Miracle-dz/UniFAR-FTUs huggingface dataset:
Epigenetic regulation of DACH1, a novel Wnt signaling component in colorectal cancer

Colorectal cancer (CRC) is one of the common malignant tumors worldwide. Both genetic and epigenetic changes are regarded as important factors of colorectal carcinogenesis. Loss of DACH1 expression was found in breast, prostate, and endometrial cancer. To analyze the regulation and function of DACH1 in CRC, 5 colorectal cancer cell lines, 8 cases of normal mucosa, 15 cases of polyps and 100 cases of primary CRC were employed in this study. In CRC cell lines, loss of DACH1 expression was correlated with promoter region hypermethylation, and re-expression of DACH1 was induced by 5-Aza-2'-deoxyazacytidine treatment. We found that DACH1 was frequently methylated in primary CRC and this methylation was associated with reduction in DACH1 expression. These results suggest that DACH1 expression is regulated by promoter region hypermethylation in CRC. DACH1 methylation was associated with late tumor stage, poor differentiation, and lymph node metastasis. Re-expression of DACH1 reduced TCF/LEF luciferase reporter activity and inhibited the expression of Wnt signaling downstream targets (c-Myc and cyclinD1). In xenografts of HCT116 cells in which DACH1 was re-expressed, tumor size was smaller than in controls. In addition, restoration of DACH1 expression induced G2/M phase arrest and sensitized HCT116 cells to docetaxel. DACH1 suppresses CRC growth by inhibiting Wnt signaling both in vitro and in vivo. Silencing of DACH1 expression caused resistance of CRC cells to docetaxel. In conclusion, DACH1 is frequently methylated in human CRC and methylation of DACH1 may serve as detective and prognostic marker in CRC.
WDM-IDMA solution for NG-PON2 enabled by coherent technology and colorless ONUs

We propose a novel hybrid solution for next generation passive optical network (NG-PON2) combining wavelength-division multiplexing (WDM) and interleave-division multiple-access (IDMA). Results demonstrate the uplink transmission supporting more than 90 colorless ONUs at 1.25 Gb/s each over 100 km reach.
The Effects of Spatially Heterogeneous Prey Distributions on Detection Patterns in Foraging Seabirds

Many attempts to relate animal foraging patterns to landscape heterogeneity are focused on the analysis of foragers movements. Resource detection patterns in space and time are not commonly studied, yet they are tightly coupled to landscape properties and add relevant information on foraging behavior. By exploring simple foraging models in unpredictable environments we show that the distribution of intervals between detected prey (detection statistics) is mostly determined by the spatial structure of the prey field and essentially distinct from predator displacement statistics. Detections are expected to be Poissonian in uniform random environments for markedly different foraging movements (e.g. Lévy and ballistic). This prediction is supported by data on the time intervals between diving events on short-range foraging seabirds such as the thick-billed murre (Uria lomvia). However, Poissonian detection statistics is not observed in long-range seabirds such as the wandering albatross (Diomedea exulans) due to the fractal nature of the prey field, covering a wide range of spatial scales. For this scenario, models of fractal prey fields induce non-Poissonian patterns of detection in good agreement with two albatross data sets. We find that the specific shape of the distribution of time intervals between prey detection is mainly driven by meso and submeso-scale landscape structures and depends little on the forager strategy or behavioral responses.
Fast Greedy Algorithms for Constructing Sparse Geometric Spanners

Given a set V of n points in $\IR^d$ and a real constant t>1, we present the first O(nlog n)-time algorithm to compute a geometric t-spanner on V. A geometric t-spanner on V is a connected graph G = (V,E) with edge weights equal to the Euclidean distances between the endpoints, and with the property that, for all $u,v\in V$, the distance between u and v in G is at most t times the Euclidean distance between u and v. The spanner output by the algorithm has O(n) edges and weight $O(1)\cdot wt(MST)$, and its degree is bounded by a constant.
Associative memory Hamiltonians for structure prediction without homology: α/β proteins

