Miracle-dz/UniFAR-FTUs huggingface dataset:
Galaxies in Front of Quasars: Markarian 1456 and SDSS J114719.90+522923.2

The chance projection of the disk of Mrk 1456 onto a background QSO is similar to the case of SBS 1543+593-HS 1543+5921. Mrk 1456 is a luminous, late-type spiral galaxy at z ≈ 0.05. Although the QSO, SDSS J114719.90+522923.2 at z ≈ 2, has not yet been observed with ultraviolet spectroscopy, it shows strong Ca II absorption at the redshift of Mrk 1456, which gives evidence that it is a possible damped Lyα absorber. Spectroscopy of the star-forming nucleus of Mrk 1456 allows us to apply emission-line diagnostics to infer the chemical abundances at the center of the galaxy and to make a prediction of the expected metallicity on the sight line to the QSO.
Fumarase tumor suppressor gene and MET oncogene cooperate in upholding transformation and tumorigenesis

Loss of the fumarate hydratase (FH) tumor suppressor gene results in the development of benign tumors that rarely, but regrettably, progress to very aggressive cancers. Using mouse embryo fibroblasts (MEFs) to model transformation, we found that fh knockdown results in increased expression of the met oncogene‐encoded tyrosine kinase receptor through hypoxia‐inducible factor (hif) stabilization. MET‐in‐creased expression was alone able to stabilize hif, thus establishing a feed forward loop that might enforce tumor progression. The fh‐defective MEFs showed increased motility and protection from apoptosis. Motility, but not survival, relied on hif‐1α and was greatly enhanced by MET ligand hepatocyte growth factor. Met cooperated with a weakly oncogenic ras in making MEFs transformed and tumorigenic, as shown by in vitro and in vivo assays. Loss of fh was not equally effective by itself but enhanced the transformed and tumorigenic phenotype induced by ras and MET. Consistently, the rescue of fumarase expression abrogated the motogenic and transformed phenotype of fh‐defective MEFs. In conclusion, the data suggest that the progression of tumors where FH is lost might be boosted by activation of the MET oncogene, which is able to drive cell‐autonomous tumor progression and is a strong candidate for targeted therapy. —Costa, B. , Dettori, D. , Lorenzato, A. , Bardella, C. , Coltella, N. , Martino, C. , Cammarata, C. , Carmeliet, P., Olivero, M. , Di Renzo, M. F. Fumarase tumor suppressor gene and MET oncogene cooperate in upholding transformation and tumorigenesis. FASEB J. 24, 2680–2688 (2010). www.fasebj. org
Advances in Frequent Itemset Mining Implementations: Introduction to FIMI03

Since the introduction of association rule mining in 1993 by Agrawal Imielinski and Swami [3], the frequent itemset mining (FIM) tasks have received a great deal of attention. Within the last decade, a phenomenal number of algorithms have been developed for mining all [3–5, 10, 18, 19, 21, 23, 26, 28, 31, 33], closed [6, 12, 22, 24, 25, 27, 29, 30, 32] and maximal frequent itemsets [1, 2, 7, 11, 15–17, 20, 35]. Every new paper claims to run faster than previously existing algorithms, based on their experimental testing, which is oftentimes quite limited in scope, since many of the original algorithms are not available due to intellectual property and copyright issues. Zheng, Kohavi and Mason [34] observed that the performance of several of these algorithms is not always as claimed by its authors, when tested on some different datasets. Also, from personal experience, we noticed that even different implementations of the same algorithm could behave quite differently for various datasets and parameters. Given this proliferation of FIM algorithms, and sometimes contradictory claims, there is a pressing need to benchmark, characterize and understand the algorithmic performance space. We would like to understand why and under what conditions one algorithm outperforms another. This means testing the methods for a wide variety of parameters, and on different datasets spanning dense and sparse, real and synthetic, small and large, and so on. Given the experimental, algorithmic nature of FIM (and most of data mining in general), it is crucial that other researchers be able to independently verify the claims made in a new paper. Unfortunately, the FIM community (with few exceptions) has a very poor track record in this regard. Many new algorithms are not available even as an executable, let alone the source code. How many times have we heard “this is proprietary software, and not available. ” This is not the way other sciences work. Independent verifiability is the hallmark of sciences like physics, chemistry, biology, and so on. One may argue, that the nature of research is different, they have detailed experimental procedure that can be replicated, while we have algorithms, and there is more than one way to code an algorithm. However, a good example to emulate is the bioinformatics community. They have espoused the open-source paradigm with more alacrity than we have. It is quite common for journals and conferences in bioinformatics to require that software be available. For example, here is a direct quote from the journal Bioinformatics (http://bioinformatics.oupjournals.org/):
Molecular Link between Leaf Coloration and Gene Expression of Flavonoid and Carotenoid Biosynthesis in Camellia sinensis Cultivar ‘Huangjinya’

