bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pharmacophore, 3D‐QSAR, and Bayesian Model Analysis for Ligands Binding at the Benzodiazepine Site of GABAA Receptors: the Key Roles of Amino Group and Hydrophobic Sites
Authors: Yang Ying , Zhang Wei , Cheng Jiagao , Tang Yun , Peng Yanqing , Li Zhong 
Published: December 2012

Ligands binding at the benzodiazepine site of GABAA receptor play important pharmacological roles in clinical application. In this study, ligand‐based pharmacophore modeling, 3D‐QSAR analysis, and Bayesian model studies have been performed on a set of 84 diverse ligands binding at the benzodiazepine site. The results showed the best pharmacophore hypothesis AADHR.4, which included two hydrogen acceptors (A), one hydrogen donor (D), one hydrophobic group (H), and one aromatic ring (R). Atom‐based 3D‐QSAR model was built, and it showed good statistical significance (R2 = 0.936) and excellent predictive ability (Q2 = 0.821). Moreover, Bayesian model was developed and used to identify the key molecular features which are good or bad for the ligand binding activity. All the results from the pharmacophore, 3D‐QSAR, and Bayesian modeling studies revealed that a hydrogen‐bond donor (e.g., N‐H) and a hydrophobic group (e.g., Br) are critical structural features for the ligands binding at the benzodiazepine site.
Differential effect on cell-mediated immunity in human volunteers after intake of different lactobacilli
Authors: Rask C , Adlerberth I , Berggren A , Ahrén I L , Wold A E 
Published: December 2012

SummaryProbiotics are live microorganisms which have beneficial effects on the host when ingested in adequate amounts. Probiotic bacteria may stimulate immune effector functions in a strain-specific manner. In this blind placebo-controlled trial, we investigated the effects on the immune system following daily intake of six different strains of lactobacilli or the Gram-negative bacterium Pseudomonas lundensis for 2 or 5 weeks. Blood lymphocyte subsets were quantified by fluorescence activated cell sorter and the expression of activation and memory markers was determined. The bacterial strains were also examined for their capacity to adhere to human intestinal cells and to be phagocytosed by human peripheral blood mononuclear cells. Intake of Lactobacillus plantarum strain 299v increased the expression of the activation marker CD25 (P = 0·01) on CD8+ T cells and the memory cell marker CD45RO on CD4+ T cells (P = 0·03), whereas intake of L. paracasei tended to expand the natural killer T (NK T) cell population (P = 0·06). The phagocytic activity of granulocytes was increased following intake of L. plantarum 299v, L. plantarum HEAL, L. paracasei or L. fermentum. In contrast, ingestion of L. rhamnosus decreased the expression of CD25 and CD45RO significantly within the CD4+ cell population. The observed immune effects after in-vivo administration of the probiotic bacteria could not be predicted by either their adherence capacity or the in-vitro-induced cytokine production. The stimulation of CD8+ T cells and NK T cells suggests that intake of probiotic bacteria may enhance the immune defence against, e.g. viral infections or tumours.
Data mining based storage assignment heuristics for travel distance reduction
Authors: Ming‐Huang Chiang David , Lin Chia‐Ping , Chen Mu‐Chen 
Published: December 2012

AbstractAmong the warehousing activities in distribution centres, order picking is the most time‐consuming and labour‐intensive. As a result, order picking may become a bottleneck preventing distribution centres from maximizing the effectiveness of their warehousing activities. Although storage location assignment (or product allocation) is a tactical decision, it is especially influential on the effectiveness of order picking. In previous studies, most storage assignment approaches considered the order frequency of individual products rather than that of product groups, which often are purchased together. This paper proposes a new association measure, weighted support count (WSC), based on association rule mining, to represent both the intensity and nature of the relationships between products in a distribution centre. This paper presents two storage assignment heuristics, the modified class‐based heuristic (MCBH) and the association seed based heuristic (ASBH), designed to facilitate efficient order picking by applying WSC. The real‐world data set of a grocery distribution centre is used to verify the effectiveness of the proposed approaches. From the computational results, MCBH cuts at most 4% from the travel distance for order picking per month, as compared with the traditional class‐based approach. Meanwhile, ASBH achieves at most a 13% reduction in travel distance.
Near‐neutral surface charge and hydrophilicity prevent mineral encrustation of Fe‐oxidizing micro‐organisms
Authors: Saini G. , Chan C. S. 
Published: December 2012

