Miracle-dz/UniFAR-FTUs huggingface dataset:
N-Glycan Structures from the Major Glycoproteins of Pigeon Egg White

N-Glycans from major glycoproteins of pigeon egg white (ovotransferrin, ovomucoid, and ovalbumins) were enzymatically released and were reductively aminated with 2-aminopyridine, separated, and structurally characterized by mass spectrometry and a three-dimensional mapping technique using three different columns of high performance liquid chromatography (HPLC) (Takahashi, N., Nakagawa, H., Fujikawa, K., Kawamura, Y., and Tomiya, N. (1995) Anal. Biochem.226, 139–146). Twenty-five major N-glycan structures, all of them hitherto unknown, were identified as pyridylamino derivatives. Of these, 13 were neutral, 10 were monosialyl, and 2 were disialyl oligosaccharides. All N-glycans contain from one to four Galα(1,4)Galβ(1,4) sequences at the nonreducing terminal positions and are devoid of fucose residues. N-Acetylneuraminic acids were α(2,6)-linked only to β-galactose. The HPLC profiles of theN-glycans from four different glycoproteins were qualitatively very similar to each other, but not identical in the peak distributions. Monosialyl glycans were most abundant in all four glycoproteins, followed by neutral glycans. Disialyl glycans were lowest in ovotransferrin, and highest in ovomucoid. Triantennary structures with bisecting GlcNAc were predominant in ovotransferrin, and tetra-antennary (with and without bisecting GlcNAc-containing) structures were predominant in other glycoproteins. Penta-antennary structures (with a sialic acid and without bisecting GlcNAc residue) were also found in small quantities in all four glycoproteins. In contrast to the chicken egg white counterparts, which contain mostly high mannose and hybrid types, all N-glycan structures in the major pigeon egg white glycoproteins are complex type.
Wearable PPG sensor based alertness scoring system

Quantifying mental alertness in today's world is important as it enables the person to adopt lifestyle changes for better work efficiency. Miniaturized sensors in wearable devices have facilitated detection/monitoring of mental alertness. Photoplethysmography (PPG) sensors through Heart Rate Variability (HRV) offer one such opportunity by providing information about one's daily alertness levels without requiring any manual interference from the user. In this paper, a smartwatch based alertness estimation system is proposed. Data collected from PPG sensor of smartwatch is processed and fed to machine learning based model to get a continuous alertness score. Utility functions are designed based on statistical analysis to give a quality score on different stages of alertness such as awake, long sleep and short duration power nap. An intelligent data collection approach is proposed in collaboration with the motion sensor in the smartwatch to reduce battery drainage. Overall, our proposed wearable based system provides a detailed analysis of alertness over a period in a systematic and optimized manner. We were able to achieve an accuracy of 80.1% for sleep/awake classification along with alertness score. This opens up the possibility for quantifying alertness levels using a single PPG sensor for better management of health related activities including sleep.
Evaluation of Estrogenic Activity of Licorice Species in Comparison with Hops Used in Botanicals for Menopausal Symptoms

