Miracle-dz/UniFAR-FTUs huggingface dataset:
Study on the Viscoelastic Property of Soybean Protein Fibers

The soybean protein fiber is a new textile material. Thanks to its fine denier, light specific gravity, high strength and silk-like luster，it has so excellent cashmere handle, silk softness and heat resistant properties that it has been called manmade cashmere and found wide application. In order to understand the relationship between the inner structure and the mechanical property and the effect of bleaching and dyeing to the soybean protein fibers，four mechanical models are chosen. The tensile and relaxation property of the soybean protein fibers are analyzed. The tensile and relaxation cures are fitted with the suitable model. It shows that the relaxation property of SPF is in accordance with the standard linear solid model. Estimates of the Hookean spring modulus at 8% and at 10% are different, so some structural modifications could be produced by the strain. Bleached fibers show a higher level of relaxation than raw fibers and dyed fibers. Bleaching has a remarkable influence on decreasing tenacity at break for each test modality. Knotted and looped modalities decrease fiber tenacity remarkably in all three samples.
Dendritic Cells Pulsed with Leukemia Cell-Derived Exosomes More Efficiently Induce Antileukemic Immunities

Dendritic cells (DCs) and tumor cell-derived exosomes have been used to develop antitumor vaccines. However, the biological properties and antileukemic effects of leukemia cell-derived exosomes (LEXs) are not well described. In this study, the biological properties and induction of antileukemic immunity of LEXs were investigated using transmission electron microscopy, western blot analysis, cytotoxicity assays, and animal studies. Similar to other tumor cells, leukemia cells release exosomes. Exosomes derived from K562 leukemia cells (LEXK562) are membrane-bound vesicles with diameters of approximately 50–100 μm and harbor adhesion molecules (e.g., intercellular adhesion molecule-1) and immunologically associated molecules (e.g., heat shock protein 70). In cytotoxicity assays and animal studies, LEXs-pulsed DCs induced an antileukemic cytotoxic T-lymphocyte immune response and antileukemic immunity more effectively than did LEXs and non-pulsed DCs (P<0.05). Therefore, LEXs may harbor antigens and immunological molecules associated with leukemia cells. As such, LEX-based vaccines may be a promising strategy for prolonging disease-free survival in patients with leukemia after chemotherapy or hematopoietic stem cell transplantation.
Novel vasopressin gene-related transcripts in rat testis.

Although the arginine vasopressin (AVP) gene is predominantly expressed in specific hypothalamic neurons, immunoreactive AVP (irAVP) has also been identified in peripheral tissues, including testis. To determine whether hypothalamic and testicular ir-AVPs derive from the same or different transcripts, we examined testicular AVP gene-related transcripts by Northern blot analysis, polymerase chain reaction (PCR), and RNase mapping. We show that the testis contains three distinct AVP gene-related transcripts of 0.67, 0.83, and 2.0 kilobases (kb) which differ in size from the 0.81-kb hypothalamic AVP mRNA. As demonstrated by deadenylation, this size heterogeneity is not due to differences in the length of the poly(A) tails. By the use of exon-specific probes we determined that the 0.67- and the 0.83-kb transcripts contain exons B and C, but not A. In contrast, the 2-kb transcript is the only testicular transcript that contains an exon A-related sequence. By application of the PCR technique, we confirm the existence of testicular transcripts in which exons B and C are spliced together, but exon A is excluded. Our findings indicate that the 0.67- and 0.83-kb mRNA results from a differential splicing event that excludes exon A and that the 2-kb mRNA probably originates from the expression of an AVP-related gene. Since the nonapeptide AVP is encoded by exon A, testicular irAVP cannot arise from the translation of any of the exon B- and C-containing transcripts, and any mRNA that has so far been identified by AVP exon C probes is unrelated to the biosynthesis of AVP-immunoreactive products. (ABSTRACT TRUNCATED AT 250 WORDS)
SENSITIVITY ANALYSIS IN NONLINEAR VARIATIONAL DATA ASSIMILATION : THEORETICAL ASPECTS AND APPLICATIONS

