jimnoneill/paper-to-field-training huggingface dataset:
Selecting Near-Native Protein Structures from Predicted Decoy Sets Using Ordered Graphlet Degree Similarity

Field: Computer Science (Physical Sciences)

Effective prediction of protein tertiary structure from sequence is an important and challenging problem in computational structural biology. Ab initio protein structure prediction is based on amino acid sequence alone, thus, it has a wide application area. With the ab initio method, a large number of candidate protein structures called decoy set can be predicted, however, it is a difficult problem to select a good near-native structure from the predicted decoy set. In this work we propose a new method for selecting the near-native structure from the decoy set based on both contact map overlap (CMO) and graphlets. By generalizing graphlets to ordered graphs, and using a dynamic programming to select the optimal alignment with an introduced gap penalty, a GR_score is defined for calculating the similarity between the three-dimensional (3D) decoy structures. The proposed method was applied to all 54 single-domain targets in CASP11 and all 43 targets in CASP10, and ensemble clustering was used to cluster the protein decoy structures based on the computed CR_scores. The most popular centroid structure was selected as the near-native structure. The experiments showed that compared to the SPICKER method, which is used in I-TASSER, the proposed method can usually select better near-native structures in terms of the similarity between the selected structure and the true native structure.
Diversity of riparian plants of black water ecosystem in the Sebangau River of Central Kalimantan Indonesian

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Riparian vegetation that grows on the bank of the Sebangau river plays an important role in supporting the composition of the biota and the quality of river water. This study aims to investigate the condition of riparian vegetation in the Sebangau river. Sampling was carried out in March 2020 using quadrant methods are with various size 1 × 1 m plots for herb and grass habitus 5 × 5 m for shrub habitus, copses, lianas, and 10 × 10 m plots for tree habitus. The data analyzed were species composition, diversity, and species dominance. The results showed that the plant composition at the study location was characterized by herb and grass habitus where we found 4 families (214 individuals) of grass and herbs, 3 families (135 individuals of shrubs, copses and lianas), and 2 families (282 individuals of tree habitus). The herb and grass habitus were dominated by Hydrilla verticillata species, shrub, copse, and liana habitus were dominated by Pandanus helicopus species, and the dominant species of tree habitus was Shorea balangeran . The low diversity index was found in tree habitus, while for herb and grass habitus and shrubs, shrubs and lianas were classified as moderate diversity.
Leak detection in pipelines by frequency response method

Field: Engineering (Physical Sciences)

A new technique for the detection of leaks in a pipeline is presented utilizing its frequency response. In the system frequency response, a leak increases the amplitude of pressure oscillations at the even harmonics. Such an increase in amplitude has an oscillatory pattern; the frequency and amplitude of this pattern may be utilized to predict the location and discharge of a leak. In this technique, the pressure transient history at one location is sufficient and the history of the transient in the pipe prior to leak is not needed; this makes it advantageous over a number of other existing techniques, in addition to being simpler to use. It is shown that the technique successfully detects the location of a leak in a number of simple systems with leak discharge as low as 0.2% of the steady discharge. The technique is verified by comparing the results with those computed by using the method of characteristics. Practical issues and limitations for field implementations are discussed.
Cationic perfluorinated polyelectrolyte as an electrode modifier

Field: Chemistry (Physical Sciences)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCationic perfluorinated polyelectrolyte as an electrode modifierNoboru. Oyama, Takeo. Ohsaka, and Takeyoshi. OkajimaCite this: Anal. Chem. 1986, 58, 4, 979–981Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/ac00295a070https://doi.org/10.1021/ac00295a070research-articleACS PublicationsRequest reuse permissionsArticle Views85Altmetric-Citations30LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Investigation of Physicochemical Drug Properties to Prepare Fine Globular Granules Composed of Only Drug Substance in Fluidized Bed Rotor Granulation

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The effect of some drug properties (wettability and particle size distribution) on granule properties (mean particle size, particle size distribution, sphericity, and granule strength) were investigated in a high (>97%) drug-loading formulation using fluidized bed rotor granulation. Three drugs: acetaminophen (APAP); ibuprofen (IBU); and ethenzamide (ETZ) were used as model drugs based on their differences in wettability and particle size distribution. Granules with mean particle sizes of 100-200 µm and a narrow particle size distribution (PSD) could be prepared regardless of the drug used. IBU and ETZ granules showed a higher sphericity than APAP granules, while APAP and ETZ granules exhibited higher granule strength than IBU. The relationship between drug and granule properties suggested that the wettability and the PSD of the drugs were critical parameters affecting sphericity and granule strength, respectively. Furthermore, the dissolution profiles of granules prepared with poorly water-soluble drugs (IBU and ETZ) showed a rapid release (80% release in 20 min) because of the improved wettability with granulation. The present study demonstrated for the first time that fluidized bed rotor granulation can prepare high drug-loaded (>97%) globular granules with a mean particle size of less than 200 µm and the relationship between physicochemical drug properties and the properties of the granules obtained could be readily determined, indicating the potential for further application of this methodology to various drugs.
URBAN FURNITURE: from gazebo to digi-booth