The increased cancer risk associated with hormone therapies has encouraged many women to seek non-hormonal alternatives including botanical supplements such as hops (Humulus lupulus) and licorice (Glycyrrhiza spec.) to manage menopausal symptoms. Previous studies have shown estrogenic properties for hops, likely due to the presence of 8-prenylnarigenin, and chemopreventive effects mainly attributed to xanthohumol. Similarly, a combination of estrogenic and chemopreventive properties has been reported for various Glycyrrhiza species. The major goal of the current study was to evaluate the potential estrogenic effects of three licorice species (Glycyrrhiza glabra, G. uralensis, and G. inflata) in comparison with hops. Extracts of Glycyrrhiza species and spent hops induced estrogen responsive alkaline phosphatase activity in endometrial cancer cells, estrogen responsive element (ERE)-luciferase in MCF-7 cells, and Tff1 mRNA in T47D cells. The estrogenic activity decreased in the order H. lupulus > G. uralensis > G. inflata > G. glabra. Liquiritigenin was found to be the principle phytoestrogen of the licorice extracts; however, it exhibited lower estrogenic effects compared to 8-prenylnaringenin in functional assays. Isoliquiritigenin, the precursor chalcone of liquiritigenin, demonstrated significant estrogenic activities while xanthohumol, a metabolic precursor of 8-prenylnaringenin, was not estrogenic. Liquiritigenin showed ERβ selectivity in competitive binding assay and isoliquiritigenin was equipotent for ER subtypes. The estrogenic activity of isoliquiritigenin could be the result of its cyclization to liquiritigenin under physiological conditions. 8-Prenylnaringenin had nanomolar estrogenic potency without ER selectivity while xanthohumol did not bind ERs. These data demonstrated that Glycyrrhiza species with different contents of liquiritigenin have various levels of estrogenic activities, suggesting the importance of precise labeling of botanical supplements. Although hops shows strong estrogenic properties via ERα, licorice might have different estrogenic activities due to its ERβ selectivity, partial estrogen agonist activity, and non-enzymatic conversion of isoliquiritigenin to liquiritigenin.
Anthropometric measures, endogenous sex steroids and breast cancer risk in postmenopausal women: A study within the EPIC cohort

In a large case–control study on breast cancer risk and serum hormone concentrations, nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, we examined to what extent the relationship of excess body weight with breast cancer risk may be explained by changes in sex steroids. Height, weight, waist and hip circumferences, and serum measurements of testosterone [T], androstenedione [Δ4], dehydroepiandrosterone sulphate [DHEAS], estradiol [E2], estrone [E1] and sex‐hormone binding globulin [SHBG] were available for 613 breast cancer cases, and 1,139 matched controls, who were all menopausal at the time of blood donation. Free T [fT] and free E2 [fE2] were calculated using mass action equations. Breast cancer risk was related to body mass index (BMI) (RR = 1.11 [0.99–1.25], per 5 kg/m2 increase in BMI), and waist (RR = 1.12 [1.02–1.24], per 10 cm increase) and hip circumferences (RR = 1.14 [1.02–1.27], per 10 cm increase). The increase in breast cancer risk associated with adiposity was substantially reduced after adjustment for any estrogens, especially for fE2 (from 1.11 [0.99–1.25] to 0.99 [0.87–1.12], from 1.12 [1.02–1.24] to 1.02 [0.92–1.14] and from 1.14 [1.02–1.27] to 1.05 [0.93–1.18] for BMI, waist and hip circumferences, respectively). A modest attenuation in excess risk was observed after adjustment for fT, but the remaining androgens had little effect on the association of body adiposity with breast cancer. Our data indicate that the relationship of adiposity with breast cancer in postmenopausal women could be partially explained by the increases in endogenous estrogens, and by a decrease in levels of SHBG. © 2005 Wiley‐Liss, Inc.
A multicriteria image-based controller based on a mixed polytopic and norm-bounded representation of uncertainties

This paper presents a multicriteria image-based controller to position a 3-DOF camera with respect to a target. The proposed controller allows to stabilize the camera and determine the associated region of stability in spite of unknown value of the target points depth, bounds on admissible visual feature errors which guarantee visibility, and limits on the camera velocity and acceleration. The description of the closed-loop system is based on a mixed polytopic and norm-bounded representation of uncertainties combined with an original sector condition. This formulation allows to consider LMI-based optimization schemes for computing the feedback gain that leads to the maximization of the size of the region of stability associated to the closed-loop system. Simulations of the control method are presented in the case of a camera mounted on a pan-platform supported by a cart-like robot.
The Arabidopsis RNA Binding Protein with K Homology Motifs, SHINY1, Interacts with the C-terminal Domain Phosphatase-like 1 (CPL1) to Repress Stress-Inducible Gene Expression

