gebhart/patrepeval huggingface dataset:
Studies of <i>de novo</i> Purine Biosynthetic Complexes in Living Cells (2008)

Purines are synthesized in ten chemical steps catalyzed by six enzymes in eukaryotes. Studies in vitro have provided scant evidence for anticipated protein‐protein interactions that would enable substrate channeling and regulation of the metabolic flux. We have applied fluorescence microscopy to HeLa and human breast cancer cells and discovered that all six enzymes colocalize to form clusters in the cellular cytoplasm. The association and dissociation of these enzyme clusters can be regulated dynamically by changing the purine levels or by the addition of exogenous agents to the culture media. Collectively, the data provide strong evidence for the constitution of a multi‐enzyme complex, the purinosome, to carry out de novo purine biosynthesis in cells.
Large vocabulary continuous Mandarin speech recognition using finite state machine (2005)

The finite state transducer (FST), popularly used in the natural language processing (NLP) area to represent the grammar rules and the characteristics of a language, has been extensively used as the core in large vocabulary continuous speech recognition (LVCSR) in recent years. By means of FST, we can effectively compose the acoustic model, pronunciation lexicon, and language model to form a compact search space. In this paper, we present our approach to developing a LVCSR decoder using FST as the core. In addition, the traditional one-pass tree-copy search algorithm is also described for comparison in terms of speed, memory requirements and achieved character accuracy.
Pathway analysis of <i>Candida albicans</i> survival and virulence determinants in a murine infection model (2010)

One potentially rich source of possible targets for antifungal therapy are those Candida albicans genes deemed essential for growth under the standard culture (i.e., in vitro) conditions; however, these genes are largely unexplored as drug targets because essential genes are not experimentally amenable to conventional gene deletion and virulence studies. Using tetracycline-regulatable promoter-based conditional mutants, we investigated a murine model of candidiasis in which repressing essential genes in the host was achieved. By adding doxycycline to the drinking water starting 3 days prior to (dox - 3D) or 2 days post (dox + 2D) infection, the phenotypic consequences of temporal gene inactivation were assessed by monitoring animal survival and fungal burden in prophylaxis and acute infection settings. Of 177 selected conditional shut-off strains tested, the virulence of 102 was blocked under both repressing conditions, suggesting that the corresponding genes are essential for growth and survival in a murine host across early and established infection periods. Among these genes were those previously identified as antifungal drug targets (i.e., FKS1, ERG1, and ERG11), verifying that this methodology can be used to validate potential new targets. We also identify genes either conditionally essential or dispensable for in vitro growth but required for survival and virulence, including those in late stage ergosterol synthesis, or early steps in fatty acid or riboflavin biosynthesis. This study evaluates the role of essential genes with respect to pathogen virulence in a large-scale, systems biology context, and provides a general method for gene target validation and for uncovering unexpected antimicrobial targets.
A sealed high-repetition-rate TEA CO<sub>2</sub>laser (1978)

A compact atmospheric pressure CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> laser utilizing a double-discharge technique has been constructed and operated at repetition rates to 100 pulses/s. With the addition of small amounts of hydrogen and carbon monoxide to give a gas mixture of He:N <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> : CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> :CO:H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> = 69.3:11:15:4:0.7, sealed operational lifetimes exceeding <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2 \times 10^{6}</tex> pulses have been obtained. Operating in this mode, the output energy density is about 8-9 J/l at repetition frequencies of 30-40 pulses/s for input energy densities of 60-70 J/l. The operation of the sealed laser has been studied by means of mass spectroscopic measurements of the gas mixture. It has been determined that sealed operation is possible as long as the oxygen concentration is kept below 1-2 percent. It has also been found that the addition of small amounts of H <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> and CO will keep the oxygen concentration below 2 percent by reducing the CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> decomposition, allowing sealed operation. The experimental results are compared to the predictions of a theoretical model in which neutral and negative-ion processes have been included. The calculations indicate that when small amounts of oxygen or water are present in the discharge the negative-ion population is significantly increased and the ratio of negative-ions to electrons <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N_{n}/N_{e}</tex> can approach values near unity. These are the conditions under which discharge arcing was found to occur. The model also predicts that the dissociation equilibrium of the CO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> can be controlled by the addition of the above concentrations of hydrogen and CO.
ZeroShotCeres: Zero-Shot Relation Extraction from Semi-Structured Webpages (2020)