We describe a method for predicting the structure of α/β class proteins in the absence of information from homologous structures. The method is based on an associative memory model for short to intermediate range in sequence contacts and a contact potential for long range in sequence contacts. The coefficients in the energy function are chosen to maximize the ratio of the folding temperature to the glass transition temperature. We use the resulting optimized model to predict the structure of three α/β protein domains ranging in length from 81 to 115 residues. The resulting predictions align with low rms deviations to large portions of the native state. We have also calculated the free energy as a function of similarity to the native state for one of these three domains, and we show that, as expected from the optimization criteria, the free energy surface resembles a rough funnel to the native state. Finally, we briefly demonstrate the effect of roughness in the energy landscape on the dynamics.
Hydrogen sulfide is an endogenous modulator of leukocyte‐mediated inflammation

Hydrogen sulfide (H2S) is increasingly recognized as an important signaling molecule in the cardiovascular and nervous systems. Recently, H2S donors were reported to induce neutrophil apoptosis and to suppress expression of some leukocyte and endothelial adhesion molecules. Using rats, we examined the possibility that H2S is an endogenous regulator of key inflammatory events at the leukocyte‐endothelial interface. Via intravital microscopy, we observed that H2S donors (NaHS and Na2S) inhibited aspirin‐induced leukocyte adherence in mesenteric venules (ED50 of 5.0 µmol/kg for Na2S), likely via activation of ATP‐sensitive K+ (KATP) channels. Inhibition of endogenous H2S synthesis elicited leukocyte adherence. Leukocyte infiltration in an air pouch model was also suppressed by H2S donors (NaHS, Lawesson's reagent, and N‐acetylcysteine; ED50 of 42.7, 1.3, and 29.9 µmol/kg, respectively) and exacerbated by inhibition of endogenous H2S synthesis. Carrageenan‐induced paw edema was suppressed by H2S donors (NaHS and Na2S; ED50s of 35 and 28 µmol/kg, respectively) to the same extent as by diclofenac and enhanced by an inhibitor of H2S synthesis. Suppression of edema formation by H2S donors was mimicked by a KATP channel agonist and reversed by an antagonist of this channel. These results suggest that endogenous H2S is an important mediator of acute inflammation, acting at the leukocyte‐endothelium interface. These findings have important implications for anti‐inflammatory drug development. —Zanardo, R. C. O. , Brancaleone, V. , Distrutti, E. , Fiorucci, S. , Cirino, G. , Wallace, J. L. Hydrogen sulfide is an endogenous modulator of leukocyte‐mediated inflammation. FASEB J. 20, E1411–E1418 (2006)
Advances in Knowledge Related to Wounding, Repair, and Healing: 1885–1984

The purpose of this paper is to record objectively the contribution of Annals of Surgery to the development of the science of surgery and its application to patient care in commemoration of its Centennial. Though many other subjects could have been chosen, the literature relating to wounding, repair, and healing is pertinent to all of surgery and uniquely comprises a significant portion of its history and science. By reviewing the articles and content of the 200 volumes, a personal perspective was gained and hopefully captured in the body of the manuscript. By departing from the usual format of a bibliography, names of authors appear rather than impersonal numbers. The editorial eras are apparent, punctuated by the beginnings, the World Wars, the Wars of Korea, Vietnam, and North Africa, the development of biomedical research, and the technologies in other fields. Annals also reflects the logarithmic increase in higly competent surgeons through the burgeoning educational programs of university health centers, major hospitals, and clinics in the United States and in other parts of the world. Societal needs and problems are reflected by the scope and breadth of the surgical articles in response to the medical needs of its constituents during war and peace. The evolution of specialization is apparent from the beginning. Declining morbidity and mortality rates reflect the application of research, technology, and experience to the science of surgery and the biology of wounds through their dissemination.
Biochemical Changes Associated with Ripening : The Fruit Ripening Syndrome