AbstractMicrobial survival in mineralizing environments depends on the ability to evade surface encrustation by minerals, which could obstruct nutrient uptake and waste output. Some organisms localize mineral precipitation away from the cell; however, cell surface properties – charge and hydrophobicity – must also play a role in preventing surface mineralization. This is especially relevant for iron‐oxidizing bacteria (FeOB), which face an encrustation threat from both biotic and abiotic mineralization. We used electron microscopy and surface characterization techniques to study the surfaces of two stalk‐forming neutrophilic FeOB: the marine Zetaproteobacterium Mariprofundus ferrooxydans PV‐1 and the recently isolated freshwater Betaproteobacterium Gallionellales strain R‐1. Both organisms lack detectable iron on cell surfaces. Live and azide‐inhibited M. ferrooxydans PV‐1 cells had small negative zeta potentials (−0.34 to −2.73 mV), over the pH range 4.2–9.4; Gallionellales strain R‐1 cells exhibited an even smaller zeta potential (−0.10 to −0.19 mV) over pH 4.2–8.8. Cells have hydrophilic surfaces, according to water contact angle measurements and microbial adhesion to hydrocarbons tests. Thermodynamic and extended Derjaguin–Landau–Verwey–Overbeek (XDLVO) calculations showed that as low charge causes low electrostatic attraction, hydrophilic repulsion dominates cell–mineral interactions. Therefore, we conclude that surface properties help enable these FeOB to survive in highly mineralizing environments. Given both mineral‐repelling surface properties and the ability to sequester Fe(III) biominerals in an organomineral stalk, these two FeOB have a well‐coordinated system to localize both biotic and abiotic mineral distribution.
Growth, leaf photosynthesis and canopy light use efficiency under differing irradiance and soil N supplies in the forage grass Brachiaria decumbens Stapf
Authors: Gómez S. , Guenni O. , Bravo de Guenni L. 
Published: December 2012

AbstractIrradiance and soil nitrogen effects on growth, net photosynthesis and radiation use efficiency (RUE) of Brachiaria decumbens were investigated in fertilized and non‐fertilized stands. Three levels of photosynthetic photon flux (PPF: S0 = 100%, S1 = 50% and S2 = 30%) and two N supplies, with (N+) and without (N−), were used. Forage biomass and nutrient accumulation, specific leaf area (SLA), leaf area index (LAI), fractional intercepted photosynthetic photon flux (fPPF), leaf photosynthetic response to light and efficiency of radiation use at leaf (A/Q) and canopy (RUE) levels were measured. Shade effects were mostly independent of soil N. Final yield was decreased by 34% (S1) and 57% (S2). Shade increased SLA (25–46%), so maximum LAI (2·4–3·3) was similar among light regimes. In N− stands, reductions in leaf biomass (14%), SLA (17%) and LAI (27%) were recorded, although forage yield was similar between soil N conditions. Under shade, peaks of A were comparable to those at full light, so A/Q was higher around midday. Derived parameters of the A‐PPF curves were similar between S0 and S2. A maximum fPPF = 0·8 (S0N+, S1N+) was recorded at LAI = 3–4. Under limited sunlight, relatively high RUE (1·6–2·8 g MJ−1) were observed over both soil N conditions. We concluded that B. decumbens had a high plasticity to shade, thus explaining its success under silvopastoral systems.
A comparison of six vetches (Vicia spp.) for developmental rate, herbage yield and seed yield in semi‐arid central Turkey
Authors: Fırıncıoğlu Hüseyin Kansur 
Published: December 2012

AbstractSix vetches (Vicia spp.), represented by 96 accessions, were evaluated for herbage yield, seed yield and related characters in three consecutive growing seasons (1995‐98) in semi‐arid central Turkey. Data were analysed by multiple statistical procedures: principal component analysis, restricted maximum‐likelihood method and simple linear regression analysis. In the first growing season (Y1), the growing period was curtailed by summer drought, and in the second (Y2) by heavy rainfall. In the third season (Y3), conditions were more temperate. Vicia pannonica ssp. pannonica (Pan) and V. villosa ssp. villosa (Vil) produced more biomass in Y3 than in Y1 and Y2, while V. pannonica ssp. purpurascens (Pur) and V. villosa ssp. dasycarpa (Das) produced more biomass in the wetter Y2. In the shorter growing seasons (Y1 and Y2), the earliness of Pur and Das resulted in high seed yield. V. narbonensis (Nar) in Y3 was particularly sensitive to widely fluctuating air temperatures with the accompanying high rainfall at the vegetative stage, which resulted in vigorous vegetative growth, hindered flowering and reduced seed yield. In V. sativa ssp. sativa (Sat), biomass and seed yield were significantly increased by the longer period of favourable growing weather during Y3. In agricultural practice, Pan and Vil have great potential for herbage production and grazing; Pur, Nar and Sat for grain and straw production; and Das for both hay and grain crops.
Impact of spatial heterogeneity of plant species on herbage productivity, herbage quality and ewe and lamb performance of continuously stocked, perennial ryegrass–white clover swards
Authors: Sharp J. M. , Edwards G. R. , Jeger M. J. 
Published: December 2012