In many documents, such as semi-structured webpages, textual semantics are augmented with additional information conveyed using visual elements including layout, font size, and color. Prior work on information extraction from semi-structured websites has required learning an extraction model specific to a given template via either manually labeled or distantly supervised data from that template. In this work, we propose a solution for "zero-shot" open-domain relation extraction from webpages with a previously unseen template, including from websites with little overlap with existing sources of knowledge for distant supervision and websites in entirely new subject verticals. Our model uses a graph neural network-based approach to build a rich representation of text fields on a webpage and the relationships between them, enabling generalization to new templates. Experiments show this approach provides a 31% F1 gain over a baseline for zero-shot extraction in a new subject vertical.
Cotranslational assembly of myosin heavy chain in developing cultured skeletal muscle. (1987)

To examine how nascent myosin heavy chains associate with the cytoskeletons of developing muscle cells, we used pulse labeling, cell fractionation, and immunoprecipitation. More than 80% of nascent myosin heavy chains associate with the cytoskeleton. More than one-third of these nascent chains are not released by puromycin and/or RNase. The fraction of nascent heavy chains that resists release increases during development of muscle cells in culture. Treatment with cytochalasin D but not nocodazole decreases myosin heavy chain cotranslational assembly. These results indicate that (i) cotranslational assembly of myosin heavy chains is developmentally regulated, (ii) structures containing actin and not microtubules may mediate initial association of the heavy chains with the cytoskeleton, and (iii) the site of translation dictates where a significant fraction of the heavy chains will be inserted into the cytoskeleton.
Copy number changes of CRISP3 in oral squamous cell carcinoma (2011)

The aim of this study was to identify tumor suppressor genes (TSGs) in oral squamous cell carcinoma (OSCC) using whole-genome analysis of microarray technology and real-time quantitative polymerase chain reaction (QPCR). We applied whole-genome analysis of TSGs in the specimens from 3 patients of OSCC by microarray technology. A total of 11 genes, CRISP3, SCGB3A1, AGR2, PIP, C20orf114, TFF1, STATH, AZGP1, MUC7, DMBT1 and LOC389429, were found to be down-regulated, and 2, matrix metallopeptidase (MMP) 1 and MMP3, were found to be up-regulated in the 3 OSCC patients using microarray technology. In this study, we selected the CRISP3 gene. CRISP3 belongs to the cystein-rich secretary protein gene family in chromosome 6p12.3. CRISP3 has been found in the salivary gland, spleen and prostate gland and is a prominent biomarker in the gene expression of prostate cancer. Down-regulation of this gene was previously observed in OSCC. No studies examining the DNA copy number of CRISP3 in detail exist. We analyzed the DNA copy number of CRISP3 in 5 OSCC-derived cell lines (SAS, Ca9-22, KON, HSC2 and HSC4) and 60 OSCC tissues by real-time QPCR. The DNA copy number loss of CRISP3 was observed in 2 of the 5 OSCC-derived cell lines (SAS, HSC2) and in 24 of 60 patients (40.0%) using real-time QPCR. A significant statistical correlation between the copy number loss and gender and T classification was observed. These results indicate that the inactivation of CRISP3 is an early event in OSCC, since the T1/T2 classification is correlated with DNA copy number loss of CRISP3, whereas T3/T4 classification is not. We conclude that CRISP3 may be involved in the carcinogenesis of OSCC.
Fast color fiducial detection and dynamic workspace extension in video see-through self-tracking augmented reality (2002)

