Miracle-dz/UniFAR-FTUs huggingface dataset:
MBBC: Model-Based Bayesian Clustering

MBBC (Model-Based Bayesian Clustering) is developed to cluster lon- gitudinal microarray data using a Bayesian objective function. This algo- rithm has advantages over conventional methods in that it clusters genes based on temporal changes of gene expressions and searches for the op- timal number of clusters, as well as members of each cluster, without needing prior information. It is implemented using a stochastic search al- gorithm which avoids local maxima. Input and output for users is through R, and the main computational parts are written in C++ to achieve a high computational speed. MBBC.r and all other related files are available at http://www.phhp. ufl.edu/ yjoo/MBBC.
First-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Implications For Inflation

We confront predictions of inflationary scenarios with the Wilkinson Microwave Anisotropy Probe (WMAP) data, in combination with complementary small-scale cosmic microwave background (CMB) measurements and large-scale structure data. The WMAP detection of a large-angle anticorrelation in the temperature-polarization cross-power spectrum is the signature of adiabatic superhorizon fluctuations at the time of decoupling. The WMAP data are described by pure adiabatic fluctuations: we place an upper limit on a correlated cold dark matter (CDM) isocurvature component. Using WMAP constraints on the shape of the scalar power spectrum and the amplitude of gravity waves, we explore the parameter space of inflationary models that is consistent with the data. We place limits on inflationary models; for example, a minimally coupled λϕ4 is disfavored at more than 3 σ using WMAP data in combination with smaller scale CMB and large-scale structure survey data. The limits on the primordial parameters using WMAP data alone are ns(k0 = 0.002 Mpc-1) = 1.20, dns/d ln k = -0.077, A(k0 = 0.002 Mpc-1) = 0.71 (68% CL), and r(k0 = 0.002 Mpc-1) < 1.28 (95% CL).
A Recovery Method for Kinect-Like Depth Map Based on Color Image Segmentation

The original depth map captured by low-cost depth cameras such as Kinect suffers from problems of depth missing and noise, which restrict its further application. In this paper, we propose a novel recovery method of Kinect-like depth map utilizing the corresponding color image. The proposed method consists of two steps: hole-filling by image in painting and denoising by fast guided filter. Experiments show that our method gives satisfactory result.
Blindsight : a case study and implications

PART 1 1. Background 2. D.B. : Clinical history and early testing PART 2 3. Reaching for randomly allocated targets 4. 'Presence' versus 'Absence' 5. Visual acuity 6. Movement thresholds 7. Discrimination of orientation 8. 'Form' discrimination 9. Detection with slow rate of onset 10. The natural blind-spot (optic disc) within the scotoma 11. Left versus right eye 12. Detection of direction of contrast 13. 'Waves' 14. Matching between impaired and intact fields 15. Matching within the impaired field 16. Double associations between form and detection 17. Standard situation PART 3 Review of other cases 19. Status, issues, and implications References Author index Subject index
DRC Protocol for the Response Time Reduction in CAN based Distributed Embedded System

Controller Area Network operational characteristic supports periodic, sporadic and event based task behavior of distributed embedded system for industrial applications. CAN connect distributed Electronics Control Units (ECU) serially in the network and share measured data of different parameters and control information from the different places. System reliability and redundancy can be affected by changing the number of connected ECUs, Bus length, data rate, etc. In this paper proposed algorithm tries to improve reliability of CAN by changing data rates, according to the length of transmission line for message transmission in the network. Also, Data Rate Change DRC protocol improves temporal behavior of the system with small CPU overheads.
DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages

We have determined the DNA sequence of the bacteriophage P2 tail genes G and H, which code for polypeptides of 175 and 669 residues, respectively. Gene H probably codes for the distal part of the P2 tail fiber, since the deduced sequence of its product contains regions similar to tail fiber proteins from phages Mu, P1, lambda, K3, and T2. The similarities of the carboxy-terminal portions of the P2, Mu, ann P1 tail fiber proteins may explain the observation that these phages in general have the same host range. The P2 H gene product is similar to the products of both lambda open reading frame (ORF) 401 (stf, side tail fiber) and its downstream ORF, ORF 314. If 1 bp is inserted near the end of ORF 401, this reading frame becomes fused with ORF 314, creating an ORF that may represent the complete stf gene that encodes a 774-amino-acid-long side tail fiber protein. Thus, a frameshift mutation seems to be present in the common laboratory strain of lambda. Gene G of P2 probably codes for a protein required for assembly of the tail fibers of the virion. The entire G gene product is very similar to the products of genes U and U' of phage Mu; a region of these proteins is also found in the tail fiber assembly proteins of phages TuIa, TuIb, T4, and lambda. The similarities in the tail fiber genes of phages of different families provide evidence that illegitimate recombination occurs at previously unappreciated levels and that phages are taking advantage of the gene pool available to them to alter their host ranges under selective pressures.
Occupying Space in American Literature and Culture: Static Heroes, Social Movements and Empowerment

