Miracle-dz/UniFAR-FTUs huggingface dataset:
Cue-Signal-Response Analysis of TNF-Induced Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data

Biological signaling networks process extracellular cues to control important cell decisions such as death-survival, growth-quiescence, and proliferation-differentiation. After receptor activation, intracellular signaling proteins change in abundance, modification state, and enzymatic activity. Many of the proteins in signaling networks have been identified, but it is not known how signaling molecules work together to control cell decisions. To begin to address this issue, we report the use of partial least squares regression as an analytical method to glean signal-response relationships from heterogeneous multivariate signaling data collected from HT-29 human colon carcinoma cells stimulated to undergo programmed cell death. By partial least squares modeling, we relate dynamic and quantitative measurements of 20-30 intracellular signals to cell survival after treatment with tumor necrosis factor alpha (a death factor) and insulin (a survival factor). We find that partial least squares models can distinguish highly informative signals from redundant uninformative signals to generate a reduced model that retains key signaling features and signal-response relationships. In these models, measurements of biochemical characteristics, based on very different techniques (Western blots, kinase assays, etc.), are grouped together as covariates, showing that heterogenous data have been effectively fused. Importantly, informative protein predictors of cell responses are always multivariate, demonstrating the multicomponent nature of the decision process.
Novosphingobium chloroacetimidivorans sp. nov., a chloroacetamide herbicide-degrading bacterium isolated from activated sludge.

Strain BUT-14(T), a Gram-reaction-negative, non-spore-forming, ellipse-shaped bacterium, was isolated from activated sludge of a chloroacetamide-herbicides-manufacturing wastewater treatment facility. The strain was able to degrade more than 90% of butachlor, acetochlor and alachlor (100 mg l(-1)) within 5 days of incubation. The taxonomic position was investigated using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain BUT-14(T) was a member of the genus Novosphingobium and showed the highest sequence similarities to Novosphingobium soli DSM 22821(T) (97.9%), N. naphthalenivorans KACC 15258(T) (97.4%), N. pentaromativorans JCM 12182(T) (97.4%) and N. barchaimii DSM 25411(T) (97.1%) and lower (<97%) sequence similarities to all other species of the genus Novosphingobium. Chemotaxonomic analysis revealed that strain BUT-14(T) possessed Q-10 as the predominant ubiquinone, spermidine as the major polyamine and C(18 : 1)ω7c (46.9%), C(17 : 1)ω6c (17.9%), summed feature 3, C(14 : 0) 2-OH (4.4%), C(15 : 0) 2-OH (3.1%) and C(16 : 0) (5.51%) as the major fatty acids. The polar lipids included lipid, glycolipid, phosphatidylglycerol, phospholipid, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and phospatidyldimethylethanolamine. Strain BUT-14(T) showed low DNA-DNA relatedness with N. soli DSM 22821(T) (41.5±2.9%), N. naphthalenivorans JCM 12182(T) (49.2±4.2%), N. pentaromativorans KACC 12295(T) (53.2±1.9%) and N. barchaimii DSM 25411 (51.2±4.5%). The DNA G+C content was 66±0.3 mol%. The combination of phylogenetic analysis, phenotypic characteristics, chemotaxonomic data and DNA-DNA hybridization supports the suggestion that strain BUT-14(T) represents a novel species of the genus Novosphingobium, for which the name Novosphingobium chloroacetimidivorans sp. nov. is proposed. The type strain is BUT-14(T) ( = CCTCC AB 2013086(T) = KACC 17147(T) = JCM 19923(T)).
The importance of pathogens in sepsis: Staphylococcus aureus story