‘Huangjinya’ is an excellent albino tea germplasm cultivated in China because of its bright color and high amino acid content. It is light sensitive, with yellow leaves under intense light while green leaves under weak light. As well, the flavonoid and carotenoid levels increased after moderate shading treatment. However, the mechanism underlying this interesting phenomenon remains unclear. In this study, the transcriptome of ‘Huangjinya’ plants exposed to sunlight and shade were analyzed by high-throughput sequencing followed by de novo assembly. Shading ‘Huangjinya’ made its leaf color turn green. De novo assembly showed that the transcriptome of ‘Huangjinya’ leaves comprises of 127,253 unigenes, with an average length of 914 nt. Among the 81,128 functionally annotated unigenes, 207 differentially expressed genes were identified, including 110 up-regulated and 97 down-regulated genes under moderate shading compared to full light. Gene ontology (GO) indicated that the differentially expressed genes are mainly involved in protein and ion binding and oxidoreductase activity. Antioxidation-related pathways, including flavonoid and carotenoid biosynthesis, were highly enriched in these functions. Shading inhibited the expression of flavonoid biosynthesis-associated genes and induced carotenoid biosynthesis-related genes. This would suggest that decreased flavonoid biosynthetic gene expression coincides with increased flavonoids (e.g., catechin) content upon moderate shading, while carotenoid levels and biosynthetic gene expression are positively correlated in ‘Huangjinya. ’ In conclusion, the leaf color changes in ‘Huangjinya’ are largely determined by the combined effects of flavonoid and carotenoid biosynthesis.
Loss of Physiologic Hepatic Blood Flow Control (“Hepatic Arterial Buffer Response”) During CO2-Pneumoperitoneum in the Rat

We analyzed whether a compensatory increase of hepatic arterial (HA) flow, known as the “hepatic arterial buffer response” (HABR), may serve for maintenance of liver blood supply during laparoscopy-associated portal venous (PV) flow reduction. We assessed HA and PV flow, as well as hepatic tissue oxygenation (Po2) during CO2-pneumoperitoneum in anesthetized and mechanically ventilated Sprague-Dawley rats (n = 7). Control animals (n = 7) without pneumoperitoneum, but tourniquet-induced PV flow reduction served to demonstrate physiologic HABR. Although stepwise tourniquet-induced reduction of PV flow to 20% of baseline values led to a significant (P < 0.05) increase of HA flow from 4.3 ± 0.7 mL/min to 9.9 ± 1.7 mL/min, stepwise intraabdominal pressure-induced decrease of PV flow was paralleled by a linear reduction of HA flow from 2.4 ± 0.3 mL/min to 1.2 ± 0.5 mL/min at 18 mm Hg intraabdominal pressure. This loss of HABR was sustained during a subsequent 2 h-period of CO2- pneumoperitoneum contrasting the 2 h of maintenance of HABR in controls. Hepatic tissue Po2 decreased during the 2 h-period of pressure- and tourniquet-induced PV flow reduction by 35% to 51%, respectively. On tourniquet release, all variables regained baseline values, whereas evacuation of the pneumoperitoneum allowed all variables except hepatic Po2 to return to baseline, indicating prolonged tissue hypoxia despite restored total liver blood flow in the Laparoscopic group. Concomitantly, increased liver enzyme activities reflected moderate tissue damage after 2 h of pneumoperitoneum. In conclusion, intraabdominal CO2- insufflation-induced hemodynamic alterations may impair tissue oxygenation and enzyme release, indicating the potential risk for hepatic tissue damage after prolonged periods of laparoscopic interventions.
Effects of azathioprine on mucociliary clearance after bronchial section and anastomosis in a rat experimental model.

