bluuebunny/crossref_metadata_2025_split huggingface dataset:
A methodology for utilization of predictive genomic signatures in FFPE samples
Authors: Freedman Jennifer A , Augustine Christina K , Selim Angelica M , Holshausen Kirsten C , Wei Zhengzheng , Tsamis Katherine A , Hsu David S , Dressman Holly K , Barry William T , Tyler Douglas S , Nevins Joseph R 
Published: August 2011

Abstract

Background
Gene expression signatures developed to measure the activity of oncogenic signaling pathways have been used to dissect the heterogeneity of tumor samples and to predict sensitivity to various cancer drugs that target components of the relevant pathways, thus potentially identifying therapeutic options for subgroups of patients. To facilitate broad use, including in a clinical setting, the ability to generate data from formalin-fixed, paraffin-embedded (FFPE) tissues is essential.

Methods
Patterns of pathway activity in matched fresh-frozen and FFPE xenograft tumor samples were generated using the MessageAmp Premier methodology in combination with assays using Affymetrix arrays. Results generated were compared with those obtained from fresh-frozen samples using a standard Affymetrix assay. In addition, gene expression data from patient matched fresh-frozen and FFPE melanomas were also utilized to evaluate the consistency of predictions of oncogenic signaling pathway status.

Results
Significant correlation was observed between pathway activity predictions from paired fresh-frozen and FFPE xenograft tumor samples. In addition, significant concordance of pathway activity predictions was also observed between patient matched fresh-frozen and FFPE melanomas.

Conclusions
Reliable and consistent predictions of oncogenic pathway activities can be obtained from FFPE tumor tissue samples. The ability to reliably utilize FFPE patient tumor tissue samples for genomic analyses will lead to a better understanding of the biology of disease progression and, in the clinical setting, will provide tools to guide the choice of therapeutics to those most likely to be effective in treating a patient's disease.
A cross‐sectional assessment of population demographics, HIV risks and human rights contexts among men who have sex with men in Lesotho
Authors: Baral Stefan , Adams Darrin , Lebona Judith , Kaibe Bafokeng , Letsie Puleng , Tshehlo Relebohile , Wirtz Andrea , Beyrer Chris 
Published: August 2011

BackgroundEvidence is increasing of high HIV risks among southern African men who have sex with men (MSM). This represents the first study of HIV risks and human rights contexts among MSM in Lesotho.MethodsTwo hundred and fifty‐two men who reported ever having anal sex with another man were accrued with snowball sampling and were administered a structured quantitative instrument in October and November 2009.ResultsOf the participants, 96.4% (240/249) were ethnic Basotho with a mean age of 26.3 years (range 18‐56), 49.6% (124/250) were currently employed, and 95.2% (238/250) had at least a secondary‐level education. Self‐reported HIV prevalence was 11.6% (22/190); 54.5% (128/235) reported being tested for HIV in the last year. HIV knowledge was low; only 3.7% (8/212) of MSM knew that receptive anal intercourse was the highest risk for HIV and that a water‐based lubricant was most appropriate to use with condoms.Bivariate associations of wearing condoms during last intercourse with men include: having easy access to condoms (OR 3.1, 95% CI 1.2‐8.5, p < 0.05); being older than 26 years (OR 2.3, 95% CI 1.3‐4.2, p < 0.01); knowing that receptive anal intercourse is higher risk than insertive anal intercourse (OR 2.6, 95% CI 1.2‐5.9, p < 0.05); wearing condoms with female sexual partners (OR 3.5, 95% 1.4‐8.3, p < 0.01); using water‐based lubricants (OR 2.8, 95% CI 1.4‐5.5, p < 0.01); being less likely to report having been diagnosed with a sexually transmitted infecton (OR 0.21, 95% CI 0.06‐0.76, p < 0.05); and being more likely to have been tested for HIV in the last year (OR 2.0, 95% CI 1.2‐3.6, p > 0.05).Human rights abuses were common: 76.2% (170/223) reported at least one abuse, including rape (9.8%, 22/225), blackmail (21.3%, 47/221), fear of seeking healthcare (22.2%, 49/221), police discrimination (16.4%, 36/219), verbal or physical harassment (59.8%, 140/234), or having been beaten (18.9%, 43/228).ConclusionsMSM in Lesotho are at high risk for HIV infection and human rights abuses. Evidence‐based and rights‐affirming HIV prevention programmes supporting the needs of MSM should be developed and implemented.
Postural control deficits in people with fibromyalgia: a pilot study
Authors: Jones Kim D , King Laurie A , Mist Scott D , Bennett Robert M , Horak Fay B 
Published: August 2011

