bluuebunny/crossref_metadata_2025_split huggingface dataset:
SNHG16 is regulated by the Wnt pathway in colorectal cancer and affects genes involved in lipid metabolism
Authors: Christensen Lise Lotte , True Kirsten , Hamilton Mark P. , Nielsen Morten M. , Damas Nkerorema D. , Damgaard Christian K. , Ongen Halit , Dermitzakis Emmanouil , Bramsen Jesper B. , Pedersen Jakob S. , Lund Anders H. , Vang Søren , Stribolt Katrine , Madsen Mogens R. , Laurberg Søren , McGuire Sean E. , Ørntoft Torben F. , Andersen Claus L. 
Published: June 2016

It is well established that lncRNAs are aberrantly expressed in cancer where they have been shown to act as oncogenes or tumor suppressors. RNA profiling of 314 colorectal adenomas/adenocarcinomas and 292 adjacent normal colon mucosa samples using RNA‐sequencing demonstrated that the snoRNA host gene 16 (SNHG16) is significantly up‐regulated in adenomas and all stages of CRC. SNHG16 expression was positively correlated to the expression of Wnt‐regulated transcription factors, including ASCL2, ETS2, and c‐Myc. In vitro abrogation of Wnt signaling in CRC cells reduced the expression of SNHG16 indicating that SNHG16 is regulated by the Wnt pathway. Silencing of SNHG16 resulted in reduced viability, increased apoptotic cell death and impaired cell migration. The SNHG16 silencing particularly affected expression of genes involved in lipid metabolism. A connection between SNHG16 and genes involved in lipid metabolism was also observed in clinical tumors. Argonaute CrossLinking and ImmunoPrecipitation (AGO‐CLIP) demonstrated that SNHG16 heavily binds AGO and has 27 AGO/miRNA target sites along its length, indicating that SNHG16 may act as a competing endogenous RNA (ceRNA) “sponging” miRNAs off their cognate targets. Most interestingly, half of the miRNA families with high confidence targets on SNHG16 also target the 3′UTR of Stearoyl‐CoA Desaturase (SCD). SCD is involved in lipid metabolism and is down‐regulated upon SNHG16 silencing. In conclusion, up‐regulation of SNHG16 is a frequent event in CRC, likely caused by deregulated Wnt signaling. In vitro analyses demonstrate that SNHG16 may play an oncogenic role in CRC and that it affects genes involved in lipid metabolism, possible through ceRNA related mechanisms.
Geochronology and tectonic settings of Late Jurassic – Early Cretaceous intrusive rocks in the Ulanhot region, central and southern Da Xingan Range
Authors: LIU CHANGFENG , ZHOU ZHIGUANG , TANG YONGJU , WU CHEN , LI HONGYING , ZHU YAN , JIANG TIAN , LIU WENCAN , YE BAOYING 
Published: June 2016

AbstractZircon U–Pb dating and whole-rock geochemical analysis have been performed on Late Jurassic – Early Cretaceous intrusive rocks of the Ulanhot area, NE China, with the aim of constraining the tectonic evolution of the central and southern Da Xingan Range. Zircon U–Pb dating indicates that Late Jurassic – Early Cretaceous magmatic events experienced four stages at:c.155 Ma;c.144 Ma; 135–130 Ma; andc.126 Ma. Thec.155 Ma magmatic event consists of quartz diorite and granite-porphyryp with the geochemical characteristic of high Sr and Sr/Y or high A/CNK (1.38), implying the primary magma was derived from partial melting of a thickened lower crust which induced the closure of the Mongol–Okhotsk Ocean. Thec.144 Ma magmatic event consists of quartz monzodiorite with the geochemical characteristics of alkaline series, and indicates the delamination of a thickened crust. The 135–130 Ma magmatic event consists of syenogranite and granite-porphyry with characteristics of both I-type and A-type granites, which induced both the subduction of the Palaeo-Pacific oceanic plate and the post-orogenic extension of the Mongol–Okhotsk Orogenic Belt. Thec.126 Ma magmatic event consisted of highly fractionated I-type biotite granite and alkaline series gabbro, marking the end of the Mongol–Okhotsk Orogen, and implying that the study area was controlled by the circum-Pacific tectonic system during this stage.
Modular elements of the TPR domain in the Mps1 N terminus differentially target Mps1 to the centrosome and kinetochore
Authors: Marquardt Joseph R. , Perkins Jennifer L. , Beuoy Kyle J. , Fisk Harold A. 
Published: June 2016