The phosphorylation state of the C-terminal domain (CTD) of the RNA polymerase II plays crucial roles in transcription and mRNA processing. Previous studies showed that the plant CTD phosphatase-like 1 (CPL1) dephosphorylates Ser-5-specific CTD and regulates abiotic stress response in Arabidopsis. Here, we report the identification of a K-homology domain-containing protein named SHINY1 (SHI1) that interacts with CPL1 to modulate gene expression. The shi1 mutant was isolated from a forward genetic screening for mutants showing elevated expression of the luciferase reporter gene driven by a salt-inducible promoter. The shi1 mutant is more sensitive to cold treatment during vegetative growth and insensitive to abscisic acid in seed germination, resembling the phenotypes of shi4 that is allelic to the cpl1 mutant. Both SHI1 and SHI4/CPL1 are nuclear-localized proteins. SHI1 interacts with SHI4/CPL1 in vitro and in vivo. Loss-of-function mutations in shi1 and shi4 resulted in similar changes in the expression of some stress-inducible genes. Moreover, both shi1 and shi4 mutants display higher mRNA capping efficiency and altered polyadenylation site selection for some of the stress-inducible genes, when compared with wild type. We propose that the SHI1-SHI4/CPL1 complex inhibits transcription by preventing mRNA capping and transition from transcription initiation to elongation.
Pad++: A Zoomable Graphical Sketchpad For Exploring Alternate Interface Physics

We describe Pad++, a zoomable graphical sketchpad that we are exploring as an alternative to traditional window and icon-based interfaces. We discuss the motivation for Pad++, describe the implementation, and present prototype applications. In addition, we introduce an informational physics strategy for interface design and briefly contrast it with current design strategies. We envision a rich world of dynamic persistent informational entities that operate according to multiple physics specifically designed to provide cognitively facile access and serve as the basis for design of new computationally-based work materials.
Change of coronary flow by continuous-flow left ventricular assist device with cardiac beat synchronizing system (native heart load control system) in acute ischemic heart failure model.

BACKGROUND A novel control system for the EVAHEART left ventricular assist device (LVAD), known as the Native Heart Load Control System (NHLCS), can change the device's rotational speed (RS) in synchrony with the heartbeat. The system enhanced coronary flow (CoF) with the counter-pulse mode in normal goats' hearts, so we examined the change in CoF in goats with acute ischemic heart failure (HF). METHODS AND RESULTS We studied 14 goats (56.1±6.9kg) with acute ischemic HF induced by coronary microsphere embolization. We installed EVAHEART and ran the device in 4 modes [continuous support, circuit-clamp, counter-pulse (raise RS in diastole), and co-pulse (raise RS in systole)] with 50% or 100% bypass in each mode. In comparison with the circuit-clamp mode, CoF was 121.0±14.1% in the counter-pulse mode and 102.9±7.9% in the co-pulse mode, whereas it was 113.5±10.6% in the continuous mode, with 100% bypass (P<0.05). The same difference was confirmed with 50% bypass. The results indicated that a LVAD in an acute ischemic heart enhanced CoF, and that CoF was greater in the counter-pulse mode and smaller in the co-pulse mode relative to the continuous mode. CONCLUSIONS By using NHLCS to change CoF, recovery of native heart function with a LVAD has a better prognosis.
The MidasPlus molecular modeling system

MidasPlus [6, 7] is an interactive molecular modeling system used to depict three dimensional macromolecular structures such as proteins and nucleic acids, to study how these structures spatially and chemically interact, and to study how small molecules such as drugs bind with these macromolecules, Effective interaction with macromolecular structures presents several challenges: the molecules consist of thousands to tens of thousands of atoms and the scientist user is easily overwhelmed by the sheer volume of data if the displayed information is not limitied and presented in a rational manner. The intellectual process of understanding the structure and function of molecules is linked to visualizing the complex spatial relationships within these structures, and since the user ia only presented images of models, this intellectual process must proceed without being able to physically handle and make experimental “hand driven” modifications of a physical model. Finally, macromolecules are often globular in shape, of course bear no resemblance to macroscopic physical objects in the real world, and hence make it inherently difficult for the human visual system to accurately perceive the complex spatial relationships that are ao crucial to chemical activity.
Harmonic Coordinates

