bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasminogen Activation In Vivo upon Intravenous Infusion of DDAVP
Authors: Levi Marcel , Boer Jan Paul de , Roem Dorina , Cate Jan Wouter ten , Hack C Erik 
Published: July 2018

SummaryInfusion of desamino-d-arginine vasopressin (DDAVP) results in an increase in plasma plasminogen activator activity. Whether this increase results in the generation of plasmin in vivo has never been established.A novel sensitive radioimmunoassay (RIA) for the measurement of the complex between plasmin and its main inhibitor α2 antiplasmin (PAP complex) was developed using monoclonal antibodies preferentially reacting with complexed and inactivated α2-antiplasmin and monoclonal antibodies against plasmin. The assay was validated in healthy volunteers and in patients with an activated fibrinolytic system.Infusion of DDAVP in a randomized placebo controlled crossover study resulted in all volunteers in a 6.6-fold increase in PAP complex, which was maximal between 15 and 30 min after the start of the infusion. Hereafter, plasma levels of PAP complex decreased with an apparent half-life of disappearance of about 120 min. Infusion of DDAVP did not induce generation of thrombin, as measured by plasma levels of prothrombin fragment F1+2 and thrombin-antithrombin III (TAT) complex.We conclude that the increase in plasminogen activator activity upon the infusion of DDAVP results in the in vivo generation of plasmin, in the absence of coagulation activation. Studying the DDAVP induced increase in PAP complex of patients with thromboembolic disease and a defective plasminogen activator response upon DDAVP may provide more insight into the role of the fibrinolytic system in the pathogenesis of thrombosis.
Type I Congenital Plasminogen Deficiency Is not a