Abstract Different pathogens cause different outcomes for patients with sepsis. They influence intensive care unit (ICU) mortality, ICU length of stay (ICU LOS) and the need for mechanical ventilation (MV). We undertook a retrospective data-based analysis over a 6-y period. Seventy-eight patients with methicillin-sensitive Staphylococcus aureus (MSSA) and 74 patients with Escherichia coli (EC) sepsis were included in the study. ICU mortality for the MSSA group was 32 (41.0%) vs 26 (35.1%) for the EC group (p = 0.506; OR 1.28, 95% CI 0.67–2.48). There was no significant difference in ICU LOS (MSSA group: median 7.5, interquartile range (IQR) 4–14 days and EC: median 5, IQR 3–13.5 days; p = 0.214). Need for MV in the MSSA group was present in 45 (57.7%) patients vs 43 (58.1%) in the EC group. Univariate analysis did not show that MSSA was independently associated with ICU mortality (p = 0.506). Logistic regression analysis showed that after adjustment for APACHE II, the chance of ICU death doubled in the MSSA group (odds ratio 2.166; 95% confidence interval 1.004–4.858). The odds for ICU admission were 8 times higher in MSSA patients. MSSA sepsis should be considered as an independent factor for ICU mortality after adjustment for APACHE II.
BioCreative-IV virtual issue

BioCreative: Critical Assessment of Information Extraction in Biology is an international community-wide effort for evaluating text mining (TM) and information extraction systems applied to the biological domain (http://www.biocreative.org/). The Challenge Evaluations and the accompanying BioCreative Workshops bring together the TM and biology communities to drive the development of practically relevant TM systems. One of the main goals of this initiative is that the resulting systems facilitate a more efficient literature information access to biologists in general, but also provide tools that can be directly integrated into the biocuration workflow and the knowledge discovery process carried out by databases. Beyond addressing the current barriers faced by TM technologies applied to biological literature, BioCreative has further been conducting user requirement analyses, user-based evaluations and fostering standards development for TM tool reuse and integration. This DATABASE virtual issue captures the major results from the Fourth BioCreative Challenge Evaluation Workshop, and is the sixth special issue devoted to BioCreative. Built on the success of the previous Challenge Evaluations and Workshops (BioCreative I, II, II.5, III, 2012) (1–5), the BioCreative IV Workshop was held in Bethesda, MD, on October 7–9, 2013.
Partnering Patterns and Sexual Behavior Among Korean Men Who Have Sex With Men

This qualitative study investigates the different methods for selecting sex partners by Korean homosexuals considering factors related to homosexual identity and sexual behavior. We take the approach of the grounded theory to examine the issue of sexual partnering of men who have sex with men (MSM). In-depth interviews of urban MSM and bisexual men were conducted. The snowball sampled through a MSM portal web site. Three key informants from the several areas were collected through a MSM portal website, and then, participants were gradually recruited with the snowball samplings in South Korea, 2011 (n=32). The results of coding the interviews based on the grounded theory approach identified three types of partnering: 1) MSM who do not prefer anal intercourse, but pursue safe sex in long-term relationships with fixed partners; 2) those who have fixed partners and perform anal sex, a category into which both MSM and bisexuals fall; and 3) those engaged in anal sex, but enjoy a concurrent sexual relationship without having fixed partners, which was common among bisexuals. The findings from this study elucidate several MSM and bisexual partnering types practice safe sex. This diversity in MSM partnering may increase the vulnerability of some MSM to HIV infection as safe-sex practices remain a matter of individual choice. Changes in Korean societal policies are necessary to enhance capacity building and encourage the practice of safe sex at the community level.
A comparative study between TruviewPCD laryngoscope and Macintosh laryngoscope in viewing glottic opening and ease of intubation: A crossover study