This chapter presents the mathematical framework to evaluate the sensitivity of a model forecast aspect to the input parameters of a nonlinear four-dimensional variational data assimilation system (4D-Var DAS): observations, prior state (background) estimate, and the error covariance specification. A fundamental relationship is established between the forecast sensitivity with respect to the information vector and the sensitivity with respect to the DAS representation of the information error covariance. Adjoint modeling is used to obtain firstand second-order derivative information and a reduced-order approach is formulated to alleviate the computational cost associated with the sensitivity estimation. Numerical results from idealized 4D-Var experiments performed with a global shallow water model are used to illustrate the theoretical concepts.
Spectrum-Based De Novo Repeat Detection in Genomic Sequences

A novel approach to the detection of genomic repeats is presented in this paper. The technique, dubbed SAGRI (Spectrum Assisted Genomic Repeat Identifier), is based on the spectrum (set of sequence k-mers, for some k) of the genomic sequence. Specifically, the genome is scanned twice. The first scan (FindHit) detects candidate pairs of repeat-segments, by effectively reconstructing portions of the Euler path of the (k-1)-mer graph of the genome only in correspondence with likely repeat sites. This process produces candidate repeat pairs, for which the location of the leftmost term is unknown. Candidate pairs are then subjected to validation in a second scan, in which the genome is labelled for hits in the (much smaller) spectrum of the repeat candidates: high hit density is taken as evidence of the location of the first segment of a repeat, and the pair of segments is then certified by pairwise alignment. The design parameters of the technique are selected on the basis of a careful probabilistic analysis (based on random sequences). SAGRI is compared with three leading repeat-finding tools on both synthetic and natural DNA sequences, and found to be uniformly superior in versatility (ability to detect repeats of different lengths) and accuracy (the central goal of repeat finding), while being quite competitive in speed. An executable program can be downloaded at http://sagri.comp.nus.edu. sg.
Backstepping Design of Robust Output Feedback Regulators for Boundary Controlled Parabolic PDEs

In this article a backstepping-based solution of the robust output regulation problem for boundary controlled parabolic PDEs with spatially varying parameters is presented. This is achieved by stabilizing the plant extended with a finite-dimensional internal model of the exogenous signals. For the resulting PDE-ODE system with spatially varying parameters a systematic backstepping-based compensator design method is developed. The robustness of the achieved output regulation is verified for non-destabilizing model uncertainties. An uncertain parabolic system illustrates the results of the article.
Estimates of left-ventricular volumes by equilibrium radionuclide angiography: importance of attenuation correction.

To compare the accuracy of attenuated and attenuation-corrected equilibrium radionuclide angiographic (RNA) left ventricular (LV) volume estimates, we studied 23 consecutive patients with biplane contrast cineangiography (CINE). Attenuated RNA end-diastolic (ED) and end-systolic (ES) volumes were calculated from background-corrected ED and ES counts obtained from hand-drawn regions of interest that were normalized to cardiac cycles processed, frame rate, and blood activity. A simple, geometric attenuation correction was performed to obtain attenuation-corrected RNA LV volumes. The attenuated and attenuation-corrected RNA LV EDV estimates correlated with the CINE LV EDVs ; however, the attenuation-corrected RNA LV EDV estimates correlated more closely. Also, the average attenuation-corrected RNA LV EDV did not differ significantly from the mean CINE LV EDV. Attenuated and attenuation-corrected RNA LV ESV estimates also correlated with the CINE LV ESVs , but the attenuation-corrected RNA LV ESV estimates correlated more closely. Also, the average attenuation-corrected RNA LV ESV did not differ significantly from the mean biplane CINE LV ESV.
A Cbx8-Containing Polycomb Complex Facilitates the Transition to Gene Activation during ES Cell Differentiation

Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Our project aimed to identify Cbx8 binding sites in differentiating mouse embryonic stem cells. Therefore, we used a genome-wide chromatin immunoprecipitation of endogenous Cbx8 coupled to direct massive parallel sequencing (ChIP-Seq). Our analysis identified 171 high confidence peaks. By crossing our data with previously published microarray analysis, we show that several differentiation genes transiently recruit Cbx8 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. Both interaction analysis, as well as chromatin immunoprecipitation experiments support the idea that activating Cbx8 acts in the context of an intact PRC1 complex. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3 and H2A ubiquitination. The composition of PRC1 is highly modular and changes when embryonic stem cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together, our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs.
Biochemical and molecular characterization of nucleoside triphosphate hydrolase isozymes from the parasitic protozoan Toxoplasma gondii

We have previously reported the presence of a novel nucleoside triphosphate hydrolase (NTPase) in the rapidly multiplying tachyzoite form of a virulent strain (RH) of Toxoplasma gondii. On further examination, it was found that the purified enzyme was not a single enzyme but was a mixture of two isozymes termed NTPase-I and NTPase-II. The two isozymes had similar molecular masses of approximately 240-270 kDa by gel filtration and contained four identical subunits of molecular mass 66-67 kDa by SDS-polyacrylamide gel electrophoresis. Both forms of the NTPase were activated by dithiothreitol, and NTPase-I had a specific activity 4.5-fold higher than NTPase-II in hydrolysis of ATP. The primary difference between these isozymes lies in their ability to hydrolyze nucleoside triphosphate versus diphosphate substrates. While NTPase-II hydrolyzed ATP to ADP and ADP to AMP at almost the same rate, NTPase-I hydrolyzed ADP to AMP at a much slower rate (0.7% of the rate for ATP). The complete cDNAs for NTPase-I and NTPase-II were sequenced and found to encode the same size predicted open reading frame of which only 16 of 628 amino acids differed between the two isozymes. Both forms of the NTPase contained an NH2-terminal hydrophobic signal peptide, consistent with our previous findings that these enzymes are secreted into the host cell vacuole occupied by the parasite. The gene encoding NTPase-II was found in all strains of Toxoplasma, while the NTPase-I was confined only to virulent strains. Expression of this highly active ATPase (NTPase-I) may contribute to intracellular survival and virulence of T. gondii.
Conformational changes in CLIP-170 regulate its binding to microtubules and dynactin localization

Cytoplasmic linker protein (CLIP)-170, CLIP-115, and the dynactin subunit p150Glued are structurally related proteins, which associate specifically with the ends of growing microtubules (MTs). Here, we show that down-regulation of CLIP-170 by RNA interference results in a strongly reduced accumulation of dynactin at the MT tips. The NH2 terminus of p150Glued binds directly to the COOH terminus of CLIP-170 through its second metal-binding motif. p150Glued and LIS1, a dynein-associating protein, compete for the interaction with the CLIP-170 COOH terminus, suggesting that LIS1 can act to release dynactin from the MT tips. We also show that the NH2-terminal part of CLIP-170 itself associates with the CLIP-170 COOH terminus through its first metal-binding motif. By using scanning force microscopy and fluorescence resonance energy transfer-based experiments we provide evidence for an intramolecular interaction between the NH2 and COOH termini of CLIP-170. This interaction interferes with the binding of the CLIP-170 to MTs. We propose that conformational changes in CLIP-170 are important for binding to dynactin, LIS1, and the MT tips.
Carbon Fiber Reinforced Polymer for Cable Structures—A Review

Carbon Fiber Reinforced Polymer (CFRP) is an advanced composite material with the advantages of high strength, lightweight, no corrosion and excellent fatigue resistance. Therefore, unidirectional CFRP has great potential for cables and to replace steel cables in cable structures. However, CFRP is a typical orthotropic material and its strength and modulus perpendicular to the fiber direction are much lower than those in the fiber direction, which brings a challenge for anchoring CFRP cables. This paper presents an overview of application of CFRP cables in cable structures, including historical review, state of the art and prospects for the future. After introducing properties of carbon fibers, mechanical characteristics and structural forms of CFRP cables, existing CFRP cable structures in the world (all of them are cable bridges) are reviewed. Especially, their CFRP cable anchorages are presented in detail. New applications for CFRP cables, i.e., cable roofs and cable facades, are also presented, including the introduction of a prototype CFRP cable roof and the conceptual design of a novel structure—CFRP Continuous Band Winding System. In addition, other challenges that impede widespread application of CFRP cable structures are briefly introduced.
Preparation of Antioxidant Enzymatic Hydrolysates from Honeybee-Collected Pollen Using Plant Enzymes

