Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling of contrast agent kinetics in the lung using T1‐weighted dynamic contrast‐enhanced MRI

Assessment of perfusion and capillary permeability is important in both malignant and nonmalignant lung disease. Kinetic modeling of T1‐weighted dynamic contrast‐enhanced MRI (DCE‐MRI) data may provide such an assessment. This study establishes the feasibility and interrelationship of kinetic modeling approaches designed to estimate microvascular properties in malignant and nonmalignant tissues of the lung. DCE‐MRI data were acquired using a low molecular weight contrast agent with 4‐sec temporal resolution in lung cancer patients. A model‐free parameterization and three kinetic models of increasing complexity, each related to the classical Kety model, were applied. Comparison of an extended Kety model and the adiabatic approximation to the tissue homogeneity (AATH) model using Akaike's Information Criterion suggested that in most cases the best description of the lung tumor data is obtained using the AATH model. In the normal lung parenchyma the temporal resolution was insufficient to separate effects of flow and contrast agent leakage and in this case the extended Kety model yielded the best fit to the data. Magn Reson Med, 2009. © 2009 Wiley‐Liss, Inc.
Economic evaluations of Internet interventions for mental health: a systematic review

Background. Internet interventions are assumed to be cost-effective. However, it is unclear how strong this evidence is, and what the quality of this evidence is. Method. A comprehensive literature search (1990–2014) in Medline, EMBASE, the Cochrane Central Register of Controlled Trials, NHS Economic Evaluations Database, NHS Health Technology Assessment Database, Office of Health Economics Evaluations Database, Compendex and Inspec was conducted. We included economic evaluations alongside randomized controlled trials of Internet interventions for a range of mental health symptoms compared to a control group, consisting of a psychological or pharmaceutical intervention, treatment-as-usual (TAU), wait-list or an attention control group. Results. Of the 6587 abstracts identified, 16 papers met the inclusion criteria. Nine studies featured a societal perspective. Results demonstrated that guided Internet interventions for depression, anxiety, smoking cessation and alcohol consumption had favourable probabilities of being more cost-effective when compared to wait-list, TAU, group cognitive behaviour therapy (CBGT), attention control, telephone counselling or unguided Internet CBT. Unguided Internet interventions for suicide prevention, depression and smoking cessation demonstrated cost-effectiveness compared to TAU or attention control. In general, results from cost-utility analyses using more generic health outcomes (quality of life) were less favourable for unguided Internet interventions. Most studies adhered reasonably to economic guidelines. Conclusions. Results of guided Internet interventions being cost-effective are promising with most studies adhering to publication standards, but more economic evaluations are needed in order to determine cost-effectiveness of Internet interventions compared to the most cost-effective treatment currently available.
Sports Video Classification from Multimodal Information Using Deep Neural Networks

The work presents a methodology for classification of sports videos using both audio and visual information by applying deep learning algorithms. We show a methodology to combine multiple deep learning architectures through higher layers. Our method learns two separate models trained on audio and visual part of the data. We have trained the model for the audio part of the multi-media input using two stacked layers of CRBMs forming a CDBN. We also train two layered ISA network to extract features from video part of the data. We then train deep stacked autoen-coder over both audio and visual features with discriminative fine tuning. Our results show that by combining both audio and visual features we get better accuracy as compared to single type of features.
Vesicular glutamate transporters define two sets of glutamatergic afferents to the somatosensory thalamus and two thalamocortical projections in the mouse