Background: TruviewPCD laryngoscope is specially designed to aid positioning of the endotracheal tube as well as to record entry of the tube into glottis. Aim of the study is to compare the view of glottic opening and ease of intubation between TruviewPCD laryngoscope and Macintosh laryngoscope in patients undergoing general anesthesia (GA). Methodology: Two hundred patients undergoing elective surgery, under GA were randomized into two groups, Group TV and Group ML. In Group TV, TrueviewPCD laryngoscope was used initially to visualize the vocal cords for Cormack and Lehane grading (CLG) and to spray the vocal cords with 10% lignocaine. Then the patient was ventilated for 1 min and Macintosh laryngoscope was used to visualize the vocal cords for CLG and proceed with intubation. In Group ML, Macintosh laryngoscope was used initially and later TruviewPCD laryngoscope. Time to intubation, CLG, number of attempts and hemodynamic parameters were recorded. Results: Ninety-six and 89 patients had CLG1 visualization when TruviewPCD laryngoscope was used as 1st and 2nd device respectively compared to 41 and 68 with Macintosh laryngoscope (P = 0.00). Four patients had CLG 4 visualization with Macintosh laryngoscope that turned out to be grade II visualization with TruviewPCD laryngoscope (P = 0.00). Mean time taken for intubation with TruviewPCD and Macintosh laryngoscope was 21.10 ± 5.64 s and 15.79 ± 2.76 s respectively (P = 0.00). Conclusion: Better visualization with lesser CLG was found with TruviewPCD laryngoscope but it took longer time for intubation than Macintosh laryngoscope. The hemodynamic response to intubation was significantly less with the use of TruviewPCD laryngoscope when compared to that of Macintosh laryngoscope.
Generation and Calibration of High-Resolution DEM From Single-Baseline Spaceborne Interferometry: The “Split-Swath” Approach

This paper focuses on the generation of very high resolution digital elevation models (DEMs) mainly from single-baseline spaceborne synthetic aperture radar (SAR) systems. The stringent requirements on vertical accuracy demand for frequent and accurate measures of the baselines, subject to mechanical vibrations of the boom that may be severe when long booms are exploited. This paper proposes a solution that exploits an existent coarse-resolution DEM, for example, the Shuttle Radar Topography Mission, as a set of ground control points (GCPs). A computational model and an inversion scheme are introduced to jointly take into account the information coming from the grid of GCP and the local shifts measured during image coregistration. The model properly takes account for the quality of the GCP, its location with respect to the target of interest, and the interferogram noise in correspondence to the GCP. A novel “split-swath” approach is proposed to enhance the quality of the baseline estimates. The mode exploits two narrow strips with significant diversity in incidence angle, achieved, for example, by ScanSAR or TOPSAR mode. An example of design is provided by assuming a Ka-band topographic spaceborne SAR mission.
In vitro and in vivo Biocompatibility of Alginate Dialdehyde/Gelatin Hydrogels with and without Nanoscaled Bioactive Glass for Bone Tissue Engineering Applications

In addition to good mechanical properties needed for three-dimensional tissue engineering, the combination of alginate dialdehyde, gelatin and nano-scaled bioactive glass (45S5) is supposed to combine excellent cellular adhesion, proliferation and differentiation properties, good biocompatibility and predictable degradation rates. The goal of this study was to evaluate thein vitro and in vivo biocompatibility as a first step on the way to its use as a scaffold in bone tissue engineering. In vitro evaluation showed good cell adherence and proliferation of bone marrow derived mesenchymal stem cells seeded on covalently crosslinked alginate dialdehyde-gelatin (ADA-GEL) hydrogel films with and without 0.1% nano-Bioglass®(nBG). Lactate dehydrogenase (LDH)- and mitochondrial activity significantly increased in both ADA-GEL and ADA-GEL-nBG groups compared to alginate. However, addition of 0.1% nBG seemed to have slight cytotoxic effect compared to ADA-GEL. In vivo implantation did not produce a significant inflammatory reaction, and ongoing degradation could be seen after four weeks. Ongoing vascularization was detected after four weeks. The good biocompatibility encourages future studies using ADA-GEL and nBG for bone tissue engineering application.
Channelized Epishelf Lake Drainage Beneath the Milne Ice Shelf, Ellesmere Island, Nunavut

