Miracle-dz/UniFAR-FTUs huggingface dataset:
Combinatorial Hopf algebras and generalized Dehn–Sommerville relations

A combinatorial Hopf algebra is a graded connected Hopf algebra over a field $\Bbbk$ equipped with a character (multiplicative linear functional) $\zeta\colon{\mathcal H}\to \Bbbk$. We show that the terminal object in the category of combinatorial Hopf algebras is the algebra ${\mathcal Q}{\mathit{Sym}}$ of quasi-symmetric functions; this explains the ubiquity of quasi-symmetric functions as generating functions in combinatorics. We illustrate this with several examples. We prove that every character decomposes uniquely as a product of an even character and an odd character. Correspondingly, every combinatorial Hopf algebra $({\mathcal H},\zeta)$ possesses two canonical Hopf subalgebras on which the character $\zeta$ is even (respectively, odd). The odd subalgebra is defined by certain canonical relations which we call the generalized Dehn–Sommerville relations. We show that, for ${\mathcal H}={\mathcal Q}{\mathit{Sym}}$, the generalized Dehn–Sommerville relations are the Bayer–Billera relations and the odd subalgebra is the peak Hopf algebra of Stembridge. We prove that ${\mathcal Q}{\mathit{Sym}}$ is the product (in the categorical sense) of its even and odd Hopf subalgebras. We also calculate the odd subalgebras of various related combinatorial Hopf algebras: the Malvenuto–Reutenauer Hopf algebra of permutations, the Loday–Ronco Hopf algebra of planar binary trees, the Hopf algebras of symmetric functions and of non-commutative symmetric functions.
Cloning, expression, and molecular characterization of the dermonecrotic toxin gene of Bordetella spp

A cosmid library of random fragments of Bordetella bronchiseptica genomic DNA was prepared and screened with oligonucleotides designed from the sequence of the B. pertussis dermonecrotic toxin (DNT) gene. Two cosmid clones which apparently contained the complete B. bronchiseptica DNT gene were identified, but they did not express the toxin. A 5-kb fragment containing the DNT gene was subcloned from one of the cosmid clones onto a high-copy-number plasmid, and this resulted in low-level expression of the toxin. The expression level was increased by deletion of a small region upstream of the coding sequence. Assays for biological activity, including the infant mouse dermonecrosis assay, confirmed that the product of the cloned gene was DNT. The complete sequence of the B. bronchiseptica DNT gene was determined and was more than 99% homologous to the DNT gene of B. pertussis. A putative purine nucleotide-binding motif was shown to be important for toxic activity. Extracts containing the recombinant or the native toxin induced DNA synthesis in Swiss 3T3 cells but inhibited cell division leading to binucleation.
Oracle Based Active Set Algorithm for Scalable Elastic Net Subspace Clustering

State-of-the-art subspace clustering methods are based on expressing each data point as a linear combination of other data points while regularizing the matrix of coefficients with ℓ<sub>1</sub>, ℓ<sub>2</sub> or nuclear norms. ℓ<sub>1</sub> regularization is guaranteed to give a subspace-preserving affinity (i.e., there are no connections between points from different subspaces) under broad theoretical conditions, but the clusters may not be connected. ℓ<sub>2</sub> and nuclear norm regularization often improve connectivity, but give a subspace-preserving affinity only for independent subspaces. Mixed ℓ<sub>1</sub>, ℓ<sub>2</sub> and nuclear norm regularizations offer a balance between the subspace-preserving and connectedness properties, but this comes at the cost of increased computational complexity. This paper studies the geometry of the elastic net regularizer (a mixture of the ℓ<sub>1</sub> and ℓ<sub>2</sub> norms) and uses it to derive a provably correct and scalable active set method for finding the optimal coefficients. Our geometric analysis also provides a theoretical justification and a geometric interpretation for the balance between the connectedness (due to ℓ<sub>2</sub> regularization) and subspace-preserving (due to ℓ<sub>1</sub> regularization) properties for elastic net subspace clustering. Our experiments show that the proposed active set method not only achieves state-of-the-art clustering performance, but also efficiently handles large-scale datasets.
Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins

Collective motions on ns-µs time scales are known to have a major impact on protein folding, stability, binding and enzymatic efficiency. It is also believed that these motions may have an important role in the early stages of prion protein misfolding and prion disease. In an effort to accurately characterize these motions and their potential influence on the misfolding and prion disease transmissibility we have conducted a combined analysis of molecular dynamic simulations and NMR-derived flexibility measurements over a diverse range of prion proteins. Using a recently developed numerical formalism, we have analyzed the essential collective dynamics (ECD) for prion proteins from eight different species including human, cow, elk, cat, hamster, chicken, turtle and frog. We also compared the numerical results with flexibility profiles generated by the random coil index (RCI) from NMR chemical shifts. Prion protein backbone flexibility derived from experimental NMR data and from theoretical computations show strong agreement with each other, demonstrating that it is possible to predict the observed RCI profiles employing the numerical ECD formalism. Interestingly, flexibility differences in the loop between second b strand (S2) and the second a helix (HB) appear to distinguish prion proteins from species that are susceptible to prion disease and those that are resistant. Our results show that the different levels of flexibility in the S2-HB loop in various species are predictable via the ECD method, indicating that ECD may be used to identify disease resistant variants of prion proteins, as well as the influence of prion proteins mutations on disease susceptibility or misfolding propensity.
Business Method Patents in Europe and Their Strategic Use - Evidence from Franking Device Manufacturers

There has been a wide-spread misconception based on the imprecise wording of Art. 52 of the European Patent Convention that the protection of business methods by patents is prohibited in Europe. This article investigates the legal framework set by patent laws with respect to the patentability of business methods, contrasting the situation in lege in Europe and the situation in the US. It is shown that in praxi business methods have never been excluded from patentability in Europe. In the empirical part of the article, 1901 European patent applications relating to business methods are identified and major patent indicators are computed. Further, a case study from the franking device industry which is characterized by strong competition for intellectual property rights is conducted. It contains evidence for the strategic use of business method patents leading to opposition rates against granted patents of 44%.
Cyst Fluid Carcinoembryonic Antigen Is an Accurate Diagnostic Marker of Pancreatic Mucinous Cysts

Objectives: Endoscopic ultrasound (EUS) may offer a diagnostic tool through the combination of imaging and guided fine-needle aspiration of pancreatic cysts. The purpose of this investigation was to determine the most accurate test for differentiating mucinous from nonmucinous cysts. Methods: The results of EUS imaging, cytology, and cyst fluid biochemical markers were prospectively collected and compared in a large single-center study (776 patients) using histology or malignant cytology as the final diagnostic standard in 198 patients. Results: The mean cyst fluid carcinoembryonic antigen (CEA) was greater in mucinous cysts (4703.0 ng/mL) compared with nonmucinous cysts (25.8 ng/mL) (P = 0.008). When using the optimal cutoff value of 109.9 ng/mL, the CEA was more accurate (86%, receiver operating characteristic area = 0.928) than EUS imaging (48%) and cytology (58%) in predicting a mucinous cyst (P < 0.0001). Malignant cysts had a mean cyst fluid CEA value (2558.2 ng/mL) similar to benign cysts (4700.2 ng/mL). Cytology (75%) more accurately diagnosed malignant cysts than EUS (66%) and CEA (62%) (P < 0.05). Conclusions: Cyst fluid CEA concentration provides a highly accurate test for the diagnosis of a mucinous cyst, but does not distinguish benign from malignant cysts. Cytology is the most accurate test for the diagnosis of a malignant cyst.Abbreviations: EUS - endoscopic ultrasound, CEA - carcinoembryonic antigen, MCN - mucinous cystic neoplasm, IPMN - intraductal papillary mucinous neoplasm
Targeting Phospholipid Metabolism in Cancer