Introduction: Spatial and Ideological Occupations 1. Emptying Out the Premises: Static Heroes Reclaiming Space 2. Places of Eviction and Places of Self-Exemption: The Homeless in William Kennedy's Ironweed and Don DeLillo's Cosmopolis 3. Circling the Alien: Camp Logic in Austerlitz, Citizen 13660, and Lunar Braceros 2125-2148 4. IV - Between Border and Dwelling: The Divisibility of the Line in Frozen River and Welcome 5. From Bartleby to Occupy Wall Street: The Politics of Empty Spaces
Essential oil composition and antinociceptive activity of Thymus capitatus

Abstract Context: The essential oil (EO) from Thymus capitatus Hoff. et Link. (Lamiaceae) has been traditionally used for its medicinal properties, such as anti-inflammatory, analgesic, antioxidant and antimicrobial properties. Objective: Characterize the constituents from T. capitatus EO and further evaluate the antinociceptive activity by in vivo and in vitro procedures. Materials and methods: Gas chromatography–mass spectrometry was used to identify and quantify the constituents of the T. capitatus EO. The antinociceptive activity was evaluated in vivo by the glutamate-induced nociception model in male Swiss mice (25 g), at doses of 3, 6 and 12 mg/kg, 1 h before evaluation of the licking time response (0–15 min). The mechanism of T. capitatus EO (1–500 μg/mL) on the isolated nerve excitability of Wistar rat (300 g) was assessed by the single sucrose technique. Results and discussion: The EO of T. capitatus presented 33 components, mainly monoterpenes and sesquiterpenes, carvacrol (ca. 80%) was its major constituent. T. capitatus EO induced antinociception in orally treated mice (3, 6, and 12 mg/kg) reducing the licking time from control (100.3 ± 11.9 s) to 84.8 ± 12.2, 62.7. 6 ± 9.9, and 41.5 ± 12.7 s, respectively (n = 8; p < 0.05). Additionally, we have demonstrated that T. capitatus EO (500 μg/mL) decreased the compound action potential amplitude (VCAP) of about 80.0 ± 4.3% from control recordings (n = 4; p < 0.05). Such activity was presumably mediated through a voltage-gated Na+ channels. Conclusions: The present study demonstrated the antinociceptive activity of Thymus capitatus essential oil, which acts via peripheral nervous excitability blockade.
A Novel Therapeutic Strategy to Rescue the Immune Effector Function of Proteolytically Inactivated Cancer Therapeutic Antibodies

Primary and acquired resistance to anticancer antibody immunotherapies presents significant clinical challenges. Here, we demonstrate that proteolytic inactivation of cancer-targeting antibodies is an unappreciated contributor to cancer immune evasion, and the finding presents novel opportunities for therapeutic intervention. A single peptide bond cleavage in the IgG1 hinge impairs cancer cell killing due to structural derangement of the Fc region. Hinge-cleaved trastuzumab gradually accumulated on the surfaces of HER2-expressing cancer cell lines in vitro, and was greatly accelerated when the cells were engineered to express the potent bacterial IgG-degrading proteinase (IdeS). Similar to cancer-related matrix metalloproteinases (MMP), IdeS exposes a hinge neoepitope that we have developed an antibody, mAb2095-2, to specifically target the epitope. In in vitro studies, mAb2095-2 restored the lost antibody-dependent cell-mediated cytotoxicity functionality of cell-bound single-cleaved trastuzumab (scIgG-T). In vivo, mAb2095-2 rescued the impaired Fc-dependent tumor-suppressive activity of scIgG-T in a xenograft tumor model and restored the recruitment of immune effector cells into the tumor microenvironment. More importantly, an Fc-engineered proteinase-resistant version of mAb2095-2 rescued trastuzumab antitumor efficacy in a mouse tumor model with human cancer cells secreting IdeS, whereas trastuzumab alone showed significantly reduced antitumor activity in the same model. Consistently, an Fc-engineered proteinase-resistant version of trastuzumab also greatly improved antitumor efficacy in the xenograft tumor model. Taken together, these findings point to a novel cancer therapeutic strategy to rescue proteolytic damage of antibody effector function by an Fc-engineered mAb against the hinge neoepitope and to overcome cancer evasion of antibody immunity. Mol Cancer Ther; 14(3); 681–91. ©2014 AACR.
Insights into Langerhans cell function from Langerhans cell ablation models

