Miracle-dz/UniFAR-FTUs huggingface dataset:
On the Pseudo Phase Diagram of Single Semi-Flexible Polymer Chains: A Flat-Histogram Monte Carlo Study

Local stiffness of polymer chains is instrumental in all structure formation processes of polymers, from crystallization of synthetic polymers to protein folding and DNA compactification. We present Stochastic Approximation Monte Carlo simulations—a type of flat-histogram Monte Carlo method—determining the density of states of a model class of single semi-flexible polymer chains, and, from this, their complete thermodynamic behavior. The chains possess a rich pseudo phase diagram as a function of stiffness and temperature, displaying non-trivial ground-state morphologies. This pseudo phase diagram also depends on chain length. Differences to existing pseudo phase diagrams of semi-flexible chains in the literature emphasize the fact that the mechanism of stiffness creation matters.
Genome-wide association study of the plasma triglyceride response to an n-3 polyunsaturated fatty acid supplementation[S]

Studies have shown a large interindividual variability in plasma TG response to long-chain n-3 PUFA supplementation, which may likely be attributable to genetic variability within the populations studied. The objective is to compare the frequency of SNPs in a genome-wide association study between responders (reduction in plasma TG levels ≥0.01 mM) and nonresponders (increase in plasma TG of ≥0 mM) to supplementation. Genomic DNA from 141 subjects who completed a 2-week run-in period followed by 6-week supplementation with 5 g of fish oil daily (1.9–2.2 g EPA and 1.1 g DHA daily) were genotyped on Illumina HumanOmni-5-QuadBeadChip. Thirteen loci had frequency differences between responders and nonresponders (P < 1 × 10−5), including SNPs in or near IQCJ-SCHIP1, MYB, NELL1, NXPH1, PHF17, and SLIT2 genes. A genetic risk score (GRS) was constructed by summing the number of risk alleles. This GRS explained 21.53% of the variation in TG response to n-3 PUFA supplementation when adjusted for age, sex, and BMI (P = 0.0002). Using Fish Oil Intervention and Genotype as a replication cohort, the GRS was able to explain 2% of variation in TG response when adjusted. In conclusion, subjects who decrease their plasma TG levels following n-3 PUFA supplementation may have a different genetic profile than individuals who do not respond.
Outbreak of JK diphtheroid infections associated with environmental contamination

The group JK diphtheroid organism is a multiply resistant opportunistic pathogen which infects immunocompromised patients sporadically. We describe the first reported outbreak of JK diphtheroid infections, in which four cases of bacteremia and one Hickman catheter site infection occurred during 4 weeks on a hematology ward. On this ward, JK diphtheroid was recovered from 17 of 39 patients, 10 of 17 30-ft3 (0.840-m3) air samples, surfaces in 9 of 13 patient rooms, and hands of 4 of 22 personnel. Previously identified risk factors for JK diphtheroid sepsis (male gender, broad-spectrum antibiotic therapy, granulocytopenia, and prolonged hospital stay) were present in infected patients but did not distinguish them from patients who were only colonized. Emphasis on aseptic practices was associated with termination of the outbreak and negative hand cultures from personnel, despite continued patient colonization and environmental contamination.
Product Fit Uncertainty in Online Markets: Nature, Effects and Antecedents

Product fit uncertainty defined as the degree to which a consumer cannot assess whether a product's attributes match her preference is proposed to be a major impediment to online markets with costly product returns and lack of consumer satisfaction. We conceptualize the nature of product fit uncertainty as an information problem and theorize its distinct effect on product returns and consumer satisfaction versus product quality uncertainty, particularly for experience versus search goods without product familiarity. To reduce product fit uncertainty, we propose two Internet-enabled systems---website media visualization systems and online product forums collaborative shopping systems---that are hypothesized to attenuate the effect of product type experience versus search goods on product fit uncertainty. Hypotheses that link experience goods to product returns through the mediating role of product fit uncertainty are tested with analyses of a unique data set composed of secondary data matched with primary direct data from numerous consumers who had recently participated in buy-it-now auctions. The results show the distinction between product fit uncertainty and quality uncertainty as two distinct dimensions of product uncertainty and interestingly show that, relative to product quality uncertainty, product fit uncertainty has a significantly stronger effect on product returns. Notably, whereas product quality uncertainty is mainly driven by the experience attributes of a product, product fit uncertainty is mainly driven by both experience attributes and lack of product familiarity. The results also suggest that Internet-enabled systems are differentially used to reduce product fit and quality uncertainty. Notably, the use of online product forums is shown to moderate the effect of experience goods on product fit uncertainty, and website media are shown to attenuate the effect of experience goods on product quality uncertainty. The results are robust to econometric specifications and estimation methods. The paper concludes by stressing the importance of reducing the increasingly prevalent information problem of product fit uncertainty in online markets with the aid of Internet-enabled systems.
The right compound in the right assay at the right time: an integrated discovery DMPK strategy