SignificanceThe importance of the Mps1 (monopolar spindle 1) protein kinase stems from its regulatory role in many important processes, among which are centrosome duplication and the spindle assembly checkpoint. Both of these processes help prevent mitotic errors that may lead to tumorigenesis, making it of great importance to elucidate how Mps1 is targeted to regulate two such spatially distinct processes. This study presents data that distinguish the separation of those two functions in the cell cycle and potentially help in the understanding of the different mechanisms by which Mps1 might influence tumorigenesis.
“Decoupled” Farm Program Payments are Really Decoupled: The Theory
Authors: Chambers Robert G. , Voica Daniel C. 
Published: June 2016

AbstractLump‐sum transfers to farmers are commonly believed to affect the production choices of farmers in the presence of risk and uncertainty. This paper shows that if farmers have off‐farm investment and employment opportunities, production decisions are decoupled from lump‐sum subsidies in the presence of risk and uncertainty. Our results are reconciled with existing results by showing that previously identified production adjustments are portfolio adjustments.
Additional evidence for fisheries acoustics: small cameras and angling gear provide tilt angle distributions and other relevant data for mackerel surveys
Authors: Fernandes Paul G. , Copland Phillip , Garcia Rafael , Nicosevici Tudor , Scoulding Ben 
Published: June 2016

Abstract
Fisheries acoustics surveys are effective tools in marine resource assessment and marine ecology. Significant advances have occurred in recent years with the application of multiple and broadband frequencies to enable remote species identification. There is, however, still the need to obtain additional evidence for identification, and the estimation of the size and tilt angle distribution of fish, which influences their acoustic target strength. The former two requirements are usually met by obtaining simultaneous net samples: there are limited, if any, recognized successful techniques for the latter. Here, two alternative tools for obtaining evidence for all three requirements are examined: angling gear and small video cameras. These tools were deployed during surveys of Atlantic mackerel (Scomber scombrus). In 2014, angling was actually more efficient than pelagic trawling (the standard technique) and over two survey periods (2012 and 2014) provided length frequency distributions that were not significantly different. A small video camera was deployed into mackerel schools, providing species identification and fish orientation. Image analysis was then applied, producing tilt-angle distributions of free swimming wild mackerel for the first time. Mean tilt angles from three deployments were very variable with 95% of observations falling between −70° and 39° with evidence of a multinomial frequency distribution. A video equipped lander was also deployed onto the type of rocky seabed where deployment of a trawl would be impossible: this confirmed the presence of Norway pout and suggested it was the dominant scatterer on this type of seabed. These techniques are complementary to traditional trawling methods, but provide additional insights into fish behaviour whilst satisfying standard requirements of identification and supplying biological samples. Crucially, the small cameras deployed approximate the size of the animals under observation and allow for measurement of behaviour (specifically tilt) that are more likely to represent those conditions encountered during surveying.
Water, methanol and dense gas tracers in the local ULIRG Arp 220: results from the new SEPIA Band 5 Science Verification campaign
Authors: Galametz M. , Zhang Z.-Y. , Immer K. , Humphreys E. , Aladro R. , De Breuck C. , Ginsburg A. , Madden S. C. , Møller P. , Arumugam V. 
Published: June 2016

Abstract
We present a line survey of the ultraluminous infrared galaxy Arp 220, taken with the newly installed SEPIA (Swedish-European Southern Observatory PI receiver for APEX) Band 5 instrument on APEX (Atacama Pathfinder Experiment). We illustrate the capacity of SEPIA to detect the 183.3 GHz H2O 31,3–22,0 line against the atmospheric H2O absorption feature. We confirm the previous detection of the HCN(2–1) line, and detect new transitions of standard dense gas tracers such as HNC(2–1), HCO+(2–1), CS(4–3), C34S(4–3) and HC3N(20–19). We also detect HCN(2–1) v2 = 1 and the 193.5 GHz methanol (4–3) group for the first time. The absence of time variations in the megamaser water line compared to previous observations seems to rule out an AGN nuclear origin for the line. It could, on the contrary, favour a thermal origin instead, but also possibly be a sign that the megamaser emission is associated with star-forming cores washed out in the beam. We finally discuss how the new transitions of HCN, HNC and HCO+ refine our knowledge of the interstellar medium physical conditions in Arp 220.
Defining a Patient Population With Cirrhosis
Authors: Chang Edward K. , Yu Christine Y. , Clarke Robin , Hackbarth Andrew , Sanders Timothy , Esrailian Eric , Hommes Daniel W. , Runyon Bruce A. 
Published: June 2016

Objectives:
The objective of this study was to use natural language processing (NLP) as a supplement to International Classification of Diseases, Ninth Revision (ICD-9) and laboratory values in an automated algorithm to better define and risk-stratify patients with cirrhosis.