The ventral posterior nucleus of the thalamus (VP) receives two major sets of excitatory inputs, one from the ascending somatosensory pathways originating in the dorsal horn, dorsal column nuclei, and trigeminal nuclei, and the other originating from the cerebral cortex. Both systems use glutamate as neurotransmitter, as do the thalamocortical axons relaying somatosensory information from the VP to the primary somatosensory cortex (SI). The synapses formed by these projection systems differ anatomically, physiologically, and in their capacity for short‐term synaptic plasticity. Glutamate uptake into synaptic vesicles and its release at central synapses depend on two isoforms of vesicular glutamate transporters, VGluT1 and VGluT2. Despite ample evidence of their complementary distribution, some instances exist of co‐localization in the same brain areas or at the same synapses. In the thalamus, the two transcripts coexist in cells of the VP and other nuclei but not in the posterior or intralaminar nuclei. We show that the two isoforms are completely segregated at VP synapses, despite their widespread expression throughout the dorsal and ventral thalamus. We present immunocytochemical, ultrastructural, gene expression, and connectional evidence that VGluT1 in the VP is only found at corticothalamic synapses, whereas VGluT2 is only found at terminals made by axons originating in the spinal cord and brainstem. By contrast, the two VGluT isoforms are co‐localized in thalamocortical axon terminals targeting layer IV, but not in those targeting layer I, suggesting the presence of two distinct projection systems related to the core/matrix pattern of organization of thalamocortical connectivity described in other mammals. J. Comp. Neurol. 507:1258–1276, 2008. © 2008 Wiley‐Liss, Inc.
Semiautomatic Domain Model Building from Text-Data

Our research is focused on semiautomatic domain model building from texts written in a natural language. The paper deals with defining the scope of the work and describes approaches of domain model creation and its representation. We describe the context of natural language processing focused on selected frequently solved tasks in this discipline and list some freely available tools suitable for text processing at the semantic level. We introduce appropriate tools and design methods to achieve determined goals. At the end of the paper, an experiment is conducted on which the successes of the implemented methods is verified, and suggestions and considerations for further development are presented.
BCM Search Launcher--an integrated interface to molecular biology data base search and analysis services available on the World Wide Web.

The BCM Search Launcher is an integrated set of World Wide Web (WWW) pages that organize molecular biology-related search and analysis services available on the WWW by function, and provide a single point of entry for related searches. The Protein Sequence Search Page, for example, provides a single sequence entry form for submitting sequences to WWW servers that offer remote access to a variety of different protein sequence search tools, including BLAST, FASTA, Smith-Waterman, BEAUTY, PROSITE, and BLOCKS searches. Other Launch pages provide access to (1) nucleic acid sequence searches, (2) multiple and pair-wise sequence alignments, (3) gene feature searches, (4) protein secondary structure prediction, and (5) miscellaneous sequence utilities (e.g., six-frame translation). The BCM Search Launcher also provides a mechanism to extend the utility of other WWW services by adding supplementary hypertext links to results returned by remote servers. For example, links to the NCBI's Entrez data base and to the Sequence Retrieval System (SRS) are added to search results returned by the NCBI's WWW BLAST server. These links provide easy access to auxiliary information, such as Medline abstracts, that can be extremely helpful when analyzing BLAST data base hits. For new or infrequent users of sequence data base search tools, we have preset the default search parameters to provide the most informative first-pass sequence analysis possible. We have also developed a batch client interface for Unix and Macintosh computers that allows multiple input sequences to be searched automatically as a background task, with the results returned as individual HTML documents directly to the user's system. The BCM Search Launcher and batch client are available on the WWW at URL http:@gc.bcm. tmc.edu:8088/search-launcher.html.
A Formal Semantics for Object Model Diagrams

Informal software development techniques, such as the object modeling technique (OMT), provide the user with easy to understand graphical notations for expressing a wide variety of concepts central to the presentation of software requirements. OMT combines three complementary diagramming notations for documenting requirements: object models, dynamic models, and functional models. OMT is a useful organizational tool in the requirements analysis and system design processes. Currently, the lack of formality in OMT prevents the evaluation of completeness, consistency, and content in requirements and design specifications. A formal method is a mathematical approach to software development that begins with the construction of a formal specification describing the system under development. However, constructing a formal specification directly from a prose description of requirements can be challenging. The paper presents a formal semantics for the OMT object model notations, where an object model provides the basis for the architecture of an object oriented system. A method for deriving modular algebraic specifications directly from object model diagrams is described. The formalization of object models contributes to a mathematical basis for deriving system designs. >
Riemannian Optimal System Identification Algorithm for Linear MIMO Systems

