bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thermodynamic scaling behavior in genechips
Authors: Ferrantini Alessandro , Allemeersch Joke , Van Hummelen Paul , Carlon Enrico 
Published: January 2009

Abstract

Background
Affymetrix Genechips are characterized by probe pairs, a perfect match (PM) and a mismatch (MM) probe differing by a single nucleotide. Most of the data preprocessing algorithms neglect MM signals, as it was shown that MMs cannot be used as estimators of the non-specific hybridization as originally proposed by Affymetrix. The aim of this paper is to study in detail on a large number of experiments the behavior of the average PM/MM ratio. This is taken as an indicator of the quality of the hybridization and, when compared between different chip series, of the quality of the chip design.

Results
About 250 different GeneChip hybridizations performed at the VIB Microarray Facility for Homo sapiens, Drosophila melanogaster, and Arabidopsis thaliana were analyzed. The investigation of such a large set of data from the same source minimizes systematic experimental variations that may arise from differences in protocols or from different laboratories. The PM/MM ratios are derived theoretically from thermodynamic laws and a link is made with the sequence of PM and MM probe, more specifically with their central nucleotide triplets.

Conclusion
The PM/MM ratios subdivided according to the different central nucleotides triplets follow qualitatively those deduced from the hybridization free energies in solution. It is shown also that the PM and MM histograms are related by a simple scale transformation, in agreement with what is to be expected from hybridization thermodynamics. Different quantitative behavior is observed on the different chip organisms analyzed, suggesting that some organism chips have superior probe design compared to others.
Activation of the steroid and xenobiotic receptor, SXR, induces apoptosis in breast cancer cells
Authors: Verma Suman , Tabb Michelle M , Blumberg Bruce 
Published: January 2009

AbstractBackgroundThe steroid and xenobiotic receptor, SXR, is an orphan nuclear receptor that regulates metabolism of diverse dietary, endobiotic, and xenobiotic compounds. SXR is expressed at high levels in the liver and intestine, and at lower levels in breast and other tissues where its function was unknown. Since many breast cancer preventive and therapeutic compounds are SXR activators, we hypothesized that some beneficial effects of these compounds are mediated through SXR.MethodsTo test this hypothesis, we measured proliferation of breast cancer cells in response to SXR activators and evaluated consequent changes in the expression of genes critical for proliferation and cell-cycle control using quantitative RT-PCR and western blotting. Results were confirmed using siRNA-mediated gene knockdown. Statistical analysis was by t-test or ANOVA and a P value ≤ 0.05 was considered to be significant.ResultsMany structurally and functionally distinct SXR activators inhibited the proliferation of MCF-7 and ZR-75-1 breast cancer cells by inducing cell cycle arrest at the G1/S phase followed by apoptosis. Decreased growth in response to SXR activation was associated with stabilization of p53 and up-regulation of cell cycle regulatory and pro-apoptotic genes such as p21, PUMA and BAX. These gene expression changes were preceded by an increase in inducible nitric oxide synthase and nitric oxide in these cells. Inhibition of iNOS blocked the induction of p53. p53 knockdown inhibited up-regulation of p21 and BAX. We infer that NO is required for p53 induction and that p53 is required for up-regulation of cell cycle regulatory and apoptotic genes in this system. SXR activator-induced increases in iNOS levels were inhibited by siRNA-mediated knockdown of SXR, indicating that SXR activation is necessary for subsequent regulation of iNOS expression.ConclusionWe conclude that activation of SXR is anti-proliferative in p53 wild type breast cancer cells and that this effect is mechanistically dependent upon the local production of NO and NO-dependent up-regulation of p53. These findings reveal a novel biological function for SXR and suggest that a subset of SXR activators may function as effective therapeutic and chemo-preventative agents for certain types of breast cancers.
Ebp1 expression in benign and malignant prostate
Authors: Gannon Philippe O , Koumakpayi Ismaël Hervé , Le Page Cécile , Karakiewicz Pierre I , Mes-Masson Anne-Marie , Saad Fred 
Published: January 2009

Abstract

Background
ErbB3-binding protein 1 (Ebp1) is a member of the PA2G4 family of proliferation-regulated proteins that is expressed in multiple malignant and non-malignant cells. ErbB3 and other members of the EGFR family have been implicated in cancer progression, it however remains unknown whether Ebp1 participate in prostate cancer progression in vivo. Therefore, the present study examines Ebp1 expression in cancerous and non-cancerous prostates tissues. Ebp1 expression was also correlated to known Ebp1 regulated proteins (Androgen receptor (AR), Cyclin D1 & ErbB3) and the proliferation marker Ki67. Furthermore we evaluated whether Ebp1 expression correlated with biochemical recurrence (BCR) following radical prostatectomy.