Field: Engineering (Physical Sciences)

Recent years have seen the steady increase of automated kiosks and temporary structures that begin to replace traditional building types. In this course we studied and analyzed the development of the gazebo/kiosk in urban/rural settings both inside and outside over time, assessed its value for commerce and social equity, proposed a forward projection regarding the role digital info-booths/commercial kiosks will play in our urban environment, and developed new spatial models that can become an integral part of our daily experience.
Clinical application of a stereolithographic tooth replica and surgical guide in tooth autotransplantation

Field: Dentistry (Health Sciences)

In recent years rapid prototyping technologies have been an indispensable tool in several studies on diagnosis, treatment planning and oral and maxillofacial surgery. A clinical case is presented employing a cone beam computed tomography (CBCT) based stereolithographic tooth replica and surgical guide in order to reduce injury to the periodontal ligament of the donor tooth in the autotransplantation procedure. Virtual 3D surgery is planned. A tooth replica and surgical guide were fabricated prior to surgery and used during the autotransplantation procedure. The use of stereolithographic models may be advantageous in diagnosis and treatment planning. It provides an accurate method to produce models of donor teeth that serve as prototypes for recipient site preparation in tooth autotransplantation procedures.
A population pharmacokinetic model of piperaquine in pregnant and non-pregnant women with uncomplicated Plasmodium falciparum malaria in Sudan

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

Pregnancy is associated with an increased risk of developing a malaria infection and a higher risk of developing severe malaria. The pharmacokinetic properties of many anti-malarials are also altered during pregnancy, often resulting in a decreased drug exposure. Piperaquine is a promising anti-malarial partner drug used in a fixed-dose combination with dihydroartemisinin. The aim of this study was to investigate the population pharmacokinetics of piperaquine in pregnant and non-pregnant Sudanese women with uncomplicated Plasmodium falciparum malaria.Symptomatic patients received a standard dose regimen of the fixed dose oral piperaquine-dihydroartemisinin combination treatment. Densely sampled plasma aliquots were collected and analysed using a previously described LC-MS/MS method. Data from 12 pregnant and 12 non-pregnant women were analysed using nonlinear mixed-effects modelling. A Monte Carlo Mapped Power (MCMP) analysis was conducted based on a previously published study to evaluate the power of detecting covariates in this relatively small study.A three-compartment disposition model with a transit-absorption model described the observed data well. Body weight was added as an allometric function on all clearance and volume parameters. A statistically significant decrease in estimated terminal piperaquine half-life in pregnant compared with non-pregnant women was found, but there were no differences in post-hoc estimates of total piperaquine exposure. The MCMP analysis indicated a minimum of 13 pregnant and 13 non-pregnant women were required to identify pregnancy as a covariate on relevant pharmacokinetic parameters (80% power and p=0.05). Pregnancy was, therefore, evaluated as a categorical and continuous covariate (i.e. estimate gestational age) in a full covariate approach. Using this approach pregnancy was not associated with any major change in piperaquine elimination clearance. However, a trend of increasing elimination clearance with increasing gestational age could be seen.The population pharmacokinetic properties of piperaquine were well described by a three-compartment disposition model in pregnant and non-pregnant women with uncomplicated malaria. The modelling approach showed no major difference in piperaquine exposure between the two groups and data presented here do not warrant a dose adjustment in pregnancy in this vulnerable population.
Ecological constraints and distribution of the primitive and enigmatic endemic Mexican butterflyBaronia brevicornis(Lepidoptera: Papilionidae)

Field: Agricultural and Biological Sciences (Life Sciences)

Abstract Baronia brevicornis Salvin (Lepidoptera: Papilionidae) is one of the most enigmatic butterflies in the world and possibly represents the most ancient lineage among the superfamily Papilionoidea. Its geographic distribution is remote from that of all its potential close relatives and many of its biological and ecological characteristics are unique among the suborder Rhopalocera. One of its particularities is that the occurrence plots of this species seem to be independent, each representing individual populations, despite the fact that the host plant: Acacia cochliacantha Humboldt and Bonpland ex Willdenow (Fabaceae), is one of the most common Mexican Fabaceae species. Our results show that no B. brevicornis populations occur if the host plant does not cover at least two-thirds of the locality. Even in the most favourable zones, the landscape occupancy of the butterfly does not exceed 2.5% of the available habitat even when its host plant covers 50% of the area. The average density of adults was 840 individuals/ha in favourable habitats, frequently on areas of around 3 ha, below of 1400 m. Using the BIOMOD2 package and the largest available set of abiotic conditions for Mexico implemented in the WorldClim database, we propose a revised potential distribution and discuss the results of our model with field occurrence data. Evolutionary and conservation issues are discussed in the light of our results.
Sn-Doped V2O5 Film with Enhanced Lithium-Ion Storage Performance