Background:
Identification of patients with cirrhosis by manual data collection is time-intensive and laborious, whereas using ICD-9 codes can be inaccurate. NLP, a novel computerized approach to analyzing electronic free text, has been used to automatically identify patient cohorts with gastrointestinal pathologies such as inflammatory bowel disease. This methodology has not yet been used in cirrhosis.

Study Design:
This retrospective cohort study was conducted at the University of California, Los Angeles Health, an academic medical center. A total of 5343 University of California, Los Angeles primary care patients with ICD-9 codes for chronic liver disease were identified during March 2013 to January 2015. An algorithm incorporating NLP of radiology reports, ICD-9 codes, and laboratory data determined whether these patients had cirrhosis. Of the 5343 patients, 168 patient charts were manually reviewed at random as a gold standard comparison. Positive predictive value (PPV), negative predictive value (NPV), sensitivity, and specificity of the algorithm and each of its steps were calculated.

Results:
The algorithm’s PPV, NPV, sensitivity, and specificity were 91.78%, 96.84%, 95.71%, and 93.88%, respectively. The NLP portion was the most important component of the algorithm with PPV, NPV, sensitivity, and specificity of 98.44%, 93.27%, 90.00%, and 98.98%, respectively.

Conclusions:
NLP is a powerful tool that can be combined with administrative and laboratory data to identify patients with cirrhosis within a population.
Sedation Variability Increases Incidence of Delirium in Adult Medical Intensive Care Unit Patients at a Tertiary Academic Medical Center
Authors: Ritchie Brianne M. , Torbic Heather , DeGrado Jeremy R. , Reardon David P. 
Published: June 2016

Background:
Variability in sedation may increase the incidence of delirium and mortality, as well as increased intensive care unit (ICU) and hospital lengths of stay (LOS), despite mean Richmond Agitation Sedation Scale (RASS) scores at goal. Coefficient of variation (CV) can be used to represent variability with a higher ratio indicating increased variability.

Study Question:
Do patients with an increased variability in sedation, as evaluated by CV in RASS, have an increased incidence of delirium?

Methods:
We conducted a retrospective chart review of adult medical ICU patients requiring mechanical ventilation (MV) for ≥24 hours between January and April 2013. Patients were excluded if intubated at an outside hospital, neuromuscularly blocked, suffering from anoxic brain injury, or had a goal RASS of −4 or −5. Outcomes assessed included the presence of delirium, as evaluated by the Confusion Assessment Method, RASS, CV in RASS, duration of MV, ICU, and hospital LOS, and survival.

Results:
Of 45 included patients, 32 experienced delirium during their ICU admission and 13 did not. The groups were similar at baseline. There was no difference in mean RASS when comparing the delirium and nondelirium groups (−1.6 ± 1.3 vs. −1.8 ± 0.8, respectively; P = 0.61). Patients with delirium had a greater CV in RASS (0.3 ± 0.135 vs. 0.2 ± 0.105; P = 0.02), a longer MV duration [4 (2–8) vs. 3 (2–3) days; P = 0.045], and a trend toward increased ICU LOS [8 (5–12.25) vs. 4 (3–8) days; P = 0.096], but no difference in hospital LOS [13 (10–25) vs. 18 (9–39) days; P = 0.83] and survival (71.9% vs. 69.2%; P = 1.0).

Conclusion:
Medical ICU patients with delirium had a higher CV in RASS compared with patients without delirium, suggesting that greater variability in sedation may increase the incidence of delirium. Patients with delirium also had a greater duration of MV and a trend toward longer ICU LOS.
Oral Anticoagulants With Dual Antiplatelet Therapy Versus Clopidogrel in Patients After Percutaneous Coronary Intervention: A Meta-Analysis
Authors: Palla Mohan , Briasoulis Alexandros , Kondur Ashok 
Published: June 2016

Background:
In patients on oral anticoagulation (OAC), dual antiplatelet therapy (DAPT) is often indicated after percutaneous coronary intervention (PCI).