Fruit ripening is a sophisticatedly orchestrated developmental process, unique to plants, that results in major physiological and metabolic changes, ultimately leading to fruit decay and seed dispersal. Because of their strong impact on fruit nutritional and sensory qualities, the ripeningassociated changes have been a matter of sustained investigation aiming at unravelling the molecular and genetic basis of fruit ripening. Tomato rapidly emerged as the model of choice for fleshy fruit research and a wealth of genetic resources and genomics tools have been developed, providing new entries into the regulatory mechanisms involved in the triggering and coordination of the ripening process. Some of the key components participating in the control of tomato fruit ripening have been uncovered, but our knowledge of the network of signalling pathways engaged in this complex developmental process remains fragmentary. This review highlights the main advances and emphasizes issues still to be addressed using the rapidly developing ‘omics’ approaches.
Relationship of Benign Gynecologic Diseases to Subsequent Risk of Ovarian and Uterine Tumors

Objective: Although endometriosis and uterine leiomyomas are common conditions, the extent to which either is associated with certain types of malignancies remains uncertain. Methods: Using record linkage techniques, we assessed the relationships between hospital and outpatient admissions for endometriosis or leiomyomas and the development of ovarian and uterine cancers in Denmark between 1978 and 1998. Based on a population-based cohort exceeding 99,000 women, including 2,491 ovarian cancers, 860 borderline ovarian tumors, and 1,398 uterine cancers, we derived relative risks (RR) and 95% confidence intervals (95% CI) associated with overall and histology-specific tumor risks after adjustment for calendar time and reproductive characteristics. Results: Endometriosis seemed to predispose to the development of ovarian cancer, with the association restricted to endometrioid or clear cell malignancies. Five or more years after the diagnosis of endometriosis, the RRs (95% CIs) were 2.53 (1.19-5.38) for endometrioid (7 exposed cases) and 3.37 (1.24-9.14) for clear cell (4 exposed cases) malignancies. Uterine leiomyomas were associated with increases in the risk of uterine malignancies, particularly sarcomas, where the RRs (95% CIs) were 20.80 (11.32-38.22) for women with 1 to 4 years of follow-up (11 exposed cases) and 5.70 (2.27-14.32) for those with more extended follow-up (5 exposed cases). Conclusion: In combination with clinical, pathologic, and molecular data, our results support that some endometriotic lesions may predispose to clear cell and endometrioid ovarian cancers. Uterine leiomyomas also showed a strong connection with subsequent uterine sarcomas, although it was difficult to decipher whether this reflected detection bias, shared risk factors, or an etiologic relationship. (Cancer Epidemiol Biomarkers Prev 2005;14(12):2929–35)
VIPACES, Verification Interface Primitives for the Development of AXI Compliant Elements and Systems

This paper presents VIPACES (verification interface primitives for the development of AXI compliant elements and systems), a simple environment for the verification of AMBA 3 AXI systems in verification IP (VIP) production. The elements come from the necessity of creating generic modules, in the verification phase, for this widely used protocol. These primitives are presented as a not compiled library written in SystemC where interfaces are the core of the library. The definition of interfaces instead of generic modules let the user construct custom modules improving the resources spent during the verification phase as well as easily adapting his own modules to the AMBA 3 AXI protocol. As validation scenario, results obtained for an AXI bus connecting IDCT and other processing resources for MPEG4 video decoding are presented
Aftermath of a snowball Earth