Enzymatic hydrolysates of honeybee-collected pollen were prepared using food-grade proteinase and aminopeptidases entirely of plant origin. Bromelain from pineapple stem was applied (8 mAU/g substrate) in the first hydrolysis stage. Aminopeptidase (0.05 U/g substrate) and proline iminopeptidase (0.03 U/g substrate) from cabbage leaves (Brassica oleracea var. capitata), and aminopeptidase (0.2 U/g substrate) from chick-pea cotyledons (Cicer arietinum L.) were involved in the additional hydrolysis of the peptide mixtures. The degree of hydrolysis (DH), total phenolic contents, and protein contents of these hydrolysates were as follows: DH (about 20–28%), total phenolics (15.3–27.2 μg/mg sample powder), and proteins (162.7–242.8 μg/mg sample powder), respectively. The hydrolysates possessed high antiradical scavenging activity determined with DPPH (42–46% inhibition). The prepared hydrolysates of bee-collected flower pollen may be regarded as effective natural and functional dietary food supplements due to their remarkable content of polyphenol substances and significant radical-scavenging capacity with special regard to their nutritional-physiological implications.
Effects of Varenicline on Neural Correlates of Alcohol Salience in Heavy Drinkers

Background: Preclinical and emerging clinical evidence indicates that varenicline, a nicotinic partial agonist approved for smoking cessation, attenuates alcohol seeking and consumption. Reductions of alcohol craving have been observed under varenicline treatment and suggest effects of the medication on alcohol reward processing, but this hypothesis remains untested. Methods: In this double-blind, placebo-controlled randomized experimental medicine study, 29 heavy drinkers underwent a functional magnetic resonance imaging scan after 2 weeks of varenicline (2mg/d) or placebo administration. During functional magnetic resonance imaging, participants performed the Alcohol-Food Incentive Delay task, where they could earn points for snacks or alcohol. At baseline and after 3 weeks of medication, participants underwent intravenous alcohol self-administration sessions in the laboratory. Results: During the functional magnetic resonance imaging scan, participants in the varenicline group (N=17) reported lower feelings of happiness and excitement on subjective mood scales when anticipating alcohol reward compared with the placebo group (N=12). Linear mixed effects analysis revealed that anticipation of alcohol reward was associated with significant blood oxygen level dependent activation of the ventral striatum, amygdala, and posterior insula in the placebo group; this activation was attenuated in the varenicline group. The varenicline group showed no difference in intravenous alcohol self-administration relative to the placebo group for either session. Participants with higher insula activation when anticipating alcohol reward showed higher alcohol self-administration behavior across groups. Conclusions: Our findings suggest that varenicline decreases blood oxygen level dependent activation in striato-cortico-limbic regions associated with motivation and incentive salience of alcohol in heavy drinkers. This mechanism may underlie the clinical effectiveness of varenicline in reducing alcohol intake and indicates its potential utility as a pharmacotherapy for alcohol use disorders.
PREDICTION/ESTIMATION WITH SIMPLE LINEAR MODELS: IS IT REALLY THAT SIMPLE?