The registration problem is one of the major issues in augmented reality (AR). Fiducial tracking is gaining interest as a solution to this problem in video see-through AR because of the availability of digitized real scenes. There are several AR systems using fiducial tracking, but most of them operate in small desktop workspaces. It is difficult to apply them directly to large scale applications. The wide range of work distance and non-uniform lighting conditions make fiducial detection very difficult. Adding new fiducials requires off-line processing for measuring positions of new fiducials. We propose a fast and robust fiducial detection procedure with carefully designed color fiducials and noise analysis of digitized images. We also present a dynamic workspace extension method with on-line position determination of unknown features. We present a framework for applying AR to large scale applications.
A Retrospective on Race: The View from Long Island (2019)

In the more than thirty years that I worked as a law professor, most of those years at Touro Law Center on Long Island, I wrote about race and law on multiple occasions.Most of my articles were published in law reviews, but I did write at least four articles for the local newspaper, Newsday, as racial conflict surfaced here on Long Island.On the occasion of the 50 th anniversary of Brown v. Board of Education in 2004, I offered a critique of the rhetorical device-diversity, and inclusion --used to deflect or defuse opposition to affirmative action. 1 In 2005, I wrote about the forcible eviction of undocumented immigrants from a housing in Farmingville and condemnation of a housing complex and eviction of its elderly and disabled residents. 2 In 2007, I wrote about the arrest and conviction of a black man who shot a young white man who was part of a mob in front of his house hurling racial epithets at his family and threatening his son. 3 Last, but not least, in 2008, I wrote about the persistence of racial categories even as public discourse announced the emergence of a postracial society after Barack Obama was elected President of the United States. 4 I am proud and grateful that the editors of the Journal of Race, Gender and Ethnicity have agreed to reprint these Op-Eds.I think of this essay as a retrospective examination of my journey as a law professor and a meditation on racism as a local and national phenomenon.Each of these articles is preceded by an annotation which updates my comments and analysis in light of recent developments in the United States and Long Island.The organization of the articles is not chronological but topical.I thought it might be interesting to juxtapose past articles with short introductions that provides some historical context and comments on current political rhetoric, including the "Make America Great Again" slogan (which many have interpreted to mean "make America white again"), 5 that propelled Donald Trump's political ascendancy.
Wide Variety of Point Mutations in the H Gene of Bombay and Para-Bombay Individuals That Inactivate H Enzyme (1997)

The H genes, encoding an alpha1,2fucosyltransferase, which defines blood groups with the H structure, of four Bombay and 13 para-Bombay Japanese individuals were analyzed for mutations. Four Bombay individuals were homologous for the same null H allele, which is inactivated by a single nonsense mutation at position 695 from G to A (G695A), resulting in termination of H gene translation. The allele inactivated by the G695A was designated h1. The other 13 para-Bombay individuals possessed a trace amount of H antigens on erythrocytes regardless of their secretor status. Sequence analysis of their H genes showed four additional inactivated H gene alleles, h2, h3, h4, and h5. The h2 allele possesed a single base deletion at position 990 G (990-del). The h3 and h4 alleles possessed a single missense mutation, T721C, which changes Tyr 241 to His, and G442T, which changes Asp148 to Tyr, respectively. The h5 allele possessed two missense mutations, T460C (Tyr154to His) and G1042A (Glu348to Lys). The h2, h3, h4, and h5 enzymes directed by these alleles were not fully inactivated by the deletion and the missense mutations expressing some residual enzyme activity resulting in synthesis of H antigen on erythrocytes. Thirteen para-Bombay individuals whose erythrocytes retained a trace amount of H antigen were determined to be heterozygous or homozygous for at least one of h2, h3, h4, or h5 alleles. This clarified that the levels (null to trace amount) of H antigen expression on erythrocytes of Bombay and para-Bombay individuals are determined solely by H enzyme activity. These mutations found in the Japanese H alleles differ from a nonsense mutation found in the Indonesian population. To determine the roles of the H, Se, and Le genes in the expression of H antigen in secretions and Lewis blood group antigen on erythrocytes, the Lewis and secretor genes were also examined in these Bombay and para-Bombay individuals. The Lewis blood group phenotype, Le(alpha- b+), was determined by the combinatorial activity of two fucosyltransferases, the Lewis enzyme and the secretor enzyme, and the secretor status was solely determined by the secretor enzyme activity, not by H enzyme activity. Bombay individuals were confirmed to be homozygous for the inactivated H and Se genes. As expected from the very low frequency of Bombay and para-Bombay individuals in the population, ie, approximately one in two or 300,000, the H gene mutations were found to be very variable, unlike the cases of the point mutations in the other glycosyltransferase genes; the ABO genes, the Lewis gene, and the secretor gene.
Colorectal cancers soon after colonoscopy: a pooled multicohort analysis (2013)