AbstractThe benefits of white clover (Trifolium repens L.) in pastures are widely recognized. However, white clover is perceived as being unreliable due to its typically low content and spatial and temporal variability in mixed (grass‐legume) pastures. One solution to increase the clover proportion and quality of herbage available to grazing animals may be to spatially separate clover from grass within the same field. In a field experiment, perennial ryegrass (Lolium perenne L.) and white clover were sown as a mixture and compared with alternating strips of ryegrass and clover (at 1·5 and 3 m widths), or in adjacent monocultures (strips of 18 m width within a 36‐m‐wide field). Pastures were stocked by ewes and lambs for three 10‐month grazing periods. Over the 3 years of the experiment, spatial separation of grass and clover, compared with a grass–clover mixture, increased clover herbage production, although its proportion in the sward declined through time (0·49–0·54 vs 0·34 in the mixture in the first year, 0·28–0·33 vs 0·15 in the second year and 0·03–0·18 vs 0·01 in the third year). Total herbage production in the growing season in the spatially separated treatments decreased from 11384 kg DM ha−1 in the first year to 8150 kg DM ha−1 in the third year. Crude protein concentration of clover and grass components in the 18‐m adjacent monoculture treatment was greater than the mixture treatment for both clover (310 vs 280 g kg−1 DM) and grass (200 vs 180 g kg−1 DM). There was no clear benefit in liveweight gain beyond the first year in response to spatially separating grass and clover into monocultures within the same field.
Triggers in Allodynic and Non‐Allodynic Migraineurs. A Clinic Setting Study
Authors: Baldacci Filippo , Vedovello Marcella , Ulivi Martina , Vergallo Andrea , Poletti Michele , Borelli Paolo , Cipriani Gabriele , Nuti Angelo , Bonuccelli Ubaldo 
Published: December 2012

BackgroundAllodynia is considered a phenomenon of central sensitization that may lead to migraine transformation, lowering the attack threshold. Migraine triggers are factors that may induce headache attacks in susceptible individuals. We hypothesize that because allodynia decreases the migraine‐attack threshold, allodynic migraineurs are more susceptible to triggers than the non‐allodynic ones.ObjectiveTo determine if the number of headache triggers differs between migraineurs with no/mild allodynia and those with moderate/severe allodynia.Materials and MethodsWe recruited 120 consecutive migraineurs. Other primary headache comorbidity and migraine prophylaxis were exclusion criteria. Each patient was interviewed according a structured questionnaire including general features about migraine, depression, and anxiety symptoms. Patients reported any migraine trigger both spontaneously and by selecting from a specific list. Allodynia during the migraine attack was measured using the Allodynia Symptoms Check‐List 12 (ASC‐12): a cut‐off of ASC‐12 score of >2 defined allodynic patients; 3‐5 score indicated mild allodynia; a 6‐8 score moderate allodynia; and score of >8 severe allodynia.ResultsThe total number of identified triggers was significantly and positively related to allodynia measured with ASC‐12 (ρs 0.33; P < .001). In a logistic regression model, allodynia independently influenced the risk to have a higher number of triggers. Moderate/severe allodynic patients had an odds ratio of 2.8 to report a number of triggers >7 in respect to non‐/mild allodynic ones.ConclusionsMigraineurs with moderate/severe allodynia had more triggers than those with no/mild allodynia. It is unknown if those with moderate/severe allodynia are more susceptible to triggers, or repetitive stimulation of the trigeminal system by triggers resulted in moderate/severe allodynia.
T helper type 17 cells contribute to anti‐tumour immunity and promote the recruitment of T helper type 1 cells to the tumour
Authors: Nuñez Sarah , Saez Juan Jose , Fernandez Dominique , Flores‐Santibañez Felipe , Alvarez Karla , Tejon Gabriela , Ruiz Paulina , Maldonado Paula , Hidalgo Yessia , Manriquez Valeria , Bono Maria Rosa , Rosemblatt Mario , Sauma Daniela 
Published: December 2012