A depression running across the outer Milne Ice Shelf was hypothesized to overlie a basal channel incised by outflow from the Milne Fiord epishelf lake, a thick layer of freshwater impounded in the fiord by the ice shelf. Ice thickness mapping using ice-penetrating radar revealed the presence of a channel with incision heights of 39 to 45 m (70-80% of mean ice shelf thickness), basal widths of 57-86 m, and mean sidewall slopes of ~40° upward from horizontal. Profiles of salinity, temperature and current speed with depth showed there was a fast flowing jet of epishelf lake water in the channel, with velocities up to 60 cm s-1, confirming the channel is a drainage outlet for the epishelf lake. The presence of the channel represents a significant structural weakness along which future breakup of the ice shelf is likely to occur.
Increased Hepatic and Circulating Interleukin-6 Levels in Human Nonalcoholic Steatohepatitis

BACKGROUND:Nonalcoholic fatty liver disease (NAFLD) and type 2 diabetes (T2D) are growing public health problems, and are strongly associated. The link between the two conditions remains poorly understood. Hepatic interleukin-6 (IL-6), a major proinflammatory cytokine, expression is increased in animal models of NAFLD, while in mice, selective sustained upregulation of IL-6 in the liver results in systemic insulin resistance. The extent and clinical significance of hepatic IL-6 expression in human NAFLD, as well as potential mechanisms by which steatosis may increase IL-6 production in the liver, have not been examined.AIMS:To ascertain the occurrence and significance of IL-6 expression in the liver in human NAFLD.PATIENTS AND METHODS: Plasma was obtained at time of liver biopsy from 50 consecutive patients with suspected NAFLD. Histology was assessed blindly. Hepatic IL-6 expression was assessed by immunohistochemistry, while plasma IL-6 levels were determined by an enzyme-linked immunosorbent assay.RESULTS:IL-6 expression was markedly increased in the livers of patients with nonalcoholic steatohepatitis (NASH) as compared to patients with simple steatosis (P < 0.005) or normal biopsies (P < 0.010), confirming the presence of hepatic IL-6 expression in human NASH. A positive correlation was observed between hepatocyte IL-6 expression and degree of inflammation and stage of fibrosis. Furthermore, liver IL-6 expression positively correlated with plasma IL-6 levels and degree of systemic insulin resistance. Culture of liver cells with saturated, but not mono- or polyunsaturated, FFA resulted in a significant increase in IL-6 messenger RNA (mRNA) and protein expression.CONCLUSION:Collectively, these data suggest that increased hepatic IL-6 production may play an important role in NASH development, as well as in systemic insulin resistance and diabetes.
Does age really matter? Recall of information presented to newly referred patients with cancer.

PURPOSE To examine age- and age-related differences in recall of information provided during oncology consultations. PATIENTS AND METHODS Two hundred sixty patients with cancer diagnosed with heterogeneous cancers, seeing a medical or radiation oncologist for the first time, participated in the study. Patients completed questionnaires assessing information needs and anxiety. Recall of information provided was measured using a structured telephone interview in which patients were prompted to remember details physicians gave about diagnosis, prognosis, and treatment. Recall was checked against the actual communication in audio-recordings of the consultations. RESULTS Recall decreased significantly with age, but only when total amount of information presented was taken into account. This indicates that if more information is discussed, older patients have more trouble remembering the information than younger ones. In addition, recall was selectively influenced by prognosis. First, patients with a poorer prognosis recalled less. Next, the more information was provided about prognosis, the less information patients recalled, regardless of their actual prognosis. CONCLUSION Recall is not simply a function of patient age. Age only predicts recall when controlling for amount of information presented. Both prognosis and information about prognosis are better predictors of recall than age. These results provide important insights into intervention strategies to improve information recall in patients with cancer.
Comparison of coronary-artery bypass surgery and stenting for the treatment of multivessel disease.

