Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification and characterization of a novel enhancer for the rat neu promoter

We used chloramphenicol acetyltransferase (CAT) assays to identify and characterize cis-acting elements responsible for rat neu promoter function. Deletion of a region of the neu promoter (-504 to -312) resulted in a marked decrease in CAT activity, indicating that this promoter region corresponds to a positive cis-acting element. Using band shift assays and methylation interference analyses, we further identified a specific protein-binding sequence, AAGATAAAACC (-466 to -456), that binds a specific trans-acting factor termed RVF (for EcoRV factor on the neu promoter). The RVF-binding site is required for maximum transcriptional activity of the rat neu promoter. This same sequence is also found in the corresponding regions of both human and mouse neu promoters. Furthermore, this sequence can enhance the CAT activity driven by a minimum promoter of the thymidine kinase gene in an orientation-independent manner, and thus it behaves as an enhancer. Our results demonstrate that RVF is the major DNA-binding protein contributing to enhancer activity. In addition, Southwestern (DNA-protein) blot analysis using the RVF-binding site as a probe points to a 60-kDa polypeptide as a potential candidate for RVF.
Inhibition of cell motility after nm23 transfection of human and murine tumor cells.

Abstract nm23 gene expression has been inversely correlated with tumor metastatic potential in certain tumors including melanomas, breast carcinomas, and hepatocellular carcinomas. The cellular mechanisms by which the nm23 protein may directly or indirectly modulate the metastatic phenotype is not yet known. Because cell motility plays an essential role in metastatic dissemination, we have studied whether tumor cells transfected with nm23 complementary DNA have any alterations in their ability to migrate. Our results demonstrate that nm23 transfection inhibits the ability of murine melanoma and human breast carcinoma cells to migrate in response to serum or to defined factors such as platelet derived growth factor or insulin-like growth factor 1. Random, unstimulated cell motility was not depressed in the nm23 transfectants. The results suggest that the nm23 gene product may interact with intracellular molecules that are essential for stimulated cell motility in two different tumor cell systems.
Hydrogen evolution: A major factor affecting the efficiency of nitrogen fixation in nodulated symbionts.

Nitrogenase-dependent hydrogen evolution from detached legume nodules and from reaction mixtures containing cell-free nitrogenase has been well established, but the overall effect of hydrogen evolution on the efficiency of nitrogen fixation in vivo has not been critically assessed. This paper describes a survey which revealed that hydrogen evolution is a general phenomenon associated with nitrogen fixation by many nodulated nitrogen-fixing symbionts. An evaluation of the magnitude of energy loss in terms of the efficiency of electron transfer to nitrogen, via nitrogenase, in excised nodules suggested that hydrogen production may severely reduce nitrogen fixation in many legumes where photosynthate supply is a factor limiting fixation. With most symbionts, including soybeans, only 40-60% of the electron flow to nitrogenase was transferred to nitrogen. The remainder was lost through hydrogen evolution. In situ measurements of hydrogen evolution and acetylene reduction by nodulated soybeans confirmed the results obtained with excised nodules. In an atmosphere of air, a major portion of the total electron flux available for the reduction of atmospheric nitrogen by either excised nodules or intact nodulated plants was utilized in the production of hydrogen gas. Some non-leguminous symbionts, such as Alnus rubra, and a few legumes (i.e., Vigna sinensis) apparently have evolved mechanisms of minimizing net hydrogen production, thus increasing their efficiency of electron transfer to nitrogen. Our results indicate that the extent of hydrogen evolution during nitrogen reduction is a major factor affecting the efficiency of nitrogen fixation by many agronomically important legumes.
Delayed coronary endothelial protection 24 hours after preconditioning: role of free radicals.

BACKGROUND Preconditioning (PC) induces delayed protection against myocardial ischemia/reperfusion (I/R) injury. Whether a similar late protective effect exists in coronary endothelial cells is not known. Thus, we assessed whether PC also induces late protection against endothelial injury after I/R and the potential role of reactive oxygen species as triggers for late PC in this setting. METHODS AND RESULTS Rats were subjected to sham surgery or to PC with 1 cycle of 2 minutes I/5 minutes R and 2 cycles of 5 minutes I/5 minutes R in the absence or presence of the free radical scavenger N-2-mercaptopropionyl glycine (MPG). Twenty-four hours later, rats were subjected to 20 minutes I/60 minutes R in the absence or presence of MPG. At the end of R, coronary segments (diameter, 200 to 300 microm) were removed distal to the site of occlusion and mounted in wire myographs. I/R reduced the relaxations to acetylcholine (maximal relaxations: sham, 72+/-6%; I/R, 31+/-6%), and this impairment was prevented by MPG (64+/-7%). PC improved the response to acetylcholine (48+/-6%), but this beneficial effect was abolished by MPG (23+/-5%). CONCLUSIONS PC induces late protection against reperfusion-induced coronary endothelial injury. Moreover, in addition to being mediators of endothelial injury during reperfusion after prolonged ischemia, reactive oxygen species produced during PC also protect the coronary endothelium from reperfusion injury 24 hours later.
Track structure in radiation biology: theory and applications.