SummaryT helper type 17 (Th17) lymphocytes are found in high frequency in tumour‐burdened animals and cancer patients. These lymphocytes, characterized by the production of interleukin‐17 and other pro‐inflammatory cytokines, have a well‐defined role in the development of inflammatory and autoimmune pathologies; however, their function in tumour immunity is less clear. We explored possible opposing anti‐tumour and tumour‐promoting functions of Th17 cells by evaluating tumour growth and the ability to promote tumour infiltration of myeloid‐derived suppressor cells (MDSC), regulatory T cells and CD4+ interferon‐γ+ cells in a retinoic acid‐like orphan receptor γt (RORγt) ‐deficient mouse model. A reduced percentage of Th17 cells in the tumour microenvironment in RORγt‐deficient mice led to enhanced tumour growth, that could be reverted by adoptive transfer of Th17 cells. Differences in tumour growth were not associated with changes in the accumulation or suppressive function of MDSC and regulatory T cells but were related to a decrease in the proportion of CD4+ T cells in the tumour. Our results suggest that Th17 cells do not affect the recruitment of immunosuppressive populations but favour the recruitment of effector Th1 cells to the tumour, thereby promoting anti‐tumour responses.
Assessment of protein expression and gene status of human epidermal growth factor receptor (HER) family molecules in ameloblastomas
Authors: Oikawa Mariko , Miki Yasuhiro , Shimizu Yoshinaka , Kumamoto Hiroyuki 
Published: December 2012

BackgroundTo evaluate roles of human epidermal growth factor receptor (HER) family molecules in ameloblastomas, protein expression and gene status were analyzed in odontogenic tissues.MethodsSixty five ameloblastomas, 10 dental follicles, and 11 dentigerous cysts were immunohistochemically examined with antibodies against epidermal growth factor receptor (EGFR) and HER2, HER3, and HER4. Amplification of EGFR and HER2 was evaluated by chromogenic in situ hybridization (CISH). In 18 ameloblastomas, EGFR exons 19 and 21 were analyzed by direct DNA sequencing.ResultsImmunohistochemical reactivity for EGFR and HER2, HER3, and HER4 was detected in odontogenic epithelium. Expression of EGFR and HER4 was remarkable in these odontogenic tissues, as compared with that of HER2 and HER3. The level of HER2 immunoreactivity was significantly lower in ameloblastomas than in dental follicles and dentigerous cysts. Follicular ameloblastomas showed significantly higher expression of HER2 and HER4 than plexiform ameloblastomas. Reactivity for EGFR and HER3 was slightly stronger in recurrent ameloblastomas than in primary ameloblastomas. CISH did not reveal obvious amplification of EGFR or HER2 in ameloblastomas; however, EGFR and HER2 gene signals were significantly higher in follicular ameloblastomas than in plexiform ameloblastomas. Direct DNA sequencing of EGFR did not show any gene alteration in ameloblastomas.ConclusionExpression of HER family molecules, especially EGFR and HER4, in odontogenic tissues suggests that growth signals mediated by these receptor molecules contribute to cell proliferation, survival, and differentiation in both normal and neoplastic odontogenic epithelial tissues. Some of these molecules might be useful for predicting outcomes in patients with ameloblastomas.
International guidelines for the in vivo assessment of skin properties in non‐clinical settings: part 1. pH
Authors: Stefaniak Aleksandr B. , Plessis Johan du , John Swen M. , Eloff Fritz , Agner Tove , Chou Tzu‐Chieh , Nixon Rosemary , Steiner Markus F. C. , Kudla Irena , Linn Holness D. 
Published: December 2012

BackgroundSkin surface pH is known to influence the dissolution and partitioning of chemicals and may influence exposures that lead to skin diseases. Non‐clinical environments (e.g. workplaces) are highly variable, thereby presenting unique measurement challenges that are not typically encountered in clinical settings. Hence, guidelines are needed for consistent measurement of skin surface pH in environments that are difficult to control.MethodsAn expert workshop was convened at the 5th International Conference on Occupational and Environmental Exposure of Skin to Chemicals to review available data on factors that could influence the determination of skin surface pH in non‐clinical settings with emphasis on the workplace as a worst case scenario.ResultsThe key elements of the guidelines are: (i) minimize, to the extent feasible, the influences of relevant endogenous (anatomical position, skin health, time of day), exogenous (hand washing, barrier creams, soaps and detergents, occlusion), environmental (seasonality), and measurement (atmospheric conditions) factors; (ii) report pH measurements results as a difference or percent change (not absolute values) using a measure of central tendency and variability; and (iii) report notable deviations from these guidelines and other relevant factors that may influence measurements.ConclusionGuidelines on the measurement and reporting of skin surface pH in non‐clinical settings should promote consistency in data reporting, facilitate inter‐comparison of study results, and aid in understanding and preventing occupational skin diseases.
Farewell Speech: Stefan Dodunekov (1945-2012)
Authors: Sendov Blagovest 
Published: December 2012