Methods
The expression of Ebp1, AR, Cyclin D1, ErbB3 and Ki67 were evaluated by immunohistochemistry using three separate tissue micro-arrays containing normal prostate tissues, non-cancerous tissue adjacent to the primary tumor, hormone-sensitive and hormone-refractory cancerous tissues. Multivariate COX regression analysis was performed with four clinical parameters in order to correlate Ebp1 expression with PCa progression.

Results
The expression of Ebp1 significantly increased with the progression from normal to hormone sensitive and to hormone refractory PCa. Furthermore, we observed strong correlation between Ebp1 expression and the nuclear expression of AR, Cyclin D1 and ErbB3 in both normal adjacent and cancer tissues. The expression of AR, Cyclin D1 and ErbB3 in normal adjacent tissues correlated with PSA relapse, whereas Ebp1 on its own did not significantly predict PSA relapse. Finally, in a multivariate analysis with a base clinical model (Gleason, Pre-op PSA, surgical margins and P-stage) we identified the multi-marker combination of Ebp1+/Cyclin D1- as an independent predictor of PSA relapse with a hazard ratio of 4.79.

Conclusion
Although not related to disease recurrence, this is the first in vivo study to report that Ebp1 expression correlates with PCa progression.
Intracellular amyloid formation in muscle cells of Aβ-transgenic Caenorhabditis elegans: determinants and physiological role in copper detoxification
Authors: Minniti Alicia N , Rebolledo Daniela L , Grez Paula M , Fadic Ricardo , Aldunate Rebeca , Volitakis Irene , Cherny Robert A , Opazo Carlos , Masters Colin , Bush Ashley I , Inestrosa Nibaldo C 
Published: January 2009

Abstract

Background
The amyloid β-peptide is a ubiquitous peptide, which is prone to aggregate forming soluble toxic oligomers and insoluble less-toxic aggregates. The intrinsic and external/environmental factors that determine Aβ aggregation in vivo are poorly understood, as well as the cellular meaning of this process itself. Genetic data as well as cell biological and biochemical evidence strongly support the hypothesis that Aβ is a major player in the onset and development of Alzheimer's disease. In addition, it is also known that Aβ is involved in Inclusion Body Myositis, a common myopathy of the elderly in which the peptide accumulates intracellularly.

Results
In the present work, we found that intracellular Aβ aggregation in muscle cells of Caenorhabditis elegans overexpressing Aβ peptide is affected by two single amino acid substitutions, E22G (Arctic) and V18A (NIC). Both variations show decrease intracellular amyloidogenesis compared to wild type Aβ. We show that intracellular amyloid aggregation of wild type Aβ is accelerated by Cu2+ and diminished by copper chelators. Moreover, we demonstrate through toxicity and behavioral assays that Aβ-transgenic worms display a higher tolerance to Cu2+ toxic effects and that this resistance may be linked to the formation of amyloid aggregates.

Conclusion
Our data show that intracellular Aβ amyloid aggregates may trap excess of free Cu2+ buffering its cytotoxic effects and that accelerated intracellular Aβ aggregation may be part of a cell protective mechanism.
Schizophrenia spectrum disorders in a Nigerian family: 4 case reports
Authors: Omoaregba Joyce O , James Bawo O , Eze George O 
Published: January 2009

Abstract

Introduction
The risk of developing schizophrenia is higher among persons with an affected sibling compared to the general population. Beliefs about aetiology influence presentation, management and treatment outcomes. There are no reports on multiple occurrences of this disorder in a family in this part of the world. In this case series we also highlight how cultural beliefs hamper and shape management.