PURPOSE A brief review is presented of the basic concepts in track structure and the relative merit of various theoretical approaches adopted in Monte-Carlo track-structure codes are examined. In the second part of the paper, a formal cluster analysis is introduced to calculate cluster-distance distributions. METHOD Total experimental ionization cross-sections were least-square fitted and compared with the calculation by various theoretical methods. Monte-Carlo track-structure code Kurbuc was used to examine and compare the spectrum of the secondary electrons generated by using functions given by Born-Bethe, Jain-Khare, Gryzinsky, Kim-Rudd, Mott and Vriens' theories. The cluster analysis in track structure was carried out using the k-means method and Hartigan algorithm. RESULTS Data are presented on experimental and calculated total ionization cross-sections: inverse mean free path (IMFP) as a function of electron energy used in Monte-Carlo track-structure codes; the spectrum of secondary electrons generated by different functions for 500 eV primary electrons; cluster analysis for 4 MeV and 20 MeV alpha-particles in terms of the frequency of total cluster energy to the root-mean-square (rms) radius of the cluster and differential distance distributions for a pair of clusters; and finally relative frequency distribution for energy deposited in DNA, single-strand break and double-strand breaks for 10MeV/u protons, alpha-particles and carbon ions. CONCLUSIONS There are a number of Monte-Carlo track-structure codes that have been developed independently and the bench-marking presented in this paper allows a better choice of the theoretical method adopted in a track-structure code to be made. A systematic bench-marking of cross-sections and spectra of the secondary electrons shows differences between the codes at atomic level, but such differences are not significant in biophysical modelling at the macromolecular level. Clustered-damage evaluation shows: that a substantial proportion of dose ( 30%) is deposited by low-energy electrons; the majority of DNA damage lesions are of simple type; the complexity of damage increases with increased LET, while the total yield of strand breaks remains constant; and at high LET values nearly 70% of all double-strand breaks are of complex type.
Design of a website for home modifications for older persons with dementia

BACKGROUND: At present, persons with dementia and their family caregivers in the Netherlands are not adequately supported to modify their dwellings to match their personal needs. OBJECTIVE: To facilitate aging-in-place for persons with dementia, a website was designed. METHODS: The website was designed with persons with dementia and their spouses. In consultation sessions existing websites were discussed. Based on this discussion, a demonstration website was created and then discussed with and judged by the participants. Visits to the website were monitored using Google Analytics. RESULTS: Participants prefer a website that is easy to print. In addition, the navigation menu should have a maximum of three levels, and the website menu should be positioned on the left. Participants dislike the use of meaningless photographs because these do not add any value to the information given. CONCLUSIONS: Participants prefer a website that is as accessible as reading a book. Some differences are related to culture, such as the participants dislike for the use of English terms. Therefore, preferences or dislikes of items on a website could not be generalized as such. However, the preferences and dislikes may provide useful input for the design process of an appropriate website.
THE GENERATIVE APPROACH TO SLA AND ITS PLACE IN MODERN SECOND LANGUAGE STUDIES

Abstract This article has two main goals. The first is to summarize and comment on the current state of affairs of generative approaches to SLA (GenSLA), 35 years into its history. This discussion brings the readership of SSLA up to date on the questions driving GenSLA agendas and clears up misconceptions about what GenSLA does and does not endeavor to explain. We engage key questions, debates, and shifts within GenSLA such as focusing on the deterministic role of input in language acquisition, as well as expanding the inquiry to new populations and empirical methodologies and technologies used. The second goal is to highlight the place of GenSLA in the broader field of SLA. We argue that various theories of SLA are needed, showing that many existing SLA paradigms are much less mutually exclusive than commonly believed (cf. Rothman & VanPatten, 2013; Slabakova, Leal, & Liskin-Gasparro, 2014, 2015; VanPatten & Rothman, 2014)—especially considering their different foci and research questions.
Effects of Ectopically Expressed Neuronal Wiskott-Aldrich Syndrome Protein Domains on Rickettsia rickettsii Actin-Based Motility