Dear mournful family and all present,We are here to bow and to send to his eternal rest the President of the Bulgarian Academy of SciencesвЂ”Academician Stefan Manev Dodunekov. We have come to share together the enormous loss every one of us has suffered.The family lost their loving and caring father and husband, the mathematical community lost one of В its brightest and most active members, the Bulgarian В Academy of Sciences lost one of В its hopes for a better and more successful development, Bulgaria lost one quiet, but uncompromising patriot ...
In Memoriam: Antony Popov (1962-2012)
Authors: BIOMATH 2012 Organising Committee of 
Published: December 2012

We are deeply saddened by the sudden death at the age of 49 of our colleague Associate Professor Dr. Antony Popov, member of the Department вЂќInformation TechnologiesвЂќ, Faculty of Mathematics and Informatics, Sofia University. Tony was a very good mathematician, specializing in the area of Pattern Recognition. . . .В В
From the Guest-Editor
Authors: Markov Svetoslav 
Published: December 2012

The BIOMATH 2012 International Conference on Mathematical Methods and Models in Biosciences was held at the Bulgarian Academy of Sciences in Sofia, in June 17-22, 2012, http://www.biomath.bg/2012/.В We were happy to meet more than 70 participantsВ from twenty differentВ countries.В В More than 40 contributions were submitted for publication in the present BIOMATH proceedings.В All submitted papers have been peer-reviewed by at least two independent anonymous reviewers. Twelve selected papers are published in the first issue of this journal. This second issue contains anotherВ ten selected contributions which will be published continuously in the electronic version of the journal.В В . . .В В В В В В В
Nonlinear Filters and Characterization of the Discrete Pulse Transform of Images
Authors: Fabris-Rotelli Inger 
Published: December 2012

The Discrete Pulse Transform (DPT) for images and videos has been developed over the past few years and provides aВ theoretically sound setting for a nonlinear decomposition of an image or video. In [1] the theoretical basis of the DPT was presented. In this paper we now present a soundВ characterization of this useful nonlinear hierarchical decomposition by referring to its ability as a separator, the consistency of the decomposition, as well as the smoothing ability of the decomposition.
Quantitative Contributions of Target Alteration and Decreased Drug Accumulation to Pseudomonas aeruginosa Fluoroquinolone Resistance
Authors: Bruchmann Sebastian , Dötsch Andreas , Nouri Bianka , Chaberny Iris F. , Häussler Susanne 
Published: December 2012

ABSTRACT

Quinolone antibiotics constitute a clinically successful and widely used class of broad-spectrum antibiotics; however, the emergence and spread of resistance increasingly limits the use of fluoroquinolones in the treatment and management of microbial disease. In this study, we evaluated the quantitative contributions of quinolone target alteration and efflux pump expression to fluoroquinolone resistance in
Pseudomonas aeruginosa
. We generated isogenic mutations in hot spots of the quinolone resistance-determining regions (QRDRs) of
gyrA
,
gyrB
, and
parC
and inactivated the efflux regulator genes so as to overexpress the corresponding multidrug resistance (MDR) efflux pumps. We then introduced the respective mutations into the reference strain PA14 singly and in various combinations. Whereas the combined inactivation of two efflux regulator-encoding genes did not lead to resistance levels higher than those obtained by inactivation of only one efflux regulator-encoding gene, the combination of mutations leading to increased efflux and target alteration clearly exhibited an additive effect. This combination of target alteration and overexpression of efflux pumps was commonly observed in clinical
P. aeruginosa
isolates; however, these two mechanisms were frequently found not to be sufficient to explain the level of fluoroquinolone resistance. Our results suggest that there are additional mechanisms, independent of the expression of the MexAB-OprM, MexCD-OprJ, MexEF-OprN, and/or MexXY-OprM efflux pump, that increase ciprofloxacin resistance in isolates with mutations in the QRDRs.