Using a simple 3‐box model of the ocean‐atmosphere system, we simulate the cycling of carbon and strontium in the aftermath of a global glaciation. Model simulations include the delivery of alkalinity to seawater from intense carbonate and silicate weathering under high pCO2 conditions as well as ocean mixing, air‐sea gas exchange, and biological productivity. The δ13C of the first carbonate precipitated after the glaciation depends on the pCO2, temperature, the saturation state of the surface ocean, and kinetic effects associated with mineral precipitation. With no biological productivity, the model produces δ13C values between +1‰ and −3‰, consistent with observations. This is in direct contradiction with arguments by Kennedy et al. [2001a] , who suggest that the δ13C value of dissolved carbon in a snowball ocean (and directly afterward) must be −5‰. Kennedy et al. assume the carbon isotope cycle is in steady state, which does not apply to a global glaciation, and also neglect any effect of high pCO2 on the carbonate chemistry of seawater. A major difference between our findings and the qualitative predictions of Hoffman et al. [1998] is our interpretation of the cap dolostone as representing an interval dominated by carbonate weathering of exposed continental shelves. As a result, the ∼2‰ drop in the δ13C observed in the cap dolostone is unlikely to be the product of Rayleigh distillation of atmospheric CO2 via silicate weathering. Instead, we interpret the ∼2‰ drop in the δ13C values as indicative of an increase in sea surface temperature which lowers the fractionation between CO2 and carbonate. Kinetic isotope effects associated with rapid precipitation from a highly supersaturated surface ocean may also be important. Rayleigh distillation of atmospheric CO2 via silicate weathering is a viable explanation for the continued drop in the δ13C values in the limestone sequence above the cap dolostone, with biological productivity and carbonate weathering driving a slow increase in δ13C values once pCO2 levels decline. Our study also simulates the cycling of strontium in seawater. In contrast to the finding of Jacobsen and Kaufman [1999] and Kennedy et al. [2001a] , model simulations show a drop in 87Sr/86Sr of less than 0.001 during 5 million years of global glaciation and an increase of less than 0.001 over the entire episode of silicate weathering. Our calculations emphasize the importance of considering the changes in seawater chemistry due to high pCO2 in evaluating the Snowball Earth hypothesis.
Entropy-based clock skew measurements for mobile devices

Clock skew measurement can be realized in one-way communication by continuously collecting timestamps from the same remote device, and then find the slope of best fit to the offset dataset. However, offsets collected in mobile network may form multi-segmented distribution due to the change of base station or network adapter. This type of distribution usually cause the existing methods fail to provide accurate estimations. This paper introduces a new method to estimate the clock skew of remote network devices. In this method, a three-stage process is adapted to efficiently scan for the skew by which the entropy of adjusted offsets be minimum. Different from the existing approaches, this entropy-based method is not affected by multi-segment offset distributions and is able to deliver precise skew estimation with a short period of time. To compare our approach with existing ones, experiments of both classical and multi-segmented distributions have been conducted. The entropy-based method is the only one whose estimations be bound in 1 parts per million range.
DSDPC: Delay signatures at different process corners based hardware trojan detection technique for FPGAs

In applications such as nuclear power plant, space and military, safety critical systems play an important role, where security is one of the crucial design parameters. Similar to software Trojans (virus), Hardware Trojans (HT) are raising security concerns in recent years. HTs are malicious additions or modifications to existing circuit elements which are implemented either as always on or triggered only under certain conditions, to disable functionality, reduce reliability and leak valuable information from the integrated chip. In this paper, we consider the scenario of HTs inserted in field programmable gate array (FPGA) devices during field operating conditions and propose a delay signature based HT detection technique. Static timing analysis is performed to measure the delay signatures of original netlist with that of netlist extracted from field configuration bit file. Since the results of electronic design automation tools are repetitive, we compare both the delay signatures and any deviation will indicate that configuration bit file/ netlist file of the original design is altered. To increase the detection efficiency, we perform static timing analysis at various process corners such as slow, typical and fast corners (at different voltage and temperature combinations) which allows us to measure the best and worst circuit delay values. Using this property, we performed simulations with Xilinx ISE tool by targeting standard benchmark circuits on Xilinx device. Experimental results reflected the difference in delay signatures if configuration bit file is tampered with in the field. The delay difference between with and without HT circuit is enhanced from slow to fast process corner, which in turn increased the HT detection efficiency.
A Pilot Test of the Latin Active Hip Hop Intervention to Increase Physical Activity among Low-Income Mexican-American Adolescents