Areas of Uncertainty:
We sought to investigate the effects of triple antithrombotic therapy (TT) versus dual therapy (DT) with OAC and clopidogrel on all-cause mortality, cardiovascular death, major bleeding, myocardial infarction (MI), stroke, and stent thrombosis.

Data Sources:
We systematically searched on MEDLINE, EMBASE, and CENTRAL for randomized controlled or cohort studies, which investigated the comparative effects of TT versus DT. We performed a meta-analysis of 6 studies (1 randomized control study and 5 cohort studies).

Results:
The included studies enrolled 7259 patients; 4630 (63.8%) were on TT and 2629 (36.2%) were on DT. The average follow-up time was 1.4 years. No significant differences were found between TT and DT in all-cause mortality (P = 0.70; I
2 = 64%), stent thrombosis (P = 0.41), myocardial infarction (P = 0.43; I
2 = 0%), stroke (P = 0.36; I
2 = 0%), and major bleeding (P = 0.43; I
2 = 0%).

Conclusions:
In patients who are on OAC with vitamin K antagonist and underwent percutaneous coronary intervention, no significant differences were found in mortality, ischemic, and hemorrhagic complications between the patients treated with TT and DT. Thus, tailored treatment based on individual thromboembolic and bleeding risk might be the most reasonable approach in these patients.
A Comparison of Diarrheal Severity Scores in the MAL‐ED Multisite Community‐Based Cohort Study
Authors: Lee Gwenyth O. , Richard Stephanie A. , Kang Gagandeep , Houpt Eric R. , Seidman Jessica C. , Pendergast Laura L. , Bhutta Zulfiqar A. , Ahmed Tahmeed , Mduma Estomih R. , Lima Aldo A. , Bessong Pascal , Jennifer Mats Steffi , Hossain Md. Iqbal , Chandyo Ram Krishna , Nyathi Emanuel , Lima Ila F. , Pascal John , Soofi Sajid , Ladaporn Bodhidatta , Guerrant Richard L. , Caulfield Laura E. , Black Robert E. , Kosek Margaret N. ,   MAL‐ED Network Investigators
Published: June 2016

ABSTRACTObjectives:There is a lack of consensus on how to measure diarrheal severity. Within the context of a multisite, prospective cohort study, we evaluated the performance of a modified Vesikari score (MAL‐ED), 2 previously published scores (Clark and CODA [a diarrheal severity score (Community DiarrheA) published by Lee et al]), and a modified definition of moderate‐to‐severe diarrhea (MSD) based on dysentery and health care worker diagnosed dehydration.Methods:Scores were built using maternally reported symptoms or fieldworker‐reported clinical signs obtained during the first 7 days of a diarrheal episode. The association between these and the risk of hospitalization were tested using receiver operating characteristic analysis. Severity scores were also related to illness etiology, and the likelihood of the episode subsequently becoming prolonged or persistent.Results:Of 10,159 episodes from 1681 children, 143 (4.0%) resulted in hospitalization. The area under the curve of each score as a predictor of hospitalization was 0.84 (95% confidence interval: 0.81, 0.87) (Clark), 0.85 (0.82, 0.88) (MAL‐ED), and 0.87 (0.84, 0.89) (CODA). Severity was also associated with etiology and episode duration. Although families were more likely to seek care for severe diarrhea, approximately half of severe cases never reached the health system.Conclusions:Community‐based diarrheal severity scores are predictive of relevant child health outcomes. Because they require no assumptions about health care access or utilization, they are useful in refining estimates of the burden of diarrheal disease, in estimating the effect of disease control interventions, and in triaging children for referral in low‐ and middle‐income countries in which the rates of morbidity and mortality after diarrhea remain high.
Environmental Enteric Dysfunction Is Associated With Poor Linear Growth and Can Be Identified by Host Fecal mRNAs
Authors: Ordiz Maria Isabel , Shaikh Nurmohammad , Trehan Indi , Maleta Ken , Stauber Jennifer , Shulman Robert , Devaraj Sridevi , Tarr Phillip I. , Manary Mark J. 
Published: June 2016