Field: Materials Science (Physical Sciences)

Homogeneous Sn-doped V2O5 sol was prepared by the sol–gel method with H2O2, V2O5, and SnCl4·5H2O as precursors, and the films were fabricated by drop-casting, drying at ambient, and then annealing at 450 °C in air for 2 h. X-ray photoelectron spectroscopy (XPS) reveals that the Sn-doped V2O5 film contains 10% V4+ likely compensates with the accommodation of Sn4+ ions. Electrochemical and lithium-ion intercalation properties of both the pure and Sn-doped V2O5 films are systematically studied by means of cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and chronopotentiometry (CP) tests. The Sn-doped V2O5 film shows much enhanced lithium-ion storage capacity, faster kinetics, and improved cyclic stability in comparison with pure V2O5 film. For example, after 50 cycles, the specific capacity of the Sn-doped V2O5 film retains 334 mAh g–1 with a current density of 500 mA g–1, much higher than 157 mAh g–1 of the pure V2O5 film. Sn-doping is found to reduce the electrochemical reaction resistance, increase the electrochemical reaction reversibility, and enhance the lithium-ion diffusivity. The possible explanation for such significant enhancement in lithium-ion intercalation capacity and cyclic stability of the Sn-doped V2O5 film is discussed.
Profiling wound healing with wound effluent: Raman spectroscopic indicators of infection

Field: Medicine (Health Sciences)

The care of modern traumatic war wounds remains a significant challenge for clinicians. Many of the extremity wounds inflicted during Operation Enduring Freedom and Operation Iraqi Freedom are colonized or infected with multi-drug resistant organisms, particularly Acinetobacter baumannii. Biofilm formation and resistance to current treatments can significantly confound the wound healing process. Accurate strain identification and targeted drug administration for the treatment of wound bioburden has become a priority for combat casualty care. In this study, we use vibrational spectroscopy to examine wound exudates for bacterial load. Inherent chemical differences in different bacterial species and strains make possible the high specificity of vibrational spectroscopy.
Transgenic animals and prion diseases

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Abstract Extract Thank you for the opportunity to respond to Peter Wills's letter on transgenic animals and prion diseases. Dr Wills has written an interesting letter, but the reader must note that only extreme cases are being argued. No biotech process has yet sought to produce a biological molecule which is non-native to the transgene, and to suggest, for example, that transgenic sheep producing human growth hormone will produce an aberrant protein of pathological potential is stretching a point.
Discourses of “Democratic Racism“ in the Talk of South Asian Canadian Women

Field: Social Sciences (Social Sciences)

Despite societal norms of tolerance and diversity, covert “democratic” racism (Henry and Tator 2006) flourishes in Canada on individual and systemic levels. Democratic racism, an ideology that allows the coexistence of both egalitarian values and racist attitudes, beliefs, and behaviours, is often expressed by the dominant group through powerful discourses that shape the social reality for many minority individuals. However, racist discourses, such as blaming the target of racism and denying that racism exists, are often manifested very subtly. In this article, we use democratic racism as a framework to investigate the multiple ways in which our participants — South Asian Canadian women — described their experiences of racism. A discourse analysis of participants’ talk revealed that they used various rhetorical strategies and discursive devices to avoid attributing negative experiences as racism. Surprisingly, we found that the same discourses used by the dominant group to dismiss and erase racism are available to, and are also utilized by, members of visible minority groups. We conclude by discussing possible reasons why participants in the study might deny racism. We also note the societal implication of such denial: racism becomes invisible, both to the perpetrators and the targets, and systemic inequalities and injustices remain unchallenged. Malgré les normes sociétales de tolérance et de diversité. un racisme «démocratique» sous-jacent (Henry and Tator 2006) fleurit au Canada à deux niveaux : individuel et systémique. Idéologie qui permet la coexistence à la fois de valeurs d’égalité et d’attitudes, de croyances et de comportements raciaux, il imprègne souvent un discours drastique tenu par le groupe dominant et qui altère la réalité sociale vécue par nombre de personnes minoritaires. Le racisme, cependant, se manifeste souvent de manière très subtile, par exemple en blâmant sa cible et en niant sa propre existence. Dans cet article, sa forme démocratique nous sert de cadre pour enquêter sur les multiples façons dont nos participantes — des Canadiennes sud-asiatiques — décrivent leur expérience dans ce domaine. Une analyse discursive de leurs propos révèle qu’elles se servent de stratégies rhétoriques et de moyens d’expression variés pour éviter d’attribuer au racisme des expériences négatives. Nous avons étonnamment découvert que le discours employé par les membres de groupes de minorités visibles était le même que celui dont se sert le groupe dominant pour démentir et gommer son racisme. Nous concluons en analysant les raisons possibles qui porteraient les participantes à cette étude à un tel déni. Nous en notons aussi les implications sociétales : le racisme devient invisible, et pour les auteurs, et pour leurs cibles; par ailleurs, aucune contestation ne remet en question les inégalités et les injustices systémiques.
Botanical and microbial insecticides application in aquaponics - is there a risk for biofilter bacteria and fish?