The high rate of attrition during drug development and its associated high research and development (R&D) cost have put pressure on pharmaceutical companies to ensure that candidate drugs going to clinical testing have the appropriate quality such that the biological hypothesis could be evaluated. To help achieve this ambition, drug metabolism and pharmacokinetic (DMPK) science and increasing investment have been deployed earlier in the R&D process. To gain maximum return on investment, it is essential that DMPK concepts are both appropriately integrated into the compound design process and that compound selection is focused on accurate prediction of likely outcomes in patients. This article describes key principles that underpin the contribution of DMPK science for small-molecule research based on 15 years of discovery support in a major pharmaceutical company. It does not aim to describe the breadth and depth of DMPK science, but more the practical application for decision making in real-world situations.
Ghrelin in Chronic Kidney Disease: Too Much or Too Little?

Ghrelin is produced in the stomach and acts on growth hormone (GH) secretagogue receptors in hypothalamic regions to potently increase food intake and body weight, with additional effects on blood glucose levels and inflammation. Elevated ghrelin levels have been associated with the poor nutritional status in patients with chronic kidney disease (CKD). However, in this issue of Peritoneal Dialysis International (PDI), Szczepańska et al. report that plasma ghrelin levels are similar in CKD children on dialysis compared with patients on conservative treatment and healthy controls with normal renal function (1). This commentary highlights the confounding factors for the measurement of serum ghrelin concentrations in cross-sectional studies of patients with CKD, factors that may contribute to these seemingly contradicting results. Potential therapeutic application of ghrelin in CKD is also discussed.
Characterization of Paroxysmal and Persistent Atrial Fibrillation in the Human Left Atrium During Initiation and Sustained Episodes

Characterization of AF in the LA. Introduction: Atrial fibrillation (AF) in the left atrium (LA) is poorly defined in terms of regional differences in the degree of organization, characteristics of paroxysmal and persistent variants, and electrophysiologic events that develop at the onset of episodes.
Pharmacognostical Studies & Phytochemical Evaluation of the Stem Barks of Embilica Officinalis Gaertn.

To investigate the pharmacognostic parameter, physico-chemical parameters, fluorescence analysis, preliminary phytochemical screening, and Thin Layer Chromatographic analysis of the stem barks of the plant Embilica officinalis Gaertn. The air-dried and powder bark of the plant Embilica officinalis Gaertn (Euphorbiaceae) were studied by morphology, microscopy, florescence analysis, preliminary phytochemical screening and thin layer analysis of powdered drug. Other physicochemical parameters were also performed as per WHO guidelines. The dried powder leaves were investigated by morphology. The results of physic-chemical parameters such as loss on drying, ash values and extractive values, fluorescence analysis, preliminary phytochemical screening and TLC are summarized here. The present information on the pharmacognostic evaluation of the plant drug Embilica officinalis Gaertn delivered the qualitative and quantitative parameters serve the important information to the identity and to determine the quality and purity of the plant material in the future. It also signify the important information of the closely related other species and varieties. © 2011 IGJPS. All rights reserved.
Role of phosphate solubilizing bacteria (PSB) in enhancing P availability and promoting cotton growth.

Plant growth promoting rhizobacteria (PGPR) mediate the soil processes such as decomposition, nutrient mobilization, mineralization, solubilization, nitrogen fixation and growth hormone production. Microorganisms having the phosphate solubilizing capacity can convert the insoluble phosphates into soluble forms through the production of organic acids. Inoculation of seed with P-solubilizing microorganisms is a promising technique which may alleviate the deficiency of phosphorus. This bioavailability of soil inorganic phosphorus in the rhizosphere varies considerably with plant species and nutritional status of soil. A field experiment was conducted at Fiber Crops Section, Ayub Agricultural Research Institute (AARI) Faisalabad to assess the ability of P-solubilizing rhizobacteria to enhance the growth and yield of cotton. Isolation and screening of P-solubilizer on Pikovskaya’s medium was carried out at the Soil Bacteriology Section Faisalabad. The trial was conducted on clay loam soil with pH 8.3, EC 2.8 dSm, N 0.040 %, organic matter 0.75% and available P 10.3 mg kg with three fertilizer levels viz. 120-30, 120-60, 120-90 kg NP ha with and without P-solubilizer (Bacillus sp.) inoculum. Results revealed that bacterial inoculum produced significantly higher seed cotton yield 1630 as compared to 1511 kg ha. The highest seed cotton yield was observed at highest fertilizer level i.e. 1733 kg ha with inoculum. The physical parameters like plant height, number of bolls per plant and boll weight and soil available P determined at regular intervals (30, 60, 90, days after sowing) was also found higher in the inoculated treatments. More exploration of this area of research should be carried out in different ecologies to compensate the mineral fertilizers
Further Reading on Lock-Free Shared Data Structures for ESSCaSS 2011 Participants

