a precursor to invasive breast cancer. The progression from in situ to invasive cancer is however little understood. We compared some tumour markers in invasive and in situ breast carcinomas trying to find steps in this progression. We designed a semi-experimental setting and compared histopathological grading and tumour marker expression in pure DCIS (n = 194), small invasive lesions (n = 127) and lesions with both an invasive and in situ component (n = 305). Grading was done according to the Elston–Ellis and EORTC classification systems, respectively. Immunohistochemical staining was conducted for p53, c-erbB-2, Ki-67, ER, PR, bcl-2 and angiogenesis. All markers correlated with grade rather than with invasiveness. No marker was clearly associated with the progression from in situ to invasiveness. The expression of tumour markers was almost identical in the 2 components of mixed lesions. DCIS as a group showed a more ‘malignant picture’ than invasive cancer according to the markers, probably, due to a higher proportion of poorly differentiated lesions. The step between in situ and invasive cancer seems to occur independently of tumour grade. The results suggest that well-differentiated DCIS progress to well-differentiated invasive cancer and poorly differentiated DCIS progress to poorly differentiated invasive cancer. © 2001 Cancer Research Campaign http://www.bjcancer. com
Investigating the Role of Tbx4 in the Female Germline in Mice1

ABSTRACT Normal development of germ cells is essential for fertility and mammalian reproduction. Although abnormal development of oocytes or follicles may lead to primary ovarian insufficiency (POI), a disorder that causes infertility in 1% of women less than 40 yr of age, the genes and signaling pathways activated in POI are not as yet fully elucidated. Tbx4, a member of the T-box family of transcription factors, is expressed in embryonic germ cells and postnatal oocytes at all stages of folliculogenesis. To investigate the requirement for Tbx4 in the germline, we analyzed germ cell development in the absence of Tbx4. We show that primordial germ cells (PGCs) are reduced in Tbx4 homozygous null (Tbx4−/−) embryos at Embryonic Day (E) 10.0. Tbx4−/− embryos die by E10.5; to study later time points in vitro, a tamoxifen-inducible estrogen receptor Cre recombinase was used to delete Tbx4 conditional mutant alleles. In addition, Gdf9cre and Zp3cre, two oocyte-specific Cre recombinases, were used to delete Tbx4 from postnatal primordial and primary follicles, respectively. We show that in vitro differentiation of the gonad into morphologically distinct testes and ovaries occurs normally starting at E11.5 when Tbx4 is deleted. In Gdf9cre; Tbx4fl/− and Zp3cre; Tbx4fl/− adult females, primordial, primary, secondary, and antral follicles form, ovulation occurs, corpus luteum formation is normal, and the mice are fertile without any evidence of diminished ovarian reserve. Although postnatal deletion of Tbx4 in oocytes does not obviously impair fertility, it is possible that the reduction in PGCs observed in Tbx4 homozygous null mutant embryos could affect long-term fertility in adults.
Combined 3T Diffusion Tensor Tractography and 1H-MR Spectroscopy in Motor Neuron Disease

BACKGROUND AND PURPOSE: Diagnostic confidence in motor neuron disease may be improved by the use of advanced MR imaging techniques. Our aim was to assess the accuracy (sensitivity/specificity) and agreement of combined 1H-MR spectroscopy (proton MR spectroscopy) and diffusion tensor imaging (DTI) at 3T in patients with suspected motor neuron disease regarding detection of upper motor neuron (UMN) dysfunction. MATERIALS AND METHODS: Eighteen patients with suspected motor neuron disease were studied with MR spectroscopy/DTI and clinically rated according to the El-Escorial and ALSFRS-R scales. For MR spectroscopy, absolute N-acetylaspartate (NAA), choline (Cho), and phosphocreatine (PCr) concentrations and relative NAA/Cho and NAA/PCr ratios of corresponding volumes of interest within the primary motor cortex were calculated. For DTI, fractional anisotropy (FA) and mean diffusivity (MD) were measured bilaterally at the level of the precentral gyrus, corona radiata, internal capsule, cerebral peduncles, pons, and pyramid. FA and MD statistics were averaged on the corticospinal tracts (CSTs) as a whole to account for a region-independent analysis. RESULTS: MR spectroscopy indicated NAA reduction beyond the double SD of controls in 6 of 8 patients with clinical evidence for UMN involvement. Congruently, the mean FA of these patients was significantly lower in the upper 3 regions of measurements (P < .01). Overall, MR spectroscopy and DTI were concordant in all except 3 cases: 1 was correctly excluded from motor neuron disease by DTI (genetically proved Kennedy syndrome), whereas MR spectroscopy indicated CST involvement. MR spectroscopy and DTI each were false-positive for CST affection in 1 patient with lower motor neuron involvement only. CONCLUSION: Combined MR spectroscopy/DTI at 3T effectively adds to the detection of motor neuron disease with a high degree of accordance.
Breast Imaging: Screening and Evaluation

Breast imaging is a dynamic field, with recent and upcoming innovations aimed at improving the morbidity and mortality associated with breast disease, most importantly, breast cancer. It plays an integral role in the detection and management of breast disease, using a multimodality approach, including x-ray, ultrasound, magnetic resonance imaging, and nuclear medicine techniques. Breast imaging also encompasses image-guided procedures, performed both for the diagnosis and definitive management of breast abnormalities.