Field: Agricultural and Biological Sciences (Life Sciences)

Aquaponics is a food production system that combines aquaculture with hydroponics. The simultaneous existence of fish, beneficial bacteria and plants in the same water loop predisposes the fish and bacteria to a possible detrimental effect of plant protection products. Additionally, there is an inadequate exploration of scientific studies on the impact of pesticides on fish and bacteria in aquaponics systems. This study investigated the effects of three commercial insecticides based on the following active ingredients: pyrethrum, azadirachtin, and spinosad, on aquaponics systems. Due to ethical concerns in animal testing, applying insecticides directly to aquaponics setup was impossible. Therefore, three separate experiments were conducted: (1) Pesticide runoff rate – in which insecticides were applied to basil ( Ocimum basilicum ) plants grown in two hydroponic systems: media bed and floating raft. The concentrations of applied insecticides were measured in the water of nutrient solutions of the hydroponics after 1, 3, 6, 12, 24, 36, 48, 72 and 96h to establish a pattern of degradation of insecticides. The result from this experiment showed that pyrethrum and spinosad were detected in unquantifiable concentrations in the nutrient solutions. Hence, further experiments were conducted only with azadirachtin. In a biofilter trial (2) – azadirachtin, at three concentrations (1.5 µg L -1 ; 7.5 µg L -1 ; and 15 µg L -1 ), was added to a running biofilter to investigate the effects on nitrifying bacteria. Mild effects were recorded in the nitrification and bacteria microbiome. In the third trial (3) – Nile tilapia ( Oreochromis niloticus ) were exposed to similar concentrations of azadirachtin for seven days (and the same period for recovery) to investigate effects on fish hematology, blood biochemistry, antioxidative enzymes in the brain, gills, muscle, liver and intestine and histopathology of gills and liver. Results showed mild effects in hematology and biochemistry profile in fish and higher levels of lipid peroxidation in the liver during the exposure. The results indicate a safe use of pyrethrum and spinosad in aquaponics setup, while azadirachtin has to be used with care, especially in coupled aquaponics systems.
Biological characterization of angiopoietin‐3 and angiopoietin‐4

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

ABSTRACT The angiopoietin (Ang) family of growth factors includes Ang1, Ang2, Ang3, and Ang4, all of which bind to the endothelial receptor tyrosine kinase Tie2. Ang3 (mouse) and Ang4 (human) are interspecies orthologs. In experiments with human endothelial cell lines, Ang3 was identified as an antagonist of Tie2 and Ang4 was identified as an agonist of Tie2. However, the biological roles of Ang3 and Ang4 are unknown. We examined the biological effect of recombinant Ang3 and Ang4 proteins in primary cultured endothelial cells and in vivo in mice. Recombinant Ang3 and Ang4 formed disulfide‐linked dimers. Ang4 (400 ng/mL) markedly increased Tie2 and Akt phosphorylation in primary cultured HUVECs whereas Ang3 (400 ng/mL) did not produce significant changes. Accordingly, Ang4, but not Ang3, induced survival and migration in primary cultured HUVECs. Unexpectedly, intravenously administered Ang3 (30 µg) was more potent than Ang4 (30 µg) in phosphorylating the Tie2 receptor in lung tissue from mice in vivo. Accordingly, Ang3 was more potent than Ang4 in phosphorylating Akt in primary cultured mouse lung microvascular endothelial cells. Ang3 and Ang4 both produced potent corneal angiogenesis extending from the limbus across the mouse cornea in vivo. Thus, Ang3 and Ang4 are agonists of Tie2, but mouse Ang3 has strong activity only on endothelial cells of its own species.—Lee, H. J., Cho, C.‐H., Hwang, S.‐J., Choi, H.‐H., Kim, K.‐T., Ahn, S. Y., Kim, J.‐H., Oh, J.‐L., Lee, G. M., Koh, G. Y. Biological characterization of angiopoietin‐3 and angiopoietin‐4. FASEB J . 18, 1200–1208 (2004)