All cancers tested so far display abnormal choline and ethanolamine phospholipid metabolism, which has been detected with numerous magnetic resonance spectroscopy (MRS) approaches in cells, animal models of cancer, as well as the tumors of cancer patients. Since the discovery of this metabolic hallmark of cancer, many studies have been performed to elucidate the molecular origins of deregulated choline metabolism, to identify targets for cancer treatment, and to develop MRS approaches that detect choline and ethanolamine compounds for clinical use in diagnosis and treatment monitoring. Several enzymes in choline, and recently also ethanolamine, phospholipid metabolism have been identified, and their evaluation has shown that they are involved in carcinogenesis and tumor progression. Several already established enzymes as well as a number of emerging enzymes in phospholipid metabolism can be used as treatment targets for anticancer therapy, either alone or in combination with other chemotherapeutic approaches. This review summarizes the current knowledge of established and relatively novel targets in phospholipid metabolism of cancer, covering choline kinase α, phosphatidylcholine-specific phospholipase D1, phosphatidylcholine-specific phospholipase C, sphingomyelinases, choline transporters, glycerophosphodiesterases, phosphatidylethanolamine N-methyltransferase, and ethanolamine kinase. These enzymes are discussed in terms of their roles in oncogenic transformation, tumor progression, and crucial cancer cell properties such as fast proliferation, migration, and invasion. Their potential as treatment targets are evaluated based on the current literature.
Classifying emotion in Thai youtube comments

To add more value on YouTube, a popular portal of social media clips, it is worth recognizing automatically the mood of a media clip using the comments given to such clip. This paper presents a method to classify emotion of a Thai media clip on YouTube using the comments given to the clip. Six basic emotions considered are Anger, Disgust, Fear, Happiness, Sadness and Surprise. Performances using three alternative machine learning algorithms, namely multinomial naïve Bayes (MNB), decision tree (DT) and support vector machine (SVM) are compared. As the result, SVM achieves the highest accuracy in the commercial advertisement (AD) genre with an accuracy of 76.14% while MNB with yields the best result in the music video (MV) genre with an accuracy of 84.48%.
Factors affecting anxiety in multiple sclerosis

Purpose: Anxiety is common in people with multiple sclerosis (MS). Little is known about the factors related to anxiety. The aim was to identify factors associated with the presence of anxiety. Methods: This was a cohort study. Participants were sent questionnaires to measure factors potentially related to anxiety. The factors included disability, depression, self-efficacy, locus of control, general stress, psychological distress and factors specific to MS. Participants with significant levels of anxiety, as measured by the Hospital Anxiety and Depression Scale (HADS), were compared to those who were not anxious. Results: Of the 157 participants who took part, 89 (57%) were clinically anxious. Participants who were anxious had a lower level of self-efficacy (p < 0.001), higher level of disability (p < 0.001), higher level of depression (p < 0.001) and higher level of stress (p < 0.001). The regression analysis showed that experiencing depression (χ2 = 5.05, OR = 1.32, p < 0.05) was the only factor that significantly predicted whether someone was anxious or not, accounting for 46% of the variance. Conclusion: There was a high prevalence of anxiety in people with MS. Depression, low levels of self-efficacy, disability and stress increased the likelihood of experiencing anxiety. Implications for Rehabilitation Anxiety and depression are common in people with multiple sclerosis. It is important to identify people experiencing anxiety as it can affect their ability to engage in rehabilitation. Peoples’ perception of their disability can have a significant impact on mood. Rehabilitation programmes should incorporate ways of raising peoples’ self-efficacy.
Spiritual care needs of hospitalized children and their families: a national survey of pastoral care providers' perceptions.