ABSTRACT Neuronal Wiskott-Aldrich syndrome protein (N-WASP) and the actin-related protein 2/3 (Arp2/3) complex have emerged as critical host proteins that regulate pathogen actin-based motility. Actin tail formation and motility in Listeria monocytogenes require the Arp2/3 complex but bypasses N-WASP signaling. Motility of Shigella flexneri and vaccinia virus requires both N-WASP and the Arp2/3 complex. Functional roles for these cytoskeletal regulatory proteins in actin-based motility of Rickettsia rickettsii have not been established. In this study, functional domains of N-WASP tagged with green fluorescent protein that have characterized effects on Shigella and vaccinia virus actin-based motility were ectopically expressed in HeLa cells infected with R. rickettsii to assess their effects on rickettsial motility. S. flexneri-infected cells were used as a control. Expressed N-WASP domains did not localize to R. rickettsii or their actin tails. Expression of N-WASP missing the VCA domain (for “verprolin homology, cofilin homology, and acidic domains”), which acts as a dominant-negative form of N-WASP, completely inhibited actin-based motility of S. flexneri while only moderately inhibiting motility of R. rickettsii. Similarly, expression of the VCA domain, which acts as a dominant-negative with respect to Arp2/3 complex function, severely inhibited actin-based motility of S. flexneri (no motility observed in the majority of expressing cells) but only moderately inhibited R. rickettsii motility. These results, taken together with the differential effects on motility observed upon expression of other N-WASP domains, suggest that actin-based motility of R. rickettsii is independent of N-WASP and the Arp2/3 complex.
What can we learn from international comparisons of social inequalities in road traffic injury mortality?

Some contextual effects can be discovered only through international comparisons In contrast with the plethora of studies concerning the social inequalities in health that have been conducted since the 1980s, there are relatively few related to injuries.1,2 There are even fewer studies comparing the influence of these inequalities in different countries. So, the publication of Borrell et al ’s study on social inequalities in transportation injury mortality across European countries3 is most welcome and timely [see page 138] . Their study elucidated the effect of differing national contexts on the influence of social disparities on road traffic injury (RTI) mortality. In this commentary, we will first explain what a so-called “contextual effect” is and then illustrate that many such effects can be discovered only through international comparisons. We contend that “dissimilarities” may provide more useful information than “similarities”. Because the contextual determinants of social inequality in RTI mortality between and within countries are different, they have different implications for injury prevention. In linguistics, context refers to the text surrounding a word, giving a better understanding of what the word means. In art, contextualism refers to the way a work of art may only be understood by knowing the historical, political, or cultural circumstances when it was produced. In health research, context similarly refers to the wider situation surrounding the association between an exposure and outcome and how this wider situation may confer meaning on that association.4 The study of the effects of collective or …
Empirical evaluation of the interrelationship of articular elements involved in the pathoanatomy of knee osteoarthritis using Magnetic Resonance Imaging

Background: In this cross-sectional study, we conducted a comprehensive assessment of all articular elements that could be measured using knee MRI. We assessed the association of pathological change in multiple articular structures involved in the pathoanatomy of osteoarthritis. Methods: Knee MRI scans from patients over 45 years old were assessed using a semi-quantitative knee MRI assessment form. The form included six distinct elements: cartilage, bone marrow lesions, osteophytes, subchondral sclerosis, joint effusion and synovitis. Each type of pathology was graded using an ordinal scale with a value of zero indicating no pathology and higher values indicating increasingly severe levels of pathology. The principal dependent variable for comparison was the mean cartilage disease score (CDS), which captured the aggregate extent of involvement of articular cartilage. The distribution of CDS was compared to the individual and cumulative distributions of each articular element using the Chi-squared test. The correlations between pathological change in the various articular structures were assessed in a Spearman correlation table. Results: Data from 140 patients were available for review. The cohort had a median age of 61 years (range 4589) and was 61% female. The cohort included a wide spectrum of OA severity. Our analysis showed a statistically significant trend towards pathological change involving more articular elements as CDS worsened (p-value for trend < 0.0001). Comparison of CDS to change in the severity of pathology of individual articular elements showed statistically significant trends towards more severe pathology as CDS worsened for osteophytes (p-value for trend < 0.0001), bone marrow lesions (p = 0.0003), and subchondral sclerosis (p = 0.009), but not joint effusion or synovitis. There was a moderate correlation between cartilage damage, osteophytes and BMLs as well as a moderate correlation between joint effusion and synovitis. However, cartilage damage and osteophytes were only weakly associated with synovitis or joint effusion. Conclusion: Our results support an inter-relationship of multiple articular elements in the pathoanatomy of knee OA. Prospective studies of OA pathogenesis in humans are needed to correlate these findings to clinically relevant outcomes such as pain and function. Published: 29 October 2009 BMC Musculoskeletal Disorders 2009, 10:133 doi:10.1186/1471-2474-10-133 Received: 18 March 2009 Accepted: 29 October 2009 This article is available from: http://www.biomedcentral. com/1471-2474/10/133 © 2009 Meredith et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Metabolic Channeling of Carbamoyl Phosphate, a Thermolabile Intermediate