In this letter, a novel optimization method for the data-driven local coordinates approach to a prediction error method, which is one of system identification methods, is developed. In the proposed method, parameters of system matrices to be estimated are kept as their original forms of matrices whereas they are converted into a vector in the literature. Optimization with respect to the matrix variables can improve the computational efficiency. Furthermore, it is effective to equate input–output equivalent systems with each other since they attain the same value of the objective function. To this end, a Riemannian quotient manifold is introduced. The geometry of the proposed manifold is investigated and a novel Riemannian conjugate gradient method on the manifold is provided. Numerical experiments show that the difference of the proposed Riemannian conjugate gradient method from Euclidean one greatly improves the efficiency of the algorithm.
Scientific publication recommendations based on collaborative citation networks

To learn about the state of the art for a research project, researchers must conduct a literature survey by searching for, collecting, and reading related scientific articles. Popular search systems, online digital libraries, and Web of Science (WoS) sources such as IEEE Explorer, ACM, SpringerLink, and Google Scholar typically return results or articles that are similar to keywords in the user's query. Some digital libraries also include content-based recommenders that suggest papers similar to one the user likes based on the contents of paper, i.e., the keywords it contains. In this work, we present a recommender module that suggests papers to users based on the seed paper's Citation Network. This work takes into account the combination of the co-citation and co-reference factors to improve algorithm's effectiveness. We applied and improved the the CCIDF (Common Citation Inverse Document Frequency) algorithm used by the CiteSeer digital library. This improved algorithm, called CCIDF+, was evaluated using data collected from Microsoft Academic Search (MAS). Experimental results show that CCIDF+ outperforms CCIDF.
Micropattern array with gradient size (µPAGS) plastic surfaces fabricated by PDMS (polydimethylsiloxane) mold-based hot embossing technique for investigation of cell–surface interaction

Recently, it was found that the variations of physical environment significantly affect cell behaviors including cell proliferation, migration and differentiation. Through a plastic surface with controlled mechanical properties such as stiffness, one can change the orientation and migration of cells in a particular direction, thereby determining cell behaviors. In this study, we demonstrate a polydimethylsiloxane (PDMS) mold-based hot embossing technique for rapid, simple and low-cost replication of polystyrene (PS) surfaces having micropatterns. The PDMS mold was fabricated by UV-photolithography followed by PDMS casting; the elastomeric properties of PDMS enabled us to obtain conformal contact of the PDMS mold to a PS surface and to create high transcription quality of micropatterns on the PS surface. Two different types of circular micropillar and microwell arrays were successfully replicated on the PS surfaces based on the suggested technique. The micropatterns were designed to have various diameters (2–150 µm), spacings (2–160 µm) and heights (1.4, 2.4, 8.2 and 14.9 µm), so as to generate the gradient of physical properties on the surface. Experimental parametric studies indicated that (1) the embossing temperature became a critical processing parameter as the aspect ratio of micropattern increased and (2) the PDMS mold-based hot embossing could successfully replicate micropatterns, even having an aspect ratio of 2.7 for micropattern diameter of 6 µm, with an optimal processing condition (embossing pressure and temperature of 0.4 MPa and 130 °C, respectively) in this study. We carried out cell experiments with adipose-derived stem cells on the replicated PS surface with the height of 1.4 µm to investigate cellular behaviors in response to the micropattern array with gradient size. Cellular experiment results showed that the micropillar-arrayed surface improved cell proliferation as compared with the microwell-arrayed surface. We could also estimate the ranges of pattern sizes having the desired effects on the cellular behaviors.
Calcineurin Mediates the Gonadotropin-Releasing Hormone Effect on Expression of Both Subunits of the Follicle-Stimulating Hormone through Distinct Mechanisms