Purpose. The primary purpose of the current study was to develop, implement, and evaluate a hip hop dance intervention, Latin Active, among low-income Mexican-American adolescents. Mexican-descent adolescents tend to have disproportionate rates of low physical activity, overweight status, and obesity. Design. A 5-week intervention design with pretest and post-test self-report measures. Setting. Charter middle school (grades 6–9) health/science classes in a low-income neighborhood were the setting for the Latin Active intervention. Participants. Overall, 81 participants were recruited; 73 (n = 41, female; n = 32, male) provided active parental consent to complete pretest/post-test surveys. Intervention. The Latin Active program included 10 interactive 50-minute lessons that were delivered twice a week during science/health classes. The curriculum was created on the basis of Social Cognitive Theory, Critical Hip Hop Pedagogy, and feedback from key stakeholders. The lessons focused on increasing physical activity as well as neighborhood barriers. Measures. The self-report pretest (n = 73) and post-test (n = 56) surveys included measures for frequency of vigorous physical activity, self-efficacy, and neighborhood barriers. Analysis. Paired-sample t-test analyses were conducted to assess mean differences from pretest to post-test results for intervention outcomes by gender. Results. The Latin Active program (with 77% retention at post-test) significantly increased vigorous physical activity and dance (p < . 05) and increased self-efficacy (p < . 05) among girls, and it decreased perception of neighborhood barriers (p < . 05) among boys. Conclusion. A hip hop physical activity program, Latin Active demonstrated preliminary efficacy to increase girl's vigorous physical activity and boy's perception of neighborhood barriers to physical activity. Future research will need to use a randomized, controlled design and investigate the effect of the program on measures of body mass index.
Pathways of post-transcriptional gene regulation in mammalian germ cell development

Male germ cell development is orchestrated by complex and disparate patterns of gene expression operating in different cell types. The mechanisms of gene expression underlying these have been dissected in the mouse because of its readily available genetics. These analyses have shown that as well as the traditional transcriptional mechanisms, post-transcriptional regulatory pathways of gene expression are essential for mouse spermatogenesis. Proteins essential for germ cell development have been identified which operate at different points throughout the life cycle of RNA from pre-mRNA splicing to translation and RNA decay in the cytoplasm. Recent data suggests that these post-transcriptional pathways respond to environmental cues via signalling pathways.
Socioeconomic and country variations in knowledge of health risks of tobacco smoking and toxic constituents of smoke: results from the 2002 International Tobacco Control (ITC) Four Country Survey

Background: Socioeconomic status is strongly associated with smoking prevalence and social class differences contribute substantially to social inequalities in mortality. This research investigated socioeconomic and country variations in smokers’ knowledge that smoking causes heart disease, stroke, impotence and lung cancer, that smoke contains cyanide, mercury, arsenic and carbon monoxide, and whether nicotine causes most of the cancer. Methods: Data were from the International Tobacco Control (ITC) Four Country Survey, a cohort survey of over suppl_ adult smokers from four countries: the United States, Canada, the United Kingdom, and Australia. Data were collected via telephone interviews in 2002. Results: Higher education and income were associated with higher awareness. For example, the odds of knowing that smoking causes heart disease, stroke and lung cancer were respectively 71%, 34% and 83% larger for respondents with high versus low income. The odds of knowing that smoke contains cyanide, mercury, arsenic and carbon monoxide were respectively 66%, 26%, 44% and 108% larger for respondents with a university degree than those with a high school diploma or lower level of education. Results also revealed that awareness of harms of smoking was generally the highest in Canada and the lowest in the UK. Conclusions: Lower socioeconomic status was associated with lower awareness of the harms of smoking and misunderstanding around nicotine. There is a need to improve knowledge of the dangers of smoking among the disadvantaged segments of the population.
Mobile-Deblur: A Clear Image Will on the Smart Device

With the development of the social network, posting announcements, image ads and other fresh events with pictures play an important role. Therefor, taking clear digital pictures is an urgent need to be solved right now. However, the movement or instability of lens will cause the picture faint blur, which greatly reduces the user experience. The current solutions are to put the virtual dummy photo in the computer of a higher configuration for processing. This process seriously affected the timeliness and universality of information dissemination. In this paper, we proposed portable deblurring system for mobile terminal of fuzzy pictures based on two classic image restoration algorithm of Wiener filter and blind restoration. Proposed mobile deblurring system adaptively evaluates the degree of picture blurs, and the point diffusion function is resolved by the existing fuzzy picture feature. At the same time, the optimization of the ambiguity is made to ensure the lightweight and low latency of the Mobile-Deblur algorithm. Finally, the validity and superiority in the MobileDeblur System is proved by simulation and real environment experiment respectively in the picture to deblur on the mobile phone.