Consider the simple normal linear regression model for estimation/prediction at a new design point. When the slope parameter is not obviously nonzero, hypothesis testing and information criteria can be used for identifying the right model. We compare the performances of such methods both theoretically and empirically from different perspectives for more insight. The testing approach at the conventional size of 0.05, in spite of being the “standard approach,” performs poorly in estimation. We also found that the frequently told story “the Bayesian information criterion (BIC) is good when the true model is finite-dimensional, and the Akaike information criterion (AIC) is good when the true model is infinite-dimensional” is far from being accurate. In addition, despite some successes in the effort to go beyond the debate between AIC and BIC by adaptive model selection, it turns out that it is not possible to share the pointwise adaptation property of BIC and the minimax-rate adaptation property of AIC by any model selection method. When model selection methods have difficulty in selection, model combining is a better alternative in terms of estimation accuracy.This work was completed when the author was on leave from Iowa State University and was a New Direction Visiting Professor at the Institute for Mathematics and its Applications (IMA) at the University of Minnesota. The fundings from both IMA and ISU are greatly appreciated. The work was also partly supported by NSF CAREER grant DMS0094323. The author thanks Xiaotong Shen and Hannes Leeb for very helpful discussions. The paper also benefited from the questions and comments from the participants at the statistics seminars the author gave at the University of Minnesota and Duke University. The author is very grateful to the anonymous reviewers and the co-editor Benedikt Pötscher for carefully reading earlier versions of the paper, bringing my attention to several closely related previous and current results, and making many very valuable suggestions, which significantly improved the paper in both content and presentation.
SMASH-U: A Proposal for Etiologic Classification of Intracerebral Hemorrhage

Background and Purpose— The purpose of this study was to provide a simple and practical clinical classification for the etiology of intracerebral hemorrhage (ICH). Methods— We performed a retrospective chart review of consecutive patients with ICH treated at the Helsinki University Central Hospital, January 2005 to March 2010 (n=1013). We classified ICH etiology by predefined criteria as structural vascular lesions (S), medication (M), amyloid angiopathy (A), systemic disease (S), hypertension (H), or undetermined (U). Clinical and radiological features and mortality by SMASH-U (Structural lesion, Medication, Amyloid angiopathy, Systemic/other disease, Hypertension, Undetermined) etiology were analyzed. Results— Structural lesions, namely cavernomas and arteriovenous malformations, caused 5% of the ICH, anticoagulation 14%, and systemic disease 5% (23 liver cirrhosis, 8 thrombocytopenia, and 17 various rare conditions). Amyloid angiopathy (20%) and hypertensive angiopathy (35%) were common, but etiology remained undetermined in 21%. Interrater agreement in classifying cases was high (&kgr;, 0.89; 95% CI, 0.82–0.96). Patients with structural lesions had the smallest hemorrhages (median volume, 2.8 mL) and best prognosis (3-month mortality 4%), whereas anticoagulation-related ICHs were largest (13.4 mL) and most often fatal (54%). Overall, median ICH survival was 5½ years, varying strongly by etiology (P<0.001). After adjustment for baseline characteristics, patients with structural lesions had the lowest 3-month mortality rates (OR, 0.06; 95% CI, 0.01–0.37) and those with anticoagulation (OR, 1.9; 1.0–3.6) or other systemic cause (OR, 4.0; 1.6–10.1) the highest. Conclusions— In our patients, performing the SMASH-U classification was feasible and interrater agreement excellent. A plausible etiology was determined in most patients but remained elusive in one in 5. In this series, SMASH-U based etiology was strongly associated with survival.
Ketorolac Tromethamine – Routes and Clinical Implications

Opioids have long been used for analgesic purposes for a wide range of procedures. However, the binding of these drugs to opiate receptors has created various challenges to the clinician due to unfavorable side effect profiles and the potential for tolerance and abuse. In 1989, ketorolac became an approved nonsteroidal inflammatory drug (NSAID) for injectable use as an analgesic. Over the last 20 years, numerous studies have been conducted involving ketorolac. These studies have provided additional information about various routes of administration and their effect on the efficacy and the side effect profile of ketorolac. Moreover, ketorolac has been compared with several widely used analgesics. This review evaluates both the potential benefits and potential drawbacks of ketorolac generally, and specifically discusses routes of administration, including their advantages and disadvantages when compared to several traditional analgesics in both inpatient and outpatient settings.