Generalizations of barycentric coordinates in two and higher dimensions have been shown to have a number of applications in recent years, including finite element analysis, the definition of Spatches (n-sided generalizations of Bézier surfaces), free-form deformations, mesh parametrization, and interpolation. In this paper we present a new form of d dimensional generalized barycentric coordinates. The new coordinates are defined as solutions to Laplace’s equation subject to carefully chosen boundary conditions. Since solutions to Laplace’s equation are called harmonic functions, we call the new construction harmonic coordinates. We show that harmonic coordinates possess several properties that make them more attractive than mean value coordinates when used to define two and three dimensional deformations.
Extending VoID for Expressing Connectivity Metrics of a Semantic Warehouse

VoID (Vocabulary of Interlinked Datasets) has been proposed by W3C as the vocabulary for expressing metadata about RDF datasets. Despite its important contributions, VoID cannot express metadata that concern the connectivity of semantic warehouses. We use the term semantic warehouse to refer to a read-only set of RDF triples fetched (and transformed) from different sources that aims at serving a particular set of query requirements. Connectivity metrics are important for evaluating the value of a semantic warehouse, since they reflect its query capabilities. Moreover they also quantify the contribution of each constituent source to the warehouse. To allow the representation, exchange, and querying of such measurements, in this paper we describe an extension of VoID that allows representing them. We demonstrate its applicability through the case of a real and operational semantic warehouse for the marine domain.
AN INVESTIGATION IN TO THE CONCEPTS AND TECHNIQUES USED FOR ESTABLISHING POSTPALATAL SEAL IN UNDERGRADUATE DENTAL CURRICULUM

A survey of Pakistani Dental Colleges was conducted to determine which concepts and techniques are currently prevalent in the teaching of establishing the postpalatal seal in the undergraduate dental curriculum. A previous structured questionnaire from international article comprised seven multiple-choice questions, was distributed by mail and personal contact to 50 demonstrators and faculty members of Prosthodontics departments, of ten different (3 Government and 7 Private) Dental Colleges in the country. Of these, 42 teachers retuned the completed questionnaire, yielding a response rate of 84%. Results from this survey showed that 85.72% of the teachers were teaching a combination of phonation with other methods for determining the location of the vibrating line. The one vibrating line concept for establishing the postpalatal seal (PPS) was taught by 80.95. 7% of teachers, 52.38% of these locate the posterior termination of the maxillary denture posterior to vibrating line. Carving the PPS in the maxillary master cast was taught by 83.33% of teachers. Most of the teachers 83.33% were teaching the students to carve the PPS to a depth of 1.0–1.5 mm in the maxillary master cast. Compressibility of the palatal tissues was a consideration during PPS carving for all of the teachers. The butterfly pattern was the most frequently (88.09%) described pattern for PPS carving. No difference in Concepts and Techniques in the teaching of establishing postpalatal seal was
Deep Syntax Language Models and Statistical Machine Translation

Hierarchical Models increase the reordering capabilities of MT systems by introducing non-terminal symbols to phrases that map source language (SL) words/phrases to the correct position in the target language (TL) translation. Building translations via discontiguous TL phrases increases the difficulty of language modeling, however, introducing the need for heuristic techniques such as cube pruning (Chiang, 2005), for example. An additional possibility to aid language modeling in hierarchical systems is to use a language model that models fluency of words not using their local context in the string, as in traditional language models, but instead using the deeper context of a word. In this paper, we explore the potential of deep syntax language models providing an interesting comparison with the traditional string-based language model. We include an experimental evaluation that compares the two kinds of models independently of any MT system to investigate the possible potential of integrating a deep syntax language model into Hierarchical SMT systems.
Extracting synonymous gene and protein terms from biological literature