Case presentation
We report a case series of schizophrenia spectrum disorders affecting four women in a Nigerian family of Ibo tribal origin who responded marginally to pharmacological interventions and required insight oriented psychotherapy and family therapy in resolving psychosocial problems.

Conclusion
While western taught disease models might explain these presentations, it is not usually accepted by lay persons from developing cultures. Limitations in contemporary treatment approaches necessitate the development of culturally relevant psychotherapeutic interventions.
Membrane Bound Axin Is Sufficient for Wingless Signaling in Drosophila Embryos
Authors: Tolwinski Nicholas S 
Published: January 2009

Abstract
The Wingless signaling pathway controls various developmental processes in both vertebrates and invertebrates. Here I probe the requirement for nuclear localization of APC2 and Axin in the Wg signal transduction pathway during embryonic development of Drosophila melanogaster. I find that nuclear localization of APC2 appears to be required, but Axin can block signaling when tethered to the membrane. These results support the model where Axin regulates Armadillo localization and activity in the cytoplasm.
Prion Variants and Species Barriers Among Saccharomyces Ure2 Proteins
Authors: Edskes Herman K , McCann Lindsay M , Hebert Andrea M , Wickner Reed B 
Published: January 2009

Abstract
As hamster scrapie cannot infect mice, due to sequence differences in their PrP proteins, we find “species barriers” to transmission of the [URE3] prion in Saccharomyces cerevisiae among Ure2 proteins of S. cerevisiae, paradoxus, bayanus, cariocanus, and mikatae on the basis of differences among their Ure2p prion domain sequences. The rapid variation of the N-terminal Ure2p prion domains results in protection against the detrimental effects of infection by a prion, just as the PrP residue 129 Met/Val polymorphism may have arisen to protect humans from the effects of cannibalism. Just as spread of bovine spongiform encephalopathy prion variant is less impaired by species barriers than is sheep scrapie, we find that some [URE3] prion variants are infectious to another yeast species while other variants (with the identical amino acid sequence) are not. The species barrier is thus prion variant dependent as in mammals. [URE3] prion variant characteristics are maintained even on passage through the Ure2p of another species. Ure2p of Saccharomyces castelli has an N-terminal Q/N-rich “prion domain” but does not form prions (in S. cerevisiae) and is not infected with [URE3] from Ure2p of other Saccharomyces. This implies that conservation of its prion domain is not for the purpose of forming prions. Indeed the Ure2p prion domain has been shown to be important, though not essential, for the nitrogen catabolism regulatory role of the protein.
CD4 Counts Decline Despite Nutritional Recovery in HIV-Infected Zambian Children With Severe Malnutrition
Authors: Hughes Stephen Miles , Amadi Beatrice , Mwiya Mwiya , Nkamba Hope , Mulundu Georgina , Tomkins Andrew , Goldblatt David 
Published: January 2009

OBJECTIVE. The objective of this study was to establish the contribution that severe malnutrition makes to CD4 lymphopenia in HIV-infected and uninfected children and to determine the changes in CD4 count during nutritional rehabilitation.
METHODS. Fifty-six children with severe malnutrition and with and without HIV infection were recruited from a pediatric ward in Lusaka for measurement of CD4 counts on admission, on discharge, and at final nutritional recovery.
RESULTS. HIV-uninfected children with severe malnutrition had normal CD4 counts. In contrast, CD4 counts in HIV-infected children with severe malnutrition were reduced, more so in those without edema compared with those with edema. Mean CD4 count of HIV-infected SM children fell despite nutritional recovery so that at the time of full nutritional recovery, &gt;85% of HIV-infected children required antiretroviral therapy.
CONCLUSIONS. Severe malnutrition did not reduce the CD4 counts of children without HIV. HIV-infected children with severe malnutrition may respond well to nutritional rehabilitation, despite low CD4 counts, but nearly all require early antiretroviral therapy to prevent disease progression.
Towards Robustness in Neural Network Based Fault Diagnosis
Authors: Patan Krzysztof , Witczak Marcin , Korbicz Józef 
Published: January 2009