OBJECTIVE To evaluate the effects of azathioprine on the mucociliary system in a model of bronchial section and anastomosis in rats. METHODS Thirty-six male Wistar-Furth rats were submitted to left bronchial section and anastomosis and divided into two groups to receive either saline solution or azathioprine. After 7, 15 and 30 days of treatment, six animals from each group were killed, after which in situ mucociliary transport velocity, in vitro mucus transportability, and contact angle of mucus in the right (intact) and left (sectioned) bronchi were measured. RESULTS In situ mucociliary transport velocity was significantly lower in the sectioned bronchi than in the intact bronchi (p < 0.001). In situ mucociliary transport velocity was lower in the intact bronchi of the animals treated with azathioprine for 7 days (p < 0.05), and those bronchi presented full recovery after 30 days of treatment. The contact angle was higher in the mucus samples collected from the sectioned bronchi of the animals treated with saline solution for 30 days (p < 0.001), which is in accordance with the decreased in vitro mucus transportability observed in the same animals (p < 0.001). CONCLUSIONS We conclude that, in the sectioned bronchi of rats, treatment with azathioprine causes only transitory impairment of mucociliary transport, whereas administration of saline solution impairs mucociliary transport for up to 30 days. In addition, azathioprine protects against alterations in mucus surface properties.
Using Evolutionary Conserved Modules in Gene Networks as a Strategy to Leverage High Throughput Gene Expression Queries

Background Large-scale gene expression studies have not yielded the expected insight into genetic networks that control complex processes. These anticipated discoveries have been limited not by technology, but by a lack of effective strategies to investigate the data in a manageable and meaningful way. Previous work suggests that using a pre-determined seed-network of gene relationships to query large-scale expression datasets is an effective way to generate candidate genes for further study and network expansion or enrichment. Based on the evolutionary conservation of gene relationships, we test the hypothesis that a seed network derived from studies of retinal cell determination in the fly, Drosophila melanogaster, will be an effective way to identify novel candidate genes for their role in mouse retinal development. Methodology/Principal Findings Our results demonstrate that a number of gene relationships regulating retinal cell differentiation in the fly are identifiable as pairwise correlations between genes from developing mouse retina. In addition, we demonstrate that our extracted seed-network of correlated mouse genes is an effective tool for querying datasets and provides a context to generate hypotheses. Our query identified 46 genes correlated with our extracted seed-network members. Approximately 54% of these candidates had been previously linked to the developing brain and 33% had been previously linked to the developing retina. Five of six candidate genes investigated further were validated by experiments examining spatial and temporal protein expression in the developing retina. Conclusions/Significance We present an effective strategy for pursuing a systems biology approach that utilizes an evolutionary comparative framework between two model organisms, fly and mouse. Future implementation of this strategy will be useful to determine the extent of network conservation, not just gene conservation, between species and will facilitate the use of prior biological knowledge to develop rational systems-based hypotheses.
Safety through security

This paper illustrates that the concept of noninterference, used in theories of security, may also be used to reason about safety. It presents a technique for modelling safety properties in terms of communicating processes, and develops a practical theory of system protection from failures. A simple example is presented to illustrate the application of this technique to different classes of safety property.
The effects of journaling for women with newly diagnosed breast cancer

Forty‐three women newly diagnosed with breast cancer participated in this study, which examined the role of expressive journal writing characteristics on mood over the course of a 12‐week support group. Writing was analyzed using the linguistic inquiry and word count program. Writing characteristics that were examined included: average word count, number of journal entries, positive and negative emotion words, the ratio of positive to negative words, and the use of cognitive mechanism words (i.e. insight and causal words). Regression analyses revealed that increased levels of anxiety and depression, post‐intervention, were predicted by the prevalence of negative emotion in writing. Unique variance in mood (anxiety and depression) was accounted for by expression of negative emotion (7 and 6%, respectively). These relationships were significant (p<0.05) and remained significant even after accounting for pre‐intervention levels of distress, and for the quantity and frequency of writing. These findings suggest the need for additional research into the naturalistic application of journaling so that appropriate recommendations for writing (e.g. focus, timing, amount) can be offered to patients who might choose to utilize this approach for coping with the stresses of cancer diagnosis and treatment. Copyright © 2005 John Wiley & Sons, Ltd.
Predicting discomfort scores reported by LHD operators using whole-body vibration exposure values and musculoskeletal pain scores.