Two different approaches provided evidence for a physical interaction between the carbamate kinase-like carbamoyl-phosphate synthetase (CKase) and ornithine carbamoyltransferase (OTCase) from the hyperthermophilic archaeonPyrococcus furiosus. Affinity electrophoresis indicated that CKase and OTCase associate into a multienzyme cluster. Further evidence for a biologically significant interaction between CKase and OTCase was obtained by co-immunoprecipitation combined with formaldehyde cross-linking experiments. These experiments support the hypothesis that CKase and OTCase form an efficient channeling cluster for carbamoyl phosphate, an extremely thermolabile and potentially toxic metabolic intermediate. Therefore, by physically interacting with each other, CKase and OTCase prevent the thermodenaturation of carbamoyl phosphate in the aqueous cytoplasmic environment.
Accumulation of labelled vitamin B12 in some transplanted tumours

The accumulation of labelled vitamin B12 in four different kinds of transplanted tumour was studied using whole‐body autoradiography and impulse counting. The tumours were 90Sr‐induced soft fibroblastic osteosarcomas, spontaneous mammary carcinomas, Ehrlich ascites and Moloney virus‐induced tumours. The 90Sr‐induced soft sarcoma, which was the most rapidly growing tumour, showed the greatest uptake of radio‐B12, the concentration being higher than in any normal tissue. In all tumours the radioactivity was localized to the peripheral, still actively growing parts. It is suggested that a connection exists between growth rate and accumulation of B12 and that B12 is needed for rapid cell multiplication.
[Role of MMP-9 and TIMP-1 in renal tubular epithelial-myofibroblast transdifferentiation].

OBJECTIVE To investigate the dynamic changes of MMP-9 and TIMP-1 expressions in rat unilateral ureteral obstruction (UUO) model, and to explore the role of MMP-9 and TIMP-1 in tubular epithelialmyofibroblast transdifferentiation. METHODS Sixty-four male rats were randomly allocated to sham UUO group and UUO group. Rats were sacrificed respectively at 3, 7, 14 and 21 days after UUO or sham-surgery. The expression levels of MMP-9, TIMP-1, alpha-smooth muscle actin (alpha-SMA) and fibronectin (FN) were examined by immunohistochemistry staining at each time point. RESULTS In UUO rats, the disruption of renal tubular basement membrane (TBM) in PAS staining was found at day 3 after operation. At postoperative day 14 and 21, the TBM was observed to be thickened and wrinkled with partial and extensive disruption. On day 3 after UUO, the expressions of alpha-SMA and FN in tubulointerstitium were obviously increased. On day 7, some tubular epithelial cells also expressed alpha-SMA. In UUO rats, the strong positive expression of MMP-9 in renal tubulointerstitium was found at day 3 after operation and the expression peaked in tubulointerstitium at day 7, then decreased gradually. (4) In UUO rats, TIMP-1 expression in renal tubulointerstitium was increased progressively starting from day 3 to day 21. (5) The expression of MMP-9 in renal tubulointerstitium was significantly associated with the positive area of alpha-SMA and the disruption of TBM. CONCLUSION The expression levels of MMP-9 and TIMP-1 relate closely to the disruption of TBM. TBM structural and functional integrity depends on many intricate interactions between MMP-9 and TIMP-1, which may play an important role in tubular epithelialmyofibroblast transdifferentiation.
Linear prediction approach for sinusoidal frequency estimation in colored noise

In this paper, we consider the problem of frequency estimation of sinusoidal signals from observations corrupted with colored noise. The proposed method is based on linear prediction property of sinusoidal signals. We express Yule-Walker equations as a quadratic eigenvalue problem whose solution corresponds to the parameters of signal and noise. The performance of the proposed algorithm is evaluated by comparing with Cramer Rao bound via computer simulation.
Ocular morbidity in myopia

As ophthalmologists we have all experienced parents or patients asking how to arrest myopia progression, or what will happen to the eye and to the sight if progression continues? Is there a higher risk of complications and are these complications depending on how the eyes are used? Such simple questions have been open for discussion for more than hundred years, and still we have no clear answers. The fact that pathologic myopia has an increased risk of developing severe complications does not necessarily imply that all cases of high myopia have a visual prognosis worse than for instance that of emmetropia. Perkins’ data (1979), however, indicate that even lower degrees of myopia are associated with a higher incidence of open angle glaucoma and retinal detachment. His data further suggest that more myopes require cataract extraction than would be expected from the mere prevalence of myopia in the population. I am not convinced that these findings have a global bearing, but even if so, we still have the problem of identifying eyes at risk and pointing out possible risk factors. It would be valuable to make investigations into the distribution of refractive errors in various eye disease entities, e.g. glaucoma, cataract, retinal detachment, and chorioretinal degenerations. Such information has to be assessed against the