Towards Robustness in Neural Network Based Fault DiagnosisChallenging design problems arise regularly in modern fault diagnosis systems. Unfortunately, classical analytical techniques often cannot provide acceptable solutions to such difficult tasks. This explains why soft computing techniques such as neural networks become more and more popular in industrial applications of fault diagnosis. Taking into account the two crucial aspects, i.e., the nonlinear behaviour of the system being diagnosed as well as the robustness of a fault diagnosis scheme with respect to modelling uncertainty, two different neural network based schemes are described and carefully discussed. The final part of the paper presents an illustrative example regarding the modelling and fault diagnosis of a DC motor, which shows the performance of the proposed strategy.
The state of plant conservation in small water bodies located within the city limits of Olsztyn
Authors: Grzybowski Mirosław , Endler Zbigniew 
Published: January 2009

Abstract
The interior depressions in the Olsztyn area are characterized by high biodiversity. On the basis of floral surveys of 32 small water bodies, 200 species of vascular plants and 10 species of bryophytes were recorded. Phytosociological analysis indicated 45 plant associations. Among the phytocoenoses described, some communities require more attention, including Wolffietum arrhizae, Riccietum fluitantis, Charetum fragilis, the pondweeds Potametum nitentis and P. commpressi as well as communities with Potamogeton trichoides and P. pusillus.

In light of their significant natural value, some of the basins studied units should be protected as ecological grounds. Reservoirs located in the Jaroty District, in the vicinity of Lake Track or some reservoirs located within the Gutkowo and Kortowo districts are important points of peatwater or water accumulation. These small water bodies limit the nutrient and pollutant input into the numerous lakes located in the Olsztyn area. Some basins are of a recreational character, including the reservoir located in the central quarter of the town and the water bodies of the Kortowo District. The remaining reservoirs need restoration and litter collection to restore their recreational functions.
The distribution of lead, zinc, and chromium in fractions of bottom sediments in the Narew River and its tributaries
Authors: Skorbiłowicz Mirosław , Skorbiłowicz Elżbieta 
Published: January 2009

Abstract
The purpose of the paper was to evaluate the distribution of lead, zinc and chromium contents in different grain fractions of bottom sediments in the Narew River and some of its tributaries. This study also aimed to determine which fractions are mostly responsible for bottom sediment pollution. The studies of the Narew and its tributaries (the Supraśl, Narewka, and Orlanka) were conducted in September 2005 in the upper Narew catchment area. The analyzed bottom sediments differed regarding grain size distribution. The studies revealed the influence of the percentage of particular grain fractions present on the accumulation of heavy metals in all bottom sediments.
Surface and near-bottom water saturation with CaCO3 in the Pomeranian Bay in the vicinity of the Świna Channel mouth
Authors: Poleszczuk Gorzysław 
Published: January 2009

Abstract
Langmuir and Langelier calcite saturation indexes were calculated for water in the vicinity of the Świna Channel in the Pomeranian Bay. Measurements carried out in April-October of 1994 and 2004 indicated that CaCO3 concentrations nearly reached the saturation level, though in spring and fall the water showed slight calcite unsaturation while in summer it was oversaturated with calcite. The observed saturation levels were related with the shifts in the equilibrium between assimilation and dissimilation processes in the Pomeranian Bay ecosystem.
Water bugs (Heteroptera) in small water bodies located in Olsztyn
Authors: Kurzątkowska Alicja 
Published: January 2009

Abstract
The study was conducted on 16 water bodies located in Olsztyn, most of them natural and dominated by astatic ones (dystrophic, eutrophic, and artificial with elevated mineralization levels). Heteroptera was identified to 32 species represented by five synecological groups, i.e., species typical of dystrophic water bodies (Cymatia bonsdorffi, Hesperocorixa linnaei, H. moesta, H. sahlbergi, Gerris lateralis, G. sphagnetorum, Hebrus ruficeps), lacustrine species (Gerris argentatus, Aquarius paludum), halophilous species (Cymatia rogenhoferi, Paracorixa concinna, Gerris thoracicus), psammophilous and argilophilous species (Sigara lateralis) and eurytopic species typical of small water bodies (18). It was found that the degree of permanency of astatic water bodies affects both the species diversity and abundance of the Heteroptera fauna. Migrations play a crucial role with respect to the colonization of newly-formed bodies of water and to the abandonment of those that are drying up.
Pilot study of patient and phantom breast dose measurements in Bulgaria
Authors: Avramova-Cholakova Simona , Vassileva Jenia 
Published: January 2009