ABSTRACT Gonadotropin-releasing hormone (GnRH) regulates the expression of all three gonadotropin genes, encoding the common α subunit (αGSU) and hormone-specific β subunits, through the activation of several signal transduction pathways. We have shown that GnRH also upregulates calcineurin, and we hypothesized that calcineurin mediates the effects of GnRH on the transcription of the αGSU and follicle-stimulating hormone β (FSHβ) genes through two of its targets: nuclear factor of activated T cells (NFAT) and CREB-regulated transcription coactivator (TORC). We show that calcineurin is essential for GnRH-induced expression of both genes but that NFAT and TORC1 play quite distinct roles in activating each gene. GnRH induces calcineurin-dependent nuclear import of NFAT3, which activates the αGSU promoter, while TORC1 also mediates GnRH activation of this promoter, but not through CREB. GnRH initially stimulates the degradation of TORC1 but protects the N terminus of the newly synthesized protein to enhance its activity. Calcineurin induces Nur77 expression, likely via NFAT3, and Nur77 interacts synergistically with TORC1 and CREB to increase FSHβ promoter activity. Although TORC plays a role in the basal activity of the FSHβ promoter, it does not interact with phosphorylated CREB and probably does not play a major role in direct GnRH signaling to this gene. TORC may be part of an alternatively regulated pathway, possibly involving cross talk with other stimulatory hormones.
Crystal structure of tRNA‐guanine transglycosylase: RNA modification by base exchange.

tRNA‐guanine transglycosylases (TGT) are enzymes involved in the modification of the anticodon of tRNAs specific for Asn, Asp, His and Tyr, leading to the replacement of guanine‐34 at the wobble position by the hypermodified base queuine. In prokaryotes TGT catalyzes the exchange of guanine‐34 with the queuine (.)precursor 7‐aminomethyl‐7‐deazaguanine (preQ1). The crystal structure of TGT from Zymomonas mobilis was solved by multiple isomorphous replacement and refined to a crystallographic R‐factor of 19% at 1.85 angstrom resolution. The structure consists of an irregular (beta/alpha)8‐barrel with a tightly attached C‐terminal zinc‐containing subdomain. The packing of the subdomain against the barrel is mediated by an alpha‐helix, located close to the C‐terminus, which displaces the eighth helix of the barrel. The structure of TGT in complex with preQ1 suggests a binding mode for tRNA where the phosphate backbone interacts with the zinc subdomain and the U33G34U35 sequence is recognized by the barrel. This model for tRNA binding is consistent with a base exchange mechanism involving a covalent tRNA‐enzyme intermediate. This structure is the first example of a (beta/alpha)‐barrel protein interacting specifically with a nucleic acid.
Serum D-lactate: a useful diagnostic marker for acute appendicitis.

BACKGROUND/AIMS Acute appendicitis is the most common acute surgical infection seen in emergency department. The present study aims to evaluate the sensitivity, specificity, negative predictive value (NPV) and positive predictive value (PPV) of the serum D-lactate levels as a marker for the diagnosis of acute appendicitis. D-lactate is the stereoisomer of the mammalian L(+)-lactate, and is produced by indigenous bacteria (Escherichia coli, Klebsiella, Bacteroides, Lactobacillus) in the gastrointestinal tract. Once obstruction occurs, appendix is a good medium for bacterial proliferation, and ischemic injury leads to an increase in D-lactate levels. METHODOLOGY A total of thirty-two consecutive patients with the suspicion of acute appendicitis were prospectively included in the study. Patient characteristics, ultrasonography (US) and laboratory assessment including white blood cell (WBC), C-reactive protein (CRP), D-lactate and intraoperative findings, histology results, clinical outcome were evaluated. RESULTS WBC level above 10(9)/L had an accuracy of 66%, whereas a CRP level above 5 mg/L had an accuracy of 75%. We observed that when the D-lactate level was greater than 0.25 mmol/L in acute appendicitis, the specificity was 60%, the false negative rate was 25% and the accuracy was 90%. The false negative rate of CRP (67%) was higher than that of D-lactate levels (25%). Ultrasound had a sensitivity of 96%, specificity 40% and accuracy 87% in our study. CONCLUSIONS We found positive correlations between serum D-lactate levels and acute appendicitis and serum D-lactate had the lowest false negative rate among the other parameters. Therefore, we conclude that D-lactate might be a simple and reliable diagnostic marker for appendicitis.
Pain and pulmonary function in patients submitted to heart surgery via sternotomy.