BACKGROUND The recent recognition that coronary-artery stenting has improved the short- and long-term outcomes of patients treated with angioplasty has made it necessary to reevaluate the relative benefits of bypass surgery and percutaneous interventions in patients with multivessel disease. METHODS A total of 1205 patients were randomly assigned to undergo stent implantation or bypass surgery when a cardiac surgeon and an interventional cardiologist agreed that the same extent of revascularization could be achieved by either technique. The primary clinical end point was freedom from major adverse cardiac and cerebrovascular events at one year. The costs of hospital resources used were also determined. RESULTS At one year, there was no significant difference between the two groups in terms of the rates of death, stroke, or myocardial infarction. Among patients who survived without a stroke or a myocardial infarction, 16.8 percent of those in the stenting group underwent a second revascularization, as compared with 3.5 percent of those in the surgery group. The rate of event-free survival at one year was 73.8 percent among the patients who received stents and 87.8 percent among those who underwent bypass surgery (P<0.001 by the log-rank test). The costs for the initial procedure were $4,212 less for patients assigned to stenting than for those assigned to bypass surgery, but this difference was reduced during follow-up because of the increased need for repeated revascularization; after one year, the net difference in favor of stenting was estimated to be $2,973 per patient. CONCLUSION As measured one year after the procedure, coronary stenting for multivessel disease is less expensive than bypass surgery and offers the same degree of protection against death, stroke, and myocardial infarction. However, stenting is associated with a greater need for repeated revascularization.
ADP Receptor P2Y12 Is Expressed in Vascular Smooth Muscle Cells and Stimulates Contraction in Human Blood Vessels

Objective—ADP plays an important role in platelet aggregation by activating P2Y12 receptors. We assessed the hypothesis that P2Y12 receptors are expressed in vascular smooth muscle cells (VSMC). Methods and Results—P2Y12 receptor mRNA was found to have a high expression among the P2 receptors in human VSMC, significantly higher than the other 2 ADP receptors (P2Y1 and P2Y13, real-time polymerase chain reaction). Western blots gave a band of 50 kD, similar to that in platelets. To unmask a P2Y12 receptor-mediated vasoconstriction by simulating the in vivo situation, vessels were precontracted to a submaximal level. 2-MeSADP stimulated contractions in vessel segments from internal mammary artery (IM), IM branches and small veins (Emax=15±6% of 60mmol/L K+ contraction, pEC50=5.6±0.6, Emax=21±1%, pEC50=6.8±0.1, and Emax=48±9%, pEC50=6.6±0.4). The selective P2Y12 antagonist AR-C67085 blocked 2-MeSADP contractions. The contraction was not reduced in patients using clopidogrel, a drug inhibiting ADP-induced platelet aggregation by blocking the P2Y12 receptor. This may be explained by the high instability of the active clopidogrel metabolite that never reaches the systemic circulation. Conclusion—ADP acting on P2Y12 receptors not only is important for platelet activation but also stimulates vasoconstriction. Stable drugs with antagonistic effects on P2Y12 receptors, affecting both platelets and VSMC, could be of double therapeutic benefit in their prevention of both thrombosis and vasospasm.
The role of microRNAs in bladder cancer

Bladder cancer (BC) is the fifth most common cancer worldwide and is associated with significant morbidity and mortality. The prognosis of muscle invasive BC is poor, and recurrence is common after radical surgery or chemotherapy. Therefore, new diagnostic methods and treatment modalities are critical. MicroRNAs (miRNAs), a class of small noncoding RNAs, regulate the expression of protein-coding genes by repressing translation or cleaving RNA transcripts in a sequence-specific manner. miRNAs have important roles in the regulation of genes involved in cancer development, progression, and metastasis. The availability of genomewide miRNA expression profiles by deep sequencing technology has facilitated rapid and precise identification of aberrant miRNA expression in BC. Indeed, several miRNAs that are either upregulated or downregulated have been shown to have associations with significant cancer pathways. Furthermore, many miRNAs, including those that can be detected in urine and blood, have been studied as potential noninvasive tumor markers for diagnostic and prognostic purposes. Here, we searched PubMed for publications describing the role of miRNAs in BC by using the keywords "bladder cancer" and "microRNA" on March 1, 2016. We found 374 papers and selected articles written in English in which the level of scientific detail and reporting were sufficient and in which novel findings were demonstrated. In this review, we summarize these studies from the point of view of miRNA-related molecular networks (specific miRNAs and their targets) and miRNAs as tumor markers in BC. We also discuss future directions of miRNA studies in the context of therapeutic modalities.