Pilot study of patient and phantom breast dose measurements in Bulgaria
A pilot study of breast dose measurements on two mammography units in Bulgaria was conducted. The mean glandular doses (MGDs) to samples of approximately 60 women per unit were measured. MGD with a standard PMMA phantom was measured as well. The MGDs were calculated according to the European protocol on dosimetry in mammography as well as to the European protocol for the quality control of the physical and technical aspects of mammography screening. The measured women's MGDs were divided into three groups depending on the compressed breast thicknesses. The results for the group of thicknesses in the interval 40-60 mm were compared with the results from the measurements on the standard 45 mm PMMA phantom. Some differences were found which could be due to errors in breast thickness measurements, differences in breast and phantom densities and other factors. A standardized procedure was elaborated for patient dose measurement and calculation both from patient and phantom studies.
A Socio-Linguistic Approach to the Development of Folk Psychology
Authors: Ohreen David 
Published: January 2009

A Socio-Linguistic Approach to the Development of Folk Psychology
One of the most interesting issues central to folk psychology is how it develops in humans. Over the past few decades, two distinct theories have emerged known as the Theory-Theory and Simulation Theory. Theory-theory supporters argue that children construct theories to explain behavior, while simulation theorists extol the virtues of empathy—putting yourself in another person's shoes. I argue that each position falls short of an adequate account of how folk psychology develops. Instead, explaining behavior is a matter of acquiring folk psychological concepts within a culture and then learning how to deploy such terms with competence.
Effect of Transgenic Maize Mon 810 on Selected Non-Target Organisms: The Bird Cherry-Oat Aphid (Rhopalosiphum padi L.) and its Predator - Green Lacewing (Chrysoperla carnea Steph.)
Authors: Lewandowski Andrzej , Górecka Julia 
Published: January 2009

Effect of Transgenic Maize Mon 810 on Selected Non-Target Organisms: The Bird Cherry-Oat Aphid (Rhopalosiphum padi L.) and its Predator - Green Lacewing (Chrysoperla carnea Steph.)
The maize variety MON 810 resistant on lepidopteran pests is one of the most common and longest grown transgenic variety. It was modified to constantly produce in its tissues Cry1Ab protein derived from common bacteria Bacillus thuringensis. The Cry1Ab protein is lethally-toxic for European corn borer (Ostrinia nubilalis), significant maize pest. A study was carried out to evaluate the influence of MON 810 maize on development of two non-target species - the bird cherry-oat aphid (Rhopalosiphum padi L.) and its predator - green lacewing (Chrysoperla carnea Steph.). During comparison analysis there were no significant differences between transgenic maize vs. non-transgenic isogenic maize influence on non-target organisms.
Efficiency of Entec 26 - A New Concept Nitrogen Fertilizer in White Head Cabbage Production
Authors: Kołota Eugeniusz , Adamczewska- Sowińska Katarzyna 
Published: January 2009

Efficiency of Entec 26 - A New Concept Nitrogen Fertilizer in White Head Cabbage Production
In field experiment conducted in 2005-2007 there was evaluated the suitability of Entec 26 - a new concept nitrogen fertilizer containing DMPP nitrification inhibitor (3,4-dimethylpyrazole phosphate) and ammonium nitrate as a source of this nutrient for white cabbage. Ammonium nitrate was supplied in split doses of 75 (1/2 + 1/2), 150 (1/2 + 1/2), 225 (1/3 + 1/3 + 1/3) and 300 (1/4 + 1/4 + 1/2) kg N per hectar, as preplant and one or two top dressings. Entec 26 was used in the same amounts and terms of application as ammonium nitrate or in one preplant dose.
Results of the study showed that Entec 26 was a better source of nitrogen than ammonium nitrate, providing higher yield of marketable heads and lower nitrate contents in plants at harvest. Plants supplied with a single preplant dose of N produced similar marketable yield with lower nitrates accumulation in comparison to split application of the fertilizer. Irrespective of nitrogen form, enhancement of its dose from 75 kg·ha-1 to 300 kg·ha-1 resulted in the decrease of sugars and vitamin C contents, while the increment of total N and nitrates level in cabbage heads.