Langerhans cells (LC) are the principal dendritic cell (DC) population in the epidermis of the skin. Owing to their prominent position at the environmental barrier, LC have long been considered to be prototypic sentinel DC. More recently, the precise role of LC in the initiation and control of cutaneous immune responses has become debatable. To elucidate their contribution to immune regulation in the skin, our laboratories have generated genetically modified mice in which LC can be followed in situ by expression of enhanced green fluorescent protein and can be either inducibly or constitutively depleted in vivo. This review highlights the similarities and differences between these mouse models, discusses the discovery and functional significance of Langerin+ dermal DC, and examines some recent data that help to shed light on LC function.
Deferoxamine Therapy in High-Ferritin Diabetes

Serum ferritin and diabetes control were evaluated in 18 White patients with poorly controlled type II (noninsulin-dependent) diabetes who had no known causes of iron-storage disorder. Serum ferritin levels were found to be elevated with normal serumiron and total iron-binding capacity in 9 of the 18 patients studied. Because excess iron, typified by hemochromatosis, is associated with diabetes, and diabetes has been shown to improve after lowering total-body iron load through repeat venesection, I investigated whether regulating elevated ferritin levels could facilitate diabetes control. Deferoxamine (DFO), a known specific chelator of iron, was used because of its capacity to correct excess iron stores. All 9 patients in the high-ferritin diabetic group and 7 of 9 diabetic control subjects with normal serum ferritin levels were given DFO (10 mg/kg i.v.) twice weekly. Diabetic control, fasting glucose, triglyceride, cholesterol, HbA1c, and serum ferritin levels were monitored. Data show that lowering elevated ferritin levels correlated well with diabetes control and improved fasting glucose, triglyceride, and HbA1c in 8 of 9 patients with high ferritin levels. Lowering normal ferritin levels had no effect on diabetes control or on any ofthe other parameters in the 7 control subjects. This study shows there is a need to study iron metabolism in poorly controlled diabetes and demonstrates the value of DFO in controlling high-ferritin diabetes.
Integer-encoded massively parallel processing of fast-learning fuzzy ARTMAP neural networks

In this paper we develop techniques that are suitable for the parallel implementation of Fuzzy ARTMAP networks. Speedup and learning performance results are provided for execution on a DECmpp/Sx-1208 parallel processor consisting of a DEC RISC Workstation Front-End and MasPar MP-1 Back-End with 8,192 processors. Experiments of the parallel implementation were conducted on the Letters benchmark database developed by Frey and Slate. The results indicate a speedup on the order of 1000-fold which allows combined training and testing time of under four minutes.
[An integrative review of drug utilization by the elderly in primary health care].

OBJECTIVE To identify knowledge produced about drug utilization by the elderly in the primary health care context from 2006 to 2014. METHOD An integrative review of the PubMed, LILACS, BDENF, and SCOPUS databases, including qualitative research papers in Portuguese, English, and Spanish. It excluded papers with insufficient information regarding the methodological description. RESULTS Search found 633 papers that, after being subjected to the inclusion and exclusion criteria, made up a corpusof 76 publications, mostly in English and produced in the United States, England, and Brazil. Results were pooled in eight thematic categories showing the current trend of drug use in the elderly, notably the use of psychotropics, polypharmacy, the prevention of adverse events, and adoption of technologies to facilitate drug management by the elderly. Studies point out the risks posed to the elderly as a consequence of changes in metabolism and simultaneous use of several drugs. CONCLUSION There is strong concern about improving communications between professionals and the elderly in order to promote an exchange of information about therapy, and in this way prevent major health complications in this population.
Towards a new health prognostics method for inverters: Power SiC-GTO failures and its precursors