OBJECTIVE Although spirituality is viewed as a vital aspect of the illness experience by most Americans, little is known about this domain of pediatric health care. The objective of this study was to profile pastoral care providers' perceptions of the spiritual care needs of hospitalized children and their parents, barriers to better pastoral care, and quality of spiritual care in children's hospitals. METHODS A cross-sectional mail survey was conducted of pastoral care providers at children's hospitals throughout the United States, with a 67% response rate from 115 institutions. RESULTS Respondents estimated that, among patients they visited, 34% were chronically ill and 21% were clearly dying. Half or more of patients were thought to have spiritual care needs regarding feeling fearful or anxious, coping with pain or other physical symptoms, and regarding their relationship to their parents or the relationship between their parents. Among patients' parents, 60% to 80% were estimated to have felt fearful or anxious, had difficulty coping with their child's pain or other symptoms, sought more medical information about their child's illness, questioned why they and their child were going through this experience, asked about the meaning or purpose of suffering, and felt guilty. Respondents agreed on 3 barriers to providing spiritual care: inadequate staffing of the pastoral care office, inadequate training of health care providers to detect patients' spiritual needs, and being called to visit with patients and families too late to provide all the care that could have been provided. Overall, respondents judged that their hospitals were providing 60% of what they deemed as ideal spiritual care. CONCLUSIONS Pastoral care providers believe that the spiritual care needs of hospitalized children and their parents are diverse and extensive. With system-level barriers cited as limiting the quality of spiritual care, considerable improvement may be possible.
rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids

Identification of chemical compounds with specific biological activities is an important step in both chemical biology and drug discovery. When the structure of the intended target is available, one approach is to use molecular docking programs to assess the chemical complementarity of small molecules with the target; such calculations provide a qualitative measure of affinity that can be used in virtual screening (VS) to rank order a list of compounds according to their potential to be active. rDock is a molecular docking program developed at Vernalis for high-throughput VS (HTVS) applications. Evolved from RiboDock, the program can be used against proteins and nucleic acids, is designed to be computationally very efficient and allows the user to incorporate additional constraints and information as a bias to guide docking. This article provides an overview of the program structure and features and compares rDock to two reference programs, AutoDock Vina (open source) and Schrödinger's Glide (commercial). In terms of computational speed for VS, rDock is faster than Vina and comparable to Glide. For binding mode prediction, rDock and Vina are superior to Glide. The VS performance of rDock is significantly better than Vina, but inferior to Glide for most systems unless pharmacophore constraints are used; in that case rDock and Glide are of equal performance. The program is released under the Lesser General Public License and is freely available for download, together with the manuals, example files and the complete test sets, at http://rdock.sourceforge. net/
Ultrastructure of the mouse epididymal duct with special reference to the regional differences of the principal cells.

It is generally known that spermatozoa aquire the capacity for fertilization during passage through the proximal region of the epididymal duct and are then stored in the distal region of the duct (BEDFORD, 1975; HAMILTON, 1975). The mouse epididymal duct has been divided into five segments (I-V) by light microscopy; Segments I, II and III constitute the head of the epididymis, Segment IV the body, and Segment V the tail; Segments I, II and III seem to belong to the proximal region, and Segments IV and V to the distal region (TAKANO, 1980). In this electron microscope study, we have examined the regional differences of the principal cells of the epididymal duct to understand the functional significance of each segment.The principal cells decrease in height distalwards from Segments I to V. The nucleus is situated basally in the cells, with a well developed Golgi apparatus located above it. The endoplasmic reticulum in Segments I, II and III is generally vesicular, and is distributed throughout the cytoplasm. The ribosomes attached to the endoplasmic reticulum increase in number from Segments I to III. In Segments IV and V, flattened rough endoplasmic reticulum is seen in the basal cytoplasm of the cells. The multivesicular bodies are usually located in the supranuclear cytoplasm. They are large in Segment II and frequent in Segments II and IV. The dense bodies are specific in appearance for the cells in each segment. They are seen in the supranuclear cytoplasm in Segment I and in the infranuclear cytoplasm in Segments III, IV and V. Few dense bodies are found in Segment II. The apical cytoplasm contains coated and non-coated vesicles. These vesicles consist of large and small types in Segments I, II and III. They are of the small type in Segments IV and V. The luminal surface membrane has coated or non-coated invaginations between stereocilia.The findings suggest that the principal cells have secretory and absorptive functions specific for each segment. Discussion shall be made on the possibility that the secretion of the specific epididymal substances may provide the fertilizing ability to spermatozoa and the absorption pertains to the testicular fluid, epididymal secretions and substances bound to spermatozoa.
Antilisterial activity of lactose monolaurate in milk, drinkable yogurt and cottage cheese