Abstract
Introduction
Postural instability and falls are increasingly recognized problems in patients with fibromyalgia (FM). The purpose of this study was to determine whether FM patients, compared to age-matched healthy controls (HCs), have differences in dynamic posturography, including sensory, motor, and limits of stability. We further sought to determine whether postural instability is associated with strength, proprioception and lower-extremity myofascial trigger points (MTPs); FM symptoms and physical function; dyscognition; balance confidence; and medication use. Last, we evaluated self-reported of falls over the past six months.

Methods
In this cross-sectional study, we compared middle-aged FM patients and age-matched HCs who underwent computerized dynamic posturography testing and completed the Fibromyalgia Impact Questionnaire-Revised (FIQR) and balance and fall questionnaires. All subjects underwent a neurological and musculoskeletal examination. Descriptive statistics were used to characterize the sample and explore the relationships between variables. The relationships between subjective, clinical and objective variables were evaluated by correlation and regression analyses.

Results
Twenty-five FM patients and twenty-seven HCs (combined mean age ± standard deviation (SD): 48.6 ± 9.7 years) completed testing. FM patients scored statistically lower on composite sensory organization tests (primary outcome; P < 0.010), as well as with regard to vestibular, visual and somatosensory ratio scores on dynamic posturography. Balance confidence was significantly different between groups, with FM patients reporting less confidence than HCs (mean ± SD: 81.24 ± 19.52 vs. 98.52 ± 2.45; P < 0.001). Interestingly, 76% to 84% of FM patients had gastrocnemius and/or anterior tibialis MTPs. Postural stability was best predicted by dyscognition, FIQR score and body mass index. Regarding falls, 3 (11%) of 27 HCs had fallen only once during the past 6 months, whereas 18 (72%) of 25 FM patients had fallen at least once. Fifteen FM patients (60%) reported falling at least three times in the past six months.

Conclusions
In this study, we report that middle-aged FM patients have consistent objective sensory deficits on dynamic posturography, despite having a normal clinical neurological examination. Further study is needed to determine prospective fall rates and the significance of lower-extremity MTPs. The development of interventions to improve balance and reduce falls in FM patients may need to combine balance training with exercise and cognitive training.
Clustered Genomic Alterations in Chromosome 7p Dictate Outcomes and Targeted Treatment Responses of Lung Adenocarcinoma WithEGFR-Activating Mutations
Authors: Yuan Shinsheng , Yu Sung-Liang , Chen Hsuan-Yu , Hsu Yi-Chiung , Su Kang-Yi , Chen Huei-Wen , Chen Chih-Yi , Yu Chong-Jen , Shih Jin-Yuan , Chang Yih-Leong , Cheng Chiou-Ling , Hsu Chung-Ping , Hsia Jiun-Yi , Lin Chien-Yu , Wu Guani , Liu Chia-Hsin , Wang Chin-Di , Yang Kang-Chung , Chen Yi-Wei , Lai Yi-Ling , Hsu Chu-Chun , Lin Tai-Ching , Yang Tsung-Ying , Chen Kun-Cheieh , Hsu Kuo-Hsuan , Chen Jeremy J.W. , Chang Gee-Chen , Li Ker-Chau , Yang Pan-Chyr 
Published: August 2011