Despite recent colonoscopy with intent to remove all neoplasia, CRC will occasionally be diagnosed. These cancers primarily seem to represent lesions that were missed or incompletely removed at the prior colonoscopy and might be avoided by increased emphasis on identifying and completely removing all neoplastic lesions at colonoscopy.
Topological Mapping from Image Sequences (2006)

An autonomous agent should be able to traverse a new environment and construct a topological representation of what it has seen. We present two new semi-supervised learning techniques which allow us to segment extended sensor (image) sequences into a topological map by clustering on low-dimensional manifolds in sensor space. The general approach is based on outlier detection in manifold space, closely related to spectral clustering. The first technique fixes the s parameter of the affinity matrix, the second allows each cluster to optimize for a different s. In both cases manifold clusters can be associated with the user’s conceptual map by labelling one image per cluster. We demonstrate these techniques for indoor and outdoor sequences.
Raised cardiac troponin T levels in patients without acute coronary syndrome (2007)

Patients without ACS but with raised levels of troponin T comprised 38% of all hospitalised patients found to have raised troponin T. These patients had worse in-hospital and 6-month outcome than those having ACS with raised levels of troponin T.
Three-dimensional data input by tablet (1974)

A large-area multiple-pen tablet system for three-dimensional data input is described. The large tablet area provides space for simultaneous use of several views of the three-dimensional object being digitized. The multiple pens enable the user to indicate a single point simultaneously in two such views, thus defining the three-dimensional position of the point. Five significant techniques are outlined. First, the large-area digitizing surface with multiple pens has proved to be an instrument very different from the more familiar single-pen small tablets. Second, a pair of two-dimensional positions is converted into a four-dimensional space and then back to three dimensions. Third, the specification of view areas, viewing directions, view positions, and coordinate axis is accomplished by giving examples directly in the viewing space rather than by specifying abstract viewing parameters. Fourth, an attitude about coordinate conversion using the inverse of a basis matrix is used throughout which automatically compensates for any tilt in the views on the tablet surface and any nonperpendicularity of the tablet axis. Fifth, the mathematics of converting from pairs of perspective views or pairs of photographs, while not new, is formulated simply in an appendix with several examples.
Downregulation of carbon monoxide as well as nitric oxide contributes to peripheral chemoreflex hypersensitivity in heart failure rabbits (2008)