MOTIVATION Genes and proteins are often associated with multiple names. More names are added as new functional or structural information is discovered. Because authors can use any one of the known names for a gene or protein, information retrieval and extraction would benefit from identifying the gene and protein terms that are synonyms of the same substance. RESULTS We have explored four complementary approaches for extracting gene and protein synonyms from text, namely the unsupervised, partially supervised, and supervised machine-learning techniques, as well as the manual knowledge-based approach. We report results of a large scale evaluation of these alternatives over an archive of biological journal articles. Our evaluation shows that our extraction techniques could be a valuable supplement to resources such as SWISSPROT, as our systems were able to capture gene and protein synonyms not listed in the SWISSPROT database.
Memory Access Scheduling Based on Dynamic Multilevel Priority in Shared DRAM Systems

Interapplication interference at shared main memory severely degrades performance and increasing DRAM frequency calls for simple memory schedulers. Previous memory schedulers employ a per-application ranking scheme for high system performance or a per-group ranking scheme for low hardware cost, but few provide a balance. We propose DMPS, a memory scheduler based on dynamic multilevel priority. First, DMPS uses “memory occupancy” to measure interference quantitatively. Second, DMPS groups applications, favors latency-sensitive groups, and dynamically prioritizes applications by employing a per-level ranking scheme. The simulation results show that DMPS has 7.2% better system performance and 22% better fairness over FRFCFS at low hardware complexity and cost.
Genomic transcription regulatory element location analysis via poisson weighted lasso

The distances between DNA Transcription Regulatory Elements (TRE) provide important clues to their dependencies and function within the gene regulation process. However, the locations of those TREs as well as their cross distances between occurrences are stochastic, in part due to the inherent limitations of Next Generation Sequencing methods used to localize them, in part due to biology itself. This paper describes a novel approach to analyzing these locations and their cross distances even at long range via a Poisson random convolution. The resulting deconvolution problem is ill-posed, and sparsity regularization is used to offset this challenge. Unlike previous work on sparse Poisson inverse problems, this paper adopts a weighted LASSO estimator with data-dependent weights calculated using concentration inequalities that account for the Poisson noise. This method exhibits better squared error performance than the classical (unweighted) LASSO both in theoretical performance bounds and in simulation studies, and can easily be computed using off-the-shelf LASSO solvers.
Multiscale Reactive Molecular Dynamics for Absolute pKa Predictions and Amino Acid Deprotonation

Accurately calculating a weak acid’s pKa from simulations remains a challenging task. We report a multiscale theoretical approach to calculate the free energy profile for acid ionization, resulting in accurate absolute pKa values in addition to insights into the underlying mechanism. Importantly, our approach minimizes empiricism by mapping electronic structure data (QM/MM forces) into a reactive molecular dynamics model capable of extensive sampling. Consequently, the bulk property of interest (the absolute pKa) is the natural consequence of the model, not a parameter used to fit it. This approach is applied to create reactive models of aspartic and glutamic acids. We show that these models predict the correct pKa values and provide ample statistics to probe the molecular mechanism of dissociation. This analysis shows changes in the solvation structure and Zundel-dominated transitions between the protonated acid, contact ion pair, and bulk solvated excess proton.
Service without a smile?! Exploring the roles of customer injustice, anger and individual differences in emotional deviance

Jennifer Z. Gillespie, Advisor There is a growing body of research focused on examining how customer service workers meet organizational demands to express positive emotions, a phenomenon known as emotional labor. However, it is unreasonable to assume that employees will always display appropriate emotions on the job, yet there is a dearth of research that examines the occurrence of emotional deviance (i.e., breaking display rules). The current study integrated theories from the emotional labor, justice and counterproductive work behavior literatures in order to gain an increased understanding of emotional deviance. Specifically, customer injustice and anger were examined as important predictors of emotional deviance, and the moderating roles of self-control, display rule commitment and display rule enforcement were considered. Quantitative and qualitative survey data were collected from 257 employees in various customer service jobs. The results indicated that being treated unfairly by customers was related to emotional deviance, both directly and indirectly through feelings of anger. Furthermore, employee self-control moderated the relationship between feelings of anger and emotional deviance such that those low in self-control were more likely to deviate. Although it was posited that employees low in display rule commitment would be more likely to emotionally deviate when they experience anger, a significant relationship was not found. Finally, the results supported display rule enforcement as an