PurposeAlthough epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) have been proven more effective for patients with lung adenocarcinoma with EGFR-activating mutation rather than wild type, the former group still includes approximately 30% nonresponders. The molecular basis of this substantial response heterogeneity is unknown. Our purpose was to seek molecular aberrations contributing to disease progression at the genome-wide level and identify the prognostic signature unique to patients with EGFR-activating mutation.Patients and MethodsWe first investigated the molecular differences between tumors with EGFR-activating mutation and wild-type tumors by conducting high-density array comparative genomic hybridization on a collection of 138 adenocarcinoma tissues. We then used an independent group of 114 patients to validate the clinical relevance of copy-number alterations (CNAs) in predicting overall and disease-free survival. Finally, focusing on 23 patients with EGFR mutation receiving EGFR-TKI treatment, we investigated the association between CNAs and response to EGFR-TKIs.ResultsWe identified chromosome regions with differential CNAs between tumors with EGFR-activating mutation and wild-type tumors and found the aberration sites to cluster highly on chromosome 7p. A cluster of six representative chromosome 7p genes predicted overall and disease-free survival for patients with EGFR-activating mutation but not for those with wild type. Importantly, simultaneous presence of more genes with increased CNAs in this cluster correlated with less favorable response to EGFR-TKIs in patients with EGFR-activating mutation.ConclusionOur results shed light on why responses to EGFR-TKIs are heterogeneous among patients with EGFR-activating mutation. They may lead to better patient management in this population.
Development and validation of a yeast high-throughput screen for inhibitors of Aβ42 oligomerization
Authors: Park Sei-Kyoung , Pegan Scott D. , Mesecar Andrew D. , Jungbauer Lisa M. , LaDu Mary Jo , Liebman Susan W. 
Published: August 2011

SUMMARY
Recent reports point to small soluble oligomers, rather than insoluble fibrils, of amyloid β (Aβ), as the primary toxic species in Alzheimer’s disease. Previously, we developed a low-throughput assay in yeast that is capable of detecting small Aβ42 oligomer formation. Specifically, Aβ42 fused to the functional release factor domain of yeast translational termination factor, Sup35p, formed sodium dodecyl sulfate (SDS)-stable low-n oligomers in living yeast, which impaired release factor activity. As a result, the assay for oligomer formation uses yeast growth to indicate restored release factor activity and presumably reduced oligomer formation. We now describe our translation of this assay into a high-throughput screen (HTS) for anti-oligomeric compounds. By doing so, we also identified two presumptive anti-oligomeric compounds from a sub-library of 12,800 drug-like small molecules. Subsequent biochemical analysis confirmed their anti-oligomeric activity, suggesting that this form of HTS is an efficient, sensitive and cost-effective approach to identify new inhibitors of Aβ42 oligomerization.
Effects of washer on the stress distribution of mini-implant
Authors: Jang Hyoung-Jun , Kwon Soon-Yong , Kim Seong-Hun , Park Young-Guk , Kim Su-Jung 
Published: August 2011

Abstract

Objective:
To investigate the biomechanical effects of ‘washer’ designed for improving mini-implant stability.

Materials and Methods:
Four three-dimensional finite element models of the mini-implant and surrounding bone were constructed with washers in different spike lengths (1.5 mm, 2.0 mm, and 2.5 mm). The force was applied in two directions (45° and 90°). The stress distribution on surrounding bone and the displacement of the mini-implant were analyzed. Plots of tensile stress, compression stress, and displacement were calculated, and maximum values in each category were analyzed.

Results:
The stress distribution was different between the models with washer and without washer. However, no remarkable differences in stress distribution were observed among the models with washer, regardless of spike length. A significantly greater displacement value was observed in the model without washer compared to the models with washer, but no notable difference in displacement value was found among the models with washer. The plots of the displacement distribution of the models with washer presented notable pattern differences as compared with that of the model without washer.

Conclusion:
With the use of the washer, a more homogeneous distribution of bone stress and less displacement of the mini-implant can be achieved.
Enzymatic activity of yeasts isolated from the inflamed mammary secretion in dairy cows
Authors: Wawron W. , Bochniarz M. , Szczubiał M. 
Published: August 2011

Enzymatic activity of yeasts isolated from the inflamed mammary secretion in dairy cows
The aim of the study was to evaluate enzymatic activities of yeasts isolated from inflammatory mammary secretion. The yeasts isolated from cows with clinical and sub-clinical mastitis (134 strains) included: Candida krusei (62 strains), Candida kefyr (48 strains), Candida lusitaniae (17 strains) and Candida famata (7 strains). The API ZYM system was used containing substrates to assess 19 hydrolytic enzymes. Substantial differences in the number and activity of hydrolyses were demonstrated in individual species. In Candida krusei, acid phosphatase showed the highest activity (4.36 points), in Candida kefyr and Candida lusitaniae - leucine arylamidase (4.93 and 4.25 points, respectively), in Candida famata - α-glucosidase (4.75 points). No activity of trypsin, chymotrypsin, α-galactosidase, β-glucuronidase, α-mannosidase or α-fucosidase was observed in any of the yeasts examined.
Immunohistochemical properties of motoneurons supplying the trapezius muscle in the rat
Authors: Dudek A. , Sienkiewicz W. , Marczak M. , Kaleczyc J. 
Published: August 2011