Peripheral chemoreflex sensitivity is potentiated in clinical and experimental chronic heart failure (CHF). Downregulation of nitric oxide (NO) synthase (NOS) in the carotid body (CB) is involved in this effect. However, it remains poorly understood whether carbon monoxide (CO) also contributes to the altered peripheral chemoreflex sensitivity in CHF. This work highlights the effect of NO and CO on renal sympathetic nerve activity (RSNA) in response to graded hypoxia in conscious rabbits. Renal sympathetic nerve responses to graded hypoxia were enhanced in CHF rabbits compared with sham rabbits. The NO donor S-nitroso-N-acetylpenicillamine (SNAP, 1.2 microg x kg(-1) x min(-1)) and the CO-releasing molecule tricarbonyldichlororuthenium (II) dimer {[Ru(CO)(3)Cl(2)](2), 3.0 microg x kg(-1) x min(-1)} each attenuated hypoxia-induced RSNA increases in CHF rabbits (P < 0.05), but the degree of attenuation of RSNA induced by SNAP or [Ru(CO)(3)Cl(2)](2) was smaller than that induced by SNAP + [Ru(CO)(3)Cl(2)](2). Conversely, treatment with the NOS inhibitor N(omega)-nitro-L-arginine (30 mg/kg) + the heme oxygenase (HO) inhibitor Cr (III) mesoporphyrin IX chloride (0.5 mg/kg) augmented the renal sympathetic nerve response to hypoxia in sham rabbits to a greater extent than treatment with either inhibitor alone and was without effect in CHF rabbits. In addition, using immunostaining and Western blot analyses, we found that expression of neuronal NOS, endothelial NOS, and HO-2 protein (expressed as the ratio of NOS or HO-2 expression to beta-tubulin protein expression) was lower in CBs from CHF (0.19 +/- 0.04, 0.17 +/- 0.06, and 0.15 +/- 0.02, respectively) than sham (0.63 +/- 0.04, 0.56 +/- 0.06, and 0.27 +/- 0.03, respectively) rabbits (P < 0.05). These results suggest that a deficiency of NO and CO in the CBs augments peripheral chemoreflex sensitivity to hypoxia in CHF.
Exploiting Unlabeled Data in Smart Cities using Federated Edge Learning (2020)

Privacy concerns are considered one of the main challenges in smart cities as sharing sensitive data induces threatening problems in people's lives. Federated learning has emerged as an effective technique to avoid privacy infringement as well as increase the utilization of the data. However, there is a scarcity in the amount of labeled data and an abundance of unlabeled data collected in smart cities; hence there is a necessity to utilize semi-supervised learning. In this paper, we present the primary design aspects for enabling federated learning at the edge networks taking into account the problem of unlabeled data. We propose a semi-supervised federated edge learning method called FedSem that exploits unlabeled data in real-time. FedSem algorithm is divided into two phases. The first phase trains a global model using only the labeled data. In the second phase, Fedsem injects unlabeled data into the learning process using the pseudo labeling technique and the model developed in the first phase to improve the learning performance. We carried out several experiments using the traffic signs dataset as a case study. Our results show that FedSem can achieve accuracy by up to 8% by utilizing the unlabeled data in the learning process.
MicroRNA machinery in Parkinson’s disease: a platform for neurodegenerative diseases (2015)

MicroRNAs (miRNAs) are noncoding RNAs that recognize their protein-coding target genes and whereby subjugate them after transcription. Despite the infancy of this field of science, the role of miRNAs in neurodegeneration is well-acknowledged. This review was conducted to indicate that Parkinson's disease (PD) is not excluded from this rule. To this end, we evaluated the existing literature and arranged PD-associated miRNAs according to their mechanism of action, particularly apoptosis, autophagy, inflammation, mitochondrial dysfunction and oxidative stress. According to this arrangement, a majority of PD-associated miRNAs were indicated to influence autophagic/apoptotic pathways. We also categorized PD-associated miRNAs according to that they could exert detrimental or beneficial or both into three sets, activator, inhibitor, and double-edged, correspondingly. Considering this criterion, a majority of PD-associated miRNAs were included in the activator category. In addition, evidences from genetic association studies investigating genetic variants of or related to miRNAs in PD patients are presented. Finally, possible applications of the miRNA machinery in PD, including mechanistic networks, diagnostic, prognostic and therapeutic potentials, are discussed. But there may be additional miRNAs involved in the pathogenesis of PD which have hitherto remained unknown and thus further studies are needed to explore the issue and to extend this platform.