Lactose monolaurate (LML) was previously found to be an antimicrobial against Listeria monocytogenes in culture medium at concentrations between 3 and 5 mg ml−1. In this study, the microbial inhibitory activity of LML in dairy products inoculated with a 5‐strain cocktail of clinical isolates of L. monocytogenes was investigated. Addition of LML at a concentration of 5 mg ml−1 resulted in 4·4, 4·0 and 4·2 log reductions in 0·5% fat, 1% fat and 3·25% fat milks, respectively; 4·1, 4·4, and 3·5 log reductions in nonfat, 1% fat, and 1·5% fat yogurts, respectively; and 4·0 log reductions in both nonfat and 2% fat cottage cheese. The inhibitory effect of LML was only observed at 37°C and not 5°C. Experiments suggest that both the lauric acid and the esterified lactose moiety of LML play roles in the growth inhibition.
Bio‐based hyperbranched polyurethane/clay nanocomposites: adhesive, mechanical, and thermal properties

The unison of vegetable oil-based hyperbranched polymers with nanotechnology can unhook myriad of avant-garde applications of such materials. Thus Mesua ferrea L. seed oil-based hyperbranched polyurethane (HBPU)/clay nanocomposites and their performance, with special reference to adhesive strength, are reported for the first time. The nanocomposites of the hyperbranched polyurethane with organically modified nanoclay were obtained by ex situ solution technique and cured by bisphenol-A-based epoxy with poly(amido amine) hardener system. The partially exfoliated and well-distributed structure of nanoclay was confirmed by XRD, SEM, and TEM studies. FTIR spectra indicate the presence of H-bonding between nanoclay and the polymer matrix. Two times improvement in the adhesive strength and scratch hardness, 10 MPa increments in the tensile strength and 112°C more thermo-stability have been observed without much affecting the impact resistance, bending, and elongation at break of the nanocomposites compared to the pristine epoxy modified HBPU system. Thus, the resulted nanocomposites are promising materials for different advanced applications including adhesive. Copyright © 2009 John Wiley & Sons, Ltd.
The effect of anaesthesia and posture on the exchange of respiratory gases and on the heart rate.

RESUME On a etudie experimentalement sur des chevaux les modifications de taux de CO2 et d'O2 durant et apres 45 minutes d'anesthesie generale obtenue soit par thiopentone, soit par chloral soit par Halothane. La respiration spontanee avait lieu soit a l'aide d'un masque (air) soit par absorption sur chaux sodee (enrichi O2). Les tensions d'Oxygene etaient plus basses sur les animaux maintenus en position dorsale (air 56 mm Hg—O2 enrichi 191 mm Hg) par comparaison avec la position laterale (air 67 mm Hg—O2 enrichi 293 mm Hg). Et le retour a la normale ne s'effectuait que lorsque l'animal avait retrouve la station debout (96 mm Hg). On tire de ces observations des conclusions permettant d'accroitre la securite des animaux durant l'anesthesie. ZUSAMMENFASSUNG Bei Versuchspferden wurden die Veranderungen der arteriellen Sauerstoff- (PaO2) und Kohlensaurespannun-gen (PaCO2) wahrend und nach einer 45 Minuten dauernden Allgemeinnarkose mit Thiopenton und Chloroform oder Halothane untersucht. Die Spontanatmung erfolgte entweder durch eine Segeltuchmaske (Luft) oder durch einen Soda-Kalkabsorber (Sauerstoffreiches Gas). Die PaO2-Werte waren tiefer bei Pferden in dorsaler Lage (Luft 56 mm Hg; sauerstoffreich 191 mm Hg) als in lateraler Lage (Luft 67 mm Hg; sauerstoffreich 293 mm Hg) und kehrten nicht zur Norm zuruck (96 mm Hg) bis die Pferde wieder standen. Die PaCO2-Werte erhohten sich von 42.4 mm Hg bis auf 58 mm Hg in der dorsalen Absorber-Gruppe und auf 48 mm Hg in der lateralen Masken-Gruppe. Aufgrund dieser Beobachtungen werden Vorschlage zur Verminderung des Narkoserisikos gemacht.