BACKGROUND Laboratory studies have typically been used to establish a relationship between whole body vibration (WBV) magnitude, frequency, exposure duration and reported discomfort. However, the relationship between subjective reports of discomfort, and predicted comfort response according to International Standards Organization (ISO) 2631-1, predicted health risks according to ISO 2631-1 and reported musculoskeletal discomfort has not been examined. The purpose here was to compare discomfort values predicted by ISO 2631-1 with the subjective discomfort reported by nine Load-haul-dump (LHD) operators during typical operating conditions. METHODS Vibration exposure at the operator/seat interface was measured and processed, for one-hour duration, according to criteria established in ISO 2631-1. Vibration total values were determined for 1-minute exposure periods and the LHD operators provided a discomfort score associated with the same vibration exposure period. A linear regression analysis and correlation was carried out to determine the strength of the relationship between the predicted subjective reports of discomfort, ISO 2631-1 discomfort, objectively measured acceleration levels and reported musculoskeletal discomfort. FINDINGS Reported discomfort was poorly correlated to ISO discomfort scores (r=0.1799). Vibration exposure values and Musculo-Skeletal Disorder (MSD) variables were related to both ISO 2631-1 discomfort and to reported discomfort. The MSD scores produced stronger relationships with reported discomfort scores than did the vibration exposure values.
How the Transition Region Along the Cascadia Megathrust Influences Coseismic Behavior: Insights From 2‐D Dynamic Rupture Simulations

There is a strong need to model potential rupture behaviors for the next Cascadia megathrust earthquake. However, there exists significant uncertainty regarding the extent of downdip rupture and rupture speed. To address this problem, we study how the transition region (i.e., the gap), which separates the locked from slow‐slip regions, influences coseismic rupture propagation using 2‐D dynamic rupture simulations governed by a slip‐weakening friction law. We show that rupture propagation through the gap is strongly controlled by the amount of accumulated tectonic initial shear stress and gap friction level. A large amplitude negative dynamic stress drop is needed to arrest downdip rupture. We also observe downdip supershear rupture when the gradient in effective normal stress from the locked to slow‐slip regions is dramatic. Our results justify kinematic rupture models that extend below the gap and suggests the possibility of high‐frequency energy radiation during the next Cascadia megathrust earthquake.
Mlc1p Is a Light Chain for the Unconventional Myosin Myo2p in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, the unconventional myosin Myo2p is of fundamental importance in polarized growth. We explore the role of the neck region and its associated light chains in regulating Myo2p function. Surprisingly, we find that precise deletion of the six IQ sites in the neck region results in a myosin, Myo2-Δ6IQp, that can support the growth of a yeast strain at 90% the rate of a wild-type isogenic strain. We exploit this mutant in a characterization of the light chains of Myo2p. First, we demonstrate that the localization of calmodulin to sites of polarized growth largely depends on the IQ sites in the neck of Myo2p. Second, we demonstrate that a previously uncharacterized protein, Mlc1p, is a myosin light chain of Myo2p. MLC1 (YGL106w) is an essential gene that exhibits haploinsufficiency. Reduced levels of MYO2 overcome the haploinsufficiency of MLC1. The mutant MYO2-Δ6IQ is able to suppress haploinsufficiency but not deletion of MLC1. We used a modified gel overlay assay to demonstrate a direct interaction between Mlc1p and the neck of Myo2p. Overexpression of MYO2 is toxic, causing a severe decrease in growth rate. When MYO2 is overexpressed, Myo2p is fourfold less stable than in a wild-type strain. High copies of MLC1 completely overcome the growth defects and increase the stability of Myo2p. Our results suggest that Mlc1p is responsible for stabilizing this myosin by binding to the neck region.
Generating a supraglacial melt-lake inventory near Jakobshavn, West Greenland, using a new semi-automated lake-mapping technique