ABSTRACTObjective:Environmental enteric dysfunction (EED) can be assessed by the lactulose:mannitol (L:M) test. Our objective was to determine if selected host fecal transcripts were correlated with EED, and whether transcripts and clinical characteristics could be used to predict EED in rural African children.Methods:Demographic and sanitation characteristics, along with L:M testing and host fecal transcript analyses from 798 asymptomatic Malawian children aged 12 to 61 months were compared with linear growth over the subsequent 3 months. Fecal host mRNA analysis included quantification of expression of 18 transcripts associated with L:M. Permeability was categorized as normal (L:M ⩽ 0.15), moderate (0.15<L:M<0.45) and severe (L:M ≥ 0.45), and random forest predictive models were created.Results:L:M was inversely correlated with linear growth over the subsequent 3 months (r = −0.32, P < 0.001) and severe EED was associated with stunting (P < 0.0001). Age younger than 24 months, weight‐for‐height z score <0, domesticated animals in the child's sleep environment, lack of a pit latrine combined with a potentially contaminated water source, and a recent history of diarrhea were associated with severe EED. A random forest model using CD53, HLA‐DRA, MUC12, and TNF was 84% sensitive for severe EED and 83% sensitive for no EED.Conclusions:Selected host fecal transcripts can be used in a random forest model as a noninvasive biomarker for categories of EED in rural African children.
Mitochondrial Encephalopathy and Optic Neuropathy Due to m.10158 MT-ND3 Complex I Mutation Presenting in an Adult Patient
Authors: Vodopivec Ivana , Cho Tracey A. , Rizzo Joseph F. , Frosch Matthew P. , Sims Katherine B. 
Published: June 2016

Introduction:
Establishing a diagnosis of mitochondrial disease in adults remains a clinician’s challenge. We report a case of syndrome reminiscent of mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) in an adult patient who carries m.10158T>C mutation in complex I respiratory chain gene MT-ND3 (mitochondrially encoded NADH dehydrogenase 3).

Case Report:
This 26-year-old man from Thailand presented with new-onset headaches, seizures, stroke-like episodes, and poor vision due to optic neuropathy and cortical blindness. Instead of expected mutations in the mitochondrial tRNA gene that are frequently associated with MELAS, the mutation in MT-ND3 with variable tissue heteroplasmy (blood 5.3%, muscle 89.5%) was demonstrated. The patient’s clinical features, blood biomarkers, neuroimaging findings, muscle biopsy with histochemical and functional in vitro analysis, and genetic studies were analyzed and compared with all previously reported ND3 disease cases.

Conclusions:
ND3 disease due to m.10158T>C mutation was previously described only in patients with Leigh or Leigh-like syndrome. Our findings thus indicate that ND3 disease can manifest with atypical phenotype in adults. The diagnosis of mitochondrial disease caused by other than typical MELAS-associated mutations in adults with stroke-like episodes, headaches, and seizures should be considered. An analysis of tissue other than blood, which is more likely to harbor a tissue-specific mitochondrial DNA mutation at a measurable level, may be necessary for diagnosis.
Systematic analysis of transcriptional and post-transcriptional regulation of metabolism in yeast
Authors: Gonçalves Emanuel , Raguz Zrinka , Zampieri Mattia , Wagih Omar , Ochoa David , Sauer Uwe , Beltrao Pedro , Saez-Rodriguez Julio 
Published: June 2016

AbstractCells react to extracellular perturbations with complex and intertwined responses. Systematic identification of the regulatory mechanisms that control these responses is still a challenge and requires tailored analyses integrating different types of molecular data. Here we acquired time-resolved metabolomics measurements in yeast under salt and pheromone stimulation and developed a machine learning approach to explore regulatory associations between metabolism and signal transduction. Existing phosphoproteomics measurements under the same conditions and kinase-substrate regulatory interactions were used to estimate the enzymatic activity of signalling kinases. Our approach identified informative associations between kinases and metabolic enzymes capable of predicting metabolic changes. We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism, conveying a total of 143 unique conditions. Our approach accurately estimated the change in activity of transcription factors, kinases and phosphatases and these were capable of building predictive models to infer the metabolic adaptations of previously unseen conditions across different dynamic experiments. Time-resolved experiments were significantly more informative than genetic perturbations to infer metabolic adaptation. This difference may be due to the indirect nature of the associations and of general cellular states that can hinder the identification of causal relationships. This work provides a novel genome-scale integrative analysis to propose putative transcriptional and post-translational regulatory mechanisms of metabolic processes.