The lectures at ESSCaSS will only scratch the surface of research on lock-free data structures. The following reading list describes where to find more information on the material that was presented, and gives some pointers to interesting papers that can serve as starting points in the literature for various topics. Feel free to contact me for more information about these topics. (Contact information is on my web page www.cse.yorku.ca/∼ruppert.)
Instance-based ensemble pruning for imbalanced learning

Class-imbalance is very common in real world. However, traditional state-of-the-art classifiers do not work well on imbalanced data sets for imbalanced class distribution. This paper considers imbalance learning from the viewpoint of ensemble pruning, and proposes a novel approach called IBEP (Instance-Based Ensemble Pruning) to improve classifier’s performance on these data sets. Unlike traditional approaches which consider imbalance problem in training stage, IBEP focuses on the problem in prediction stage. Given an unlabeled instance, IBEP tries to search for the k nearest neighbors as the corresponding pruning set and adopts ensemble pruning strategy to select a subset of ensemble members to form sub-ensemble based on the pruning set to predict the instance. In this way, IBEP pays more attention to rare class and achieves better performance on imbalanced data set. Besides, two widely used sampling techniques, under-sampling and SMOTE, are skillfully combined with IBEP to further improve its performance. Experimental results on 14 data sets show that IBEP performs significantly better than many state-of-the-art classification methods on all metrics used in this paper including recall, f -measure and g-mean.
Neonatal startles, smiles, erections, and reflex sucks as related to state, sex, and individuality.

Frequencies of startles, reflex smiles, erections, and reflex sucks were recorded in the context of the state in which they occurred in 32, 2- to 3-dayold healthy neonates. States were monitored for each infant during 2 hours and 20 minutes divided in 6 observation periods. Observer agreements ranged from 80 percent to 100 percent on the infants' states and from 93 to 100 percent on the spontaneous behaviors. Results confirm Wolff's findings (1966) that there is a highly significant relation between state and the type and frequency of the spontaneous behaviors. The frequencies are highest during regular sleep when the infant is most deafferented and they diminish in direct proportion to the infant's closeness to wakefulness. Results on sex differences reflect a consistent trend that males startle more in all states and females engage more frequently in reflex smiles and bursts of rhythmical mouthing. Since the mean rate of the spontaneous behaviors is almost identical for males and females when erections are excluded, it appears that females make up in smiles and reflex sucks what they lack in startles. The data also suggest that erections are spontaneous behaviors which occur over and above the other discharge behaviors. Rank correlations showed that individual infants tend to rely heavily on specific discharge channels over states (e.g., .77 for erections, .53 for rhythmical mouthing). The discussion focuses on the possible function of the spontaneous behaviors for providing endogenous afferent stimulation under conditions of deafferentation, during a period when such stimulation may be critical for the developing central nervous system, and on the potential significance of these behaviors for later development.
The Mammalian Chitinase-like Lectin, YKL-40, Binds Specifically to Type I Collagen and Modulates the Rate of Type I Collagen Fibril Formation*

YKL-40 is expressed in arthritic cartilage and produced in large amounts by cultured chondrocytes, but its exact role is unclear, and the identities of its physiological ligands remain unknown. Purification of YKL-40 from resorbing bovine nasal cartilage and chondrocyte monolayers demonstrated the existence of three isoforms, a major and minor form from resorbing cartilage and a third species from chondrocytes. Affinity chromatography experiments with purified YKL-40 demonstrated specific binding of all three forms to collagen types I, II, and III, thus identifying collagens as potential YKL-40 ligands. Binding to immobilized type I collagen was inhibited by soluble native ligand, but not heat-denatured ligand, confirming a specific interaction. Binding of the chondrocyte-derived species to type I collagen was also demonstrated by surface plasmon resonance analysis, and the dissociation rate constant was calculated (3.42 × 10-3 to 4.50 × 10-3 s-1). The chondrocyte-derived species was found to prevent collagenolytic cleavage of type I collagen and to stimulate the rate of type I collagen fibril formation in a concentration-dependent manner. By contrast, the cartilage major form had an inhibitory effect on type I collagen fibrillogenesis. Digestion with N-glycosidase F, endoglycosidase H and lectin blotting did not reveal any difference in the carbohydrate component of these two YKL-40 species, indicating that this does not account for the opposing effects on fibril formation rate.
The enzyme and inhibitors of 4-ene-3-oxosteroid 5 alpha-oxidoreductase.