ABSTRACT We analyze Landsat-7 imagery spanning a 13-year period (2000–2012) for the Jakobshavn Ablation Region (JAR) along the west coast of Greenland. In addition, we introduce a new semi-automated technique for the mapping of melt-lakes using FoveaPro image-processing software (plug-in to Adobe Photoshop™), greatly simplifying the process, and resulting in more-precise spatial melt-lake statistics over existing manual methods. We found a total mean melt-lake area of 0.30 ± 0.12 km2 (±1σ), with maximum melt-lake area increasing at an average rate of 0.032 km2 d−1 across the study periods. Additionally, we note a yearly seasonal increase (∼1.8 m d−1) in the overall mean lake elevation (∼200 m per season) as well as an optimal elevation of the largest-area melt-lakes of ∼1320 ± 20 m (±1σ). We also found an increase in the maximum average melt-lake elevation (MAME) of ∼3.8 m a−1 (∼50 m). Based on data recorded at nearby automated weather stations, the mean seasonal temperature increased ∼1.6°C over the 13-year period at an average rate of 0.125°C a−1. Although temperature is a driver for meltwater production, we conclude that mechanisms related to the surface topography are more likely modulating the spatial pattern and characteristics of melt lakes in the ablation zone.
When Prostate Cancer Circulates in the Bloodstream

Management of patients with prostate cancer is currently based on imperfect clinical, biological, radiological and pathological evaluation. Prostate cancer aggressiveness, including metastatic potential, remains difficult to accurately estimate. In an attempt to better adapt therapeutics to an individual (personalized medicine), reliable evaluation of the intrinsic molecular biology of the tumor is warranted, and particularly for all tumor sites (primary tumors and secondary sites) at any time of the disease progression. As a consequence of their natural tendency to grow (passive invasion) or as a consequence of an active blood vessel invasion by metastase-initiating cells, tumors shed various materials into the bloodstream. Major efforts have been recently made to develop powerful and accurate methods able to detect, quantify and/or analyze all these circulating tumor materials: circulating tumors cells, disseminating tumor cells, extracellular vesicles (including exosomes), nucleic acids, etc. The aim of this review is to summarize current knowledge about these circulating tumor materials and their applications in translational research.
Transfusion medicine as of 2014

Transfusion of blood components is one of the most common medical treatments, and in spite of the time that has evolved since we started to transfuse blood routinely in the 1930s, there are issues associated with its use that we are still trying to improve. Issues such as when to transfuse and adverse effects associated with the transfusion are fields where new evidence is being generated that ideally should help us to indicate when and what to transfuse to the patients. The recognition that the evidence generated in randomized control trials was not widely applied to guide the indication of the transfusion of blood components has provoked the development of initiatives that try to reduce its unnecessary usage. Those initiatives, grouped under the name of patient blood management, have represented a significant paradigm change, and a growing number of activities in this field are performed in health-care facilities around the world. This article tries to summarize the latest publications in those fields.
Nitrous oxide emissions in the Shanghai river network: implications for the effects of urban sewage and IPCC methodology

Global nitrogen (N) enrichment has resulted in increased nitrous oxide (N2O) emission that greatly contributes to climate change and stratospheric ozone destruction, but little is known about the N2O emissions from urban river networks receiving anthropogenic N inputs. We examined N2O saturation and emission in the Shanghai city river network, covering 6300 km2, over 27 months. The overall mean saturation and emission from 87 locations was 770% and 1.91 mg N2O‐N m−2 d−1, respectively. Nitrous oxide (N2O) saturation did not exhibit a clear seasonality, but the temporal pattern was co‐regulated by both water temperature and N loadings. Rivers draining through urban and suburban areas receiving more sewage N inputs had higher N2O saturation and emission than those in rural areas. Regression analysis indicated that water ammonium (NH4+) and dissolved oxygen (DO) level had great control on N2O production and were better predictors of N2O emission in urban watershed. About 0.29 Gg N2O‐N yr−1 N2O was emitted from the Shanghai river network annually, which was about 131% of IPCC's prediction using default emission values. Given the rapid progress of global urbanization, more study efforts, particularly on nitrification and its N2O yielding, are needed to better quantify the role of urban rivers in global riverine N2O emission.