OBJECTIVE To investigate the pulmonary function and pain in adult patients undergoing heart surgery via sternotomy and to verify possible correlations of these variables with the characteristics of the surgical procedure and hospital stay. METHODS A cross-sectional study was carried out of 70 individuals undergoing heart surgery. The lung function was assessed before and after surgery by spirometry and incentive spirometry. Details of the surgical procedure were studied and patients were followed up postoperatively using a visual analogue scale and design of the human body to evaluate pain. RESULTS The pulmonary function was significantly impaired in the postoperative compared to preoperative period (P <0.01). The pain was centered in the region of the sternotomy and persisted until at least the 5th postoperative day. There was a correlation between pain and the parameters of pulmonary function (forced expiratory volume in 1 second - percentage: r = -0.271, P <0.047; peak expiratory flow: r = 0.357, P <0.008; and maximum inspiratory volume: r = -0.293, P <0.032). There was no significant correlation between pain and other variables. CONCLUSION There was significant impairment of lung function which had not recovered completely on the 5th postoperative day. Pain was a complaint that persisted throughout the study period. The parameters of pulmonary function showed a significant relationship with pain. There was no correlation between pain and the characteristics of individuals, the surgical procedure or the length of hospital stay.
Polymorphisms in Phytophthora infestans: Four Mitochondrial Haplotypes Are Detected after PCR Amplification of DNA from Pure Cultures or from Host Lesions

ABSTRACT Four pairs of primers were designed for PCR amplification of known polymorphic regions of the mitochondrial genome of Phytophthora infestans. Digestion of the amplified products with restriction enzymes allows identification of previously identified haplotypes. Product P2 cut with MspI uniquely identifies haplotypes Ib and IIa, while types Ia and IIb are differentiated by digestion of product P4 with EcoRI. Digestion of products P1 and P3 gave results similar to that with digestion of P4, but amplification of these products was less robust. Thus, all four common haplotypes are identified by amplifying and digesting products P2 and P4. Identification of haplotypes was also possible from DNA extracted directly from small, late-blight lesions on both tomato and potato leaves, making isolation of the fungus unnecessary. A rapid and efficient method of monitoring changes in the pathogen population is facilitated. These PCR primers were also useful for differentiating other Phytophthora species.
Words Speak Louder than Action?: A Mixed-Methods Case Study.

The purpose of this mixed-methods case study was to examine the dynamic of Culturally Responsive Pedagogy (Gay, 2010) among nine secondary agriculture teachers in ethnically diverse schools. By reviewing the diversity of student enrollment in the agriculture programs, the participants were separated by two groups: diverse and non-diverse. A hybrid coding system of axial and magnitude allowed an unbiased panel to quantify the comments of each teacher. Results showed a difference in magnitude codes between comments provided by teachers with a diverse student enrollment and teachers with a non-diverse student enrollment. A large difference existed among four of the six characteristics of Culturally Relevant Pedagogy (CRP) and a medium difference existed in the latter two. Recommendations toward teacher home visits, implementation of curriculum modifications and diverse community engagement were directed toward the participants and practicing secondary teachers. Additional research and opportunities for CRP among teacher training institutions are also recommended.