Since evidence of 5 alpha-reductase activity in rabbit liver homogenate was discovered in 1954, the presence of this enzyme has been demonstrated in many other organs and tissues of mammalian species. 5 alpha-Reductase selectively transforms a 4-ene-3-oxosteroid (e.g., testosterone) irreversibly to the corresponding 5 alpha-3-oxosteroid (e.g., 5 alpha-dihydrotestosterone) in the presence of NADPH as an essential coenzyme at an optimal pH. However, excessive production of 5 alpha-dihydrotestosterone is the major cause of many androgen-related disorders, such as prostate cancer, benign prostatic hyperplasia, acne, female hirsutism, and male pattern baldness; therefore, inhibition of androgenic action by 5 alpha-reductase inhibitors is a logical treatment. During the past two decades, research has focused on understanding the biological functions and effects of 5 alpha-reductase and its 5 alpha-reduced metabolites: purification of the enzyme, substrates, and metabolites; characterization of their physical, chemical, and biochemical properties; analysis of the amino acid sequence of the enzyme; synthesis of various classes of molecules as potential inhibitors; and examination of the biological activity of the inhibitors in vitro and/or in vivo. This review summarizes the biochemical studies on this enzyme, suggests the mechanisms of action of the enzyme or inhibitors, and discusses the chemistry necessary for the preparation, structure-activity relationships, and in vitro and/or in vivo data obtained from the evaluation of nonsteroidal and steroidal compounds that have been tested as inhibitors of 5 alpha-reductase. In particular, IC50 and Ki values for relevant compounds will be compared according to molecular class. This review could function as a comprehensive working reference of what research has been accomplished so far and what problems remain to be solved in the future for those engaged in this interesting field.
Toward Semantic Cryptography APIs

While several mature cryptographic frameworks exist, and have been utilized for building complex applications, developers often use these frameworks incorrectly and introduce security vulnerabilities. This stems from several challenges, including (i) an expectation that framework users understand security attacks and defenses and the subtle impact of various low level parameters, (ii) the need to take into account information external to the system to ensure security (e.g. TLS certificate revocations), and (iii) the frequent need to disable security checks during development and testing, as sometimes these checks remain disabled in production. We propose guidelines for designing cryptography APIs that are semantically meaningful for developers and that can be implemented consistently on top of existing frameworks. We also propose the Regulator design pattern, for incorporating security-critical external information, and build management hooks for isolating security workarounds needed during the development and test phases. Our API is a first step toward striking the right balance between restricting the security decisions that developers make and giving them the flexibility needed for complex applications that use cryptography.
How to Best Classify Rural and Urban?

While “agricultural and rural development” is one of the key policy areas, there is no universally accepted way on how to classify the urban and rural. On one hand, dissatisfied with the OECD approach in which a “rural area” is defined merely based on the population density, there has been a rich literature in the statistical discourse and policy debate on what other variables should be considered and included for the urban-rural typology. On the other hand, according to the rural areas observed in OECD countries, where the population has migrated to the urban and agricultural production has become less important, some people argue that the traditional way of thinking “rural” as the same of “agricultural” is not true anymore for the developed countries and the same transformation is going on in the developing countries. The salient feature of this paper is to apply an econometric logistic regression model to two datasets for Italy, an OECD country and China, a non-OECD country. The results of the model unambiguously demonstrate that, first, to classify the rural and urban, a multidimensional approach by taking into account both economic activities and geographic dimension along with population density is more appropriate; and second, agriculture is still highly relevant to the rural, and thus an important determinant factor in defining the rural area.
Single Mucosal, but Not Parenteral, Immunization with Recombinant Adenoviral-Based Vaccine Provides Potent Protection from Pulmonary Tuberculosis1

Bacillus Calmette-Guérin (BCG) vaccine has failed to control the global tuberculosis (TB) epidemic, and there is a lack of safe and effective mucosal vaccines capable of potent protection against pulmonary TB. A recombinant replication-deficient adenoviral-based vaccine expressing an immunogenic Mycobacterium tuberculosis Ag Ag85A (AdAg85A) was engineered and evaluated for its potential to be used as a respiratory mucosal TB vaccine in a murine model of pulmonary TB. A single intranasal, but not i.m. , immunization with AdAg85A provided potent protection against airway Mycobacterium tuberculosis challenge at an improved level over that by cutaneous BCG vaccination. Systemic priming with an Ag85A DNA vaccine and mucosal boosting with AdAg85A conferred a further enhanced immune protection which was remarkably better than BCG vaccination. Such superior protection triggered by AdAg85 mucosal immunization was correlated with much greater retention of Ag-specific T cells, particularly CD4 T cells, in the lung and was shown to be mediated by both CD4 and CD8 T cells. Thus, adenoviral TB vaccine represents a promising novel vaccine platform capable of potent mucosal immune protection against TB. Our study also lends strong evidence that respiratory mucosal vaccination is critically advantageous over systemic routes of vaccination against TB.