A device-based health conditions monitoring and diagnosis method for inverters is present. In the inverter, SiCGTO (Gate-Turn-Off Thyristor) is considered as the key device to achieve pulse-width modulation. So the performance degradation of SiC-GTO device induced by interface-states is critical for the health conditions of inverters. In the research, key electrical parameters, including the forward blocking voltage and the dynamic switch characteristics, are evaluated for SiC-GTO device with elevated interface-states density. Results indicate that the forward blocking voltage, turn-on/off speed and gate drive current can be used as precursors for the failure. Based on further study, a test structure and an indirect precursor are developed for feasibly application on health prognostics algorithms (data-driven or physics-based) of failure with interface-states accumulation as a mechanism.
Strategic Social Media Management and Public Relations Leadership: Insights from Industry Leaders

To understand how social media are reshaping the public relations profession, it is vital to examine the perceptions of public relations leaders who are typically involved in decisions integrating social media into communication programs. This study explored how social media use has affected leadership behaviors of 43 public relations leaders in the United States. Four key dimensions emerged from interview results on how public relations leaders can strategically use social media to establish leadership roles: exhibiting expert power, gaining decision power by demonstrating tangible outcomes, displaying leadership vision in social media use, and establishing leadership among peers. This study made theoretical contributions to the area of public relations leadership by developing three mechanisms for public relations managers to build their leadership through developing leadership capabilities in strategic social media management, gaining expert power to exert upward influence, and paralleling relationship building with peer leaders from other organizational functions. Suggested future research directions included how public relations leaders’ engagement in social media management has affected the whole leadership structure within the organization and to what extent public relations leaders could influence the ethical use of social media or the issue of social media governance.
Development of anaplastic lymphoma kinase (ALK) inhibitors and molecular diagnosis in ALK rearrangement-positive lung cancer

The fusion of echinoderm microtubule-associated protein-like 4 with anaplastic lymphoma kinase (ALK) was identified as a transforming gene for lung cancer in 2007. This genetic rearrangement accounts for 2%–5% of non-small-cell lung cancer (NSCLC) cases, occurring predominantly in younger individuals with adenocarcinoma who are never- or light smokers. A small-molecule tyrosine-kinase inhibitor of ALK, crizotinib, was rapidly approved by the US Food and Drug Administration on the basis of its pronounced clinical activity in patients with ALK rearrangement-positive NSCLC. Next-generation ALK inhibitors, such as alectinib, LDK378, and AP26113, are also being developed in ongoing clinical trials. In addition, the improvement and validation of methods for the detection of ALK rearrangement in NSCLC patients will be key to the optimal clinical use of ALK inhibitors. We here summarize recent progress in the development of new ALK inhibitors and in the molecular diagnosis of ALK rearrangement-positive NSCLC.
Year-Round Shotgun Metagenomes Reveal Stable Microbial Communities in Agricultural Soils and Novel Ammonia Oxidizers Responding to Fertilization

ABSTRACT The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for a better understanding of nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points during 1 year from two depths (0 to 5 and 20 to 30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty loam) with similar cropping histories. Although the microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural aquatic ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed a less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (are more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. IMPORTANCE Even though the impact of agricultural management on the microbial community structure has been recognized, an understanding of the dynamics of individual microbial populations and what functions each population carries are limited. Yet, this information is important for a better understanding of nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here, we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic than their marine counterparts previously studied.
Seismic Resolution and Thin Bed Reflectivity Inversion

When it c omes to thin bed resolution, c onventional wisdom usually follows the c onclusions enunciated by Widess (1973). According to the Wide ss model (which consists of an isolated thin bed) the peak frequency of the s eismic response is higher than that of the wavelet; below 1/8th of a wavelength the seismic response bec omes the derivative of the wav elet and does not change shape with changing thickness. Ou r experience with spectral de composition has led to the surprising conclusion that the Wi dess model of thin bed response is a v ery special case that is very different from most combinations of reflection coefficients. When the reflection coefficients at the top and base of a th in bed are not exactly equal and opposite, a more general behavior i s observed where the peak frequency decreases as thickness decreases below the tuning frequency. This tells us that the seismic respons e is more sensitive to thin beds than thought previously. In fact, w e find that encoded in t he spectral decomposition of a seismic trace is information that exceeds the bandwidth of the ac tual seismic signal and allows us to make inferences about thin beds that ar e far thinner than classical limits of seismic resolution. Such knowledge can be used to remove the seis mic wavelet without magnifying noise and c an thus be used to produce high resolution reflectivity secti ons that are far superior to conventional seism ic sections in resolution and interpretability (Chopra et al 2006). Real data ex amples will illustrate how hi gh resolution reflectivity inversion yields an enormous amount of detail not only in terms of extra reflection cycles, but also the fault detail. Correlation with log curves provides the final confirmation that interpreters usually look for.