Immunohistochemical properties of motoneurons supplying the trapezius muscle in the ratCombined retrograde tracing (using fluorescent tracer Fast blue) and double-labelling immunofluorescence were used to study the distribution and immunohistochemical characteristics of neurons projecting to the trapezius muscle in mature male rats (n=9). As revealed by retrograde tracing, Fast blue-positive (FB+) neurons were located within the ambiguous nucleus and accessory nucleus of the grey matter of the spinal cord. Immunohistochemistry revealed that nearly all the neurons were cholinergic in nature [choline acetyltransferase (ChAT)-positive]. Retrogradely labelled neurons displayed also immunoreactivities to calcitonin gene-related peptide (CGRP; approximately 60% of FB+neurons), nitric oxide synthase (NOS; 50%), substance P (SP; 35%), Leu5-Enkephalin (LEnk; 10%) and vasoactive intestinal polypeptide (VIP; 5%). The analysis of double-stained tissue sections revealed that all CGRP-, VIP- and LEnk-immunoreactive FB+perikarya were simultaneously ChAT-positive. The vast majority of the neurons expressing SP- or NOS-immunoreactivity were also cholinergic in nature; however, solitary somata were ChAT-negative. FB+perikarya were surrounded by numerous varicose nerve fibres (often forming basket-like structures) immunoreactive to LEnk or SP. They were also associated with some CGRP-, NOS- and neuropeptide Y-positive nerve terminals.
Genetic comparison of Campylobacter jejuni isolated from different cattle farms
Authors: Bednarski M. , Wieliczko A. , Mazurkiewicz M. 
Published: August 2011

Genetic comparison of Campylobacter jejuni isolated from different cattle farms
To compare the genotypes of Campylobacter jejuni, isolates of cattle origin were collected from 9 Polish farms and genotyped by ERIC-PCR. We identified 28 genotypes among the 43 C. jejuni isolates, and demonstrated high genomic diversity. The highest level of diversity was observed in strains isolated from stanchion-barn animals in opposition to those from the loose-housing system.
Changes in the blood coagulation profile after ovariohysterectomy in female dogs
Authors: Sobiech P. , Targoński R. , Stopyra A. , Żarczyńska K. 
Published: August 2011

Changes in the blood coagulation profile after ovariohysterectomy in female dogs
This study investigated changes in the coagulation profile of 10 healthy female dogs subjected to ovariohysterectomy. Blood samples were collected three times - before, directly after and 24 h after surgery. Plasma samples were analyzed to determine thrombin time (TT), prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen content, D-dimer content and antithrombin (AT) III activity. The results revealed post-operative haemostatic system disorders related to prolonged APTT, higher fibrinogen and D-dimer concentrations and lower levels of AT III activity.
Transgenic mammalian species, generated by somatic cell cloning, in biomedicine, biopharmaceutical industry and human nutrition/dietetics - recent achievements
Authors: Samiec M. , Skrzyszowska M. 
Published: August 2011

Transgenic mammalian species, generated by somatic cell cloning, in biomedicine, biopharmaceutical industry and human nutrition/dietetics - recent achievementsSomatic cell cloning technology in mammals promotes the multiplication of productively-valuable genetically engineered individuals, and consequently allows also for standardization of transgenic farm animal-derived products, which, in the context of market requirements, will have growing significance. Gene farming is one of the most promising areas in modern biotechnology. The use of live bioreactors for the expression of human genes in the lactating mammary gland of transgenic animals seems to be the most cost-effective method for the production/processing of valuable recombinant therapeutic proteins. Among the transgenic farm livestock species used so far, cattle, goats, sheep, pigs and rabbits are useful candidates for the expression of tens to hundreds of grams of genetically-engineered proteins or xenogeneic biopreparations in the milk. At the beginning of the new millennium, a revolution in the treatment of disease is taking shape due to the emergence of new therapies based on recombinant human proteins. The ever-growing demand for such pharmaceutical or nutriceutical proteins is an important driving force for the development of safe and large-scale production platforms. The aim of this paper is to present an overall survey of the state of the art in investigations which provide the current knowledge for deciphering the possibilities of practical application of the transgenic mammalian species generated by somatic cell cloning in biomedicine, the biopharmaceutical industry, human nutrition/dietetics and agriculture.
Charge transfer through single molecule contacts: How reliable are rate descriptions?
Authors: Kast Denis , Kecke L , Ankerhold J 
Published: August 2011

Background: The trend for the fabrication of electrical circuits with nanoscale dimensions has led to impressive progress in the field of molecular electronics in the last decade. However, a theoretical description of molecular contacts as the building blocks of future devices is challenging, as it has to combine the properties of Fermi liquids in the leads with charge and phonon degrees of freedom on the molecule. Outside of ab initio schemes for specific set-ups, generic models reveal the characteristics of transport processes. Particularly appealing are descriptions based on transfer rates successfully used in other contexts such as mesoscopic physics and intramolecular electron transfer. However, a detailed analysis of this scheme in comparison with numerically exact solutions is still elusive.Results: We show that a formulation in terms of transfer rates provides a quantitatively accurate description even in domains of parameter space where strictly it is expected to fail, e.g., at lower temperatures. Typically, intramolecular phonons are distributed according to a voltage driven steady state that can only roughly be captured by a thermal distribution with an effective elevated temperature (heating). An extension of a master equation for the charge–phonon complex, to effectively include the impact of off-diagonal elements of the reduced density matrix, provides very accurate solutions even for stronger electron–phonon coupling.Conclusion: Rate descriptions and master equations offer a versatile model to describe and understand charge transfer processes through molecular junctions. Such methods are computationally orders of magnitude less expensive than elaborate numerical simulations that, however, provide exact solutions as benchmarks. Adjustable parameters obtained, e.g., from ab initio calculations allow for the treatment of various realizations. Even though not as rigorously formulated as, e.g., nonequilibrium Green’s function methods, they are conceptually simpler, more flexible for extensions, and from a practical point of view provide accurate results as long as strong quantum correlations do not modify the properties of the relevant subunits substantially.
The EU Sustainable Development Discourse – An Analysis
Authors: Boissière Bruno 
Published: August 2011

Résumé Le développement durable semble aujourd’hui clairement déﬁni en tant que concept et dans ses implications politiques. Son usage dans les discours politiques s’est multiplié au ﬁl des années, à un point tel que certains n’hésitent pas à abuser de l’adjectif « durable », sans renoncer au dogme productiviste. L’analyse de discours de référence des institutions de l’Union européenne sur le développement durable montre que l’évolution du concept lui-même a fait évoluer le processus au niveau des institutions européennes depuis la première stratégie déﬁnie au Conseil européen de Göteborg (juin 2001). Cependant, si le concept a pénétré les discours des institutions, sa traduction opérationnelle et l’adaptation des structures organisationnelles apparaissent extrêmement lentes et souvent très partielles. On est loin d’une refonte du fonctionnement général en fonction de ce qui est annoncé comme une priorité politique, y compris dans les 3 principaux domaines concernés: économique, social et environnemental. Mais la cohérence du discours avec la pratique se vériﬁe dans la partie émergée de l’iceberg de la Commission, où la coordination et la supervision du développement durable ont été conﬁées au Secrétariat général en liaison directe avec le Président de la Commission.
Le discours sur la stratégie nationale de développement durable en France
Authors: Baechler Laurent 
Published: August 2011

Résumé Les autorités françaises présentèrent en 2003 la première stratégie officielle de développement durable. Ce premier programme fut mis à jour en 2006 pour se mettre en accord avec la stratégie européenne. Cependant, toute la stratégie fut révisée après l’élection présidentielle de 2007 dans un processus dynamique appelé « Grenelle de l’environnement ». Ce processus concerne un grand nombre d’acteurs, chacun ayant – au moins en théorie – une position sur la stratégie nationale de développement durable. Dès lors, le Grenelle est un parfait cas d’étude pour l’analyse du discours sur la stratégie nationale du développement durable en France. Deux conclusions ressortent de cette étude : le discours des acteurs est intrinsèquement dépendant de leurs positions et intérêts respectifs, ce qui signifie que l’on trouvera difficilement un discours intégrateur cohérent avec la conception à trois dimensions du développement durable. Cependant, plus les acteurs impliqués sont loin du niveau où l’on mesure le développement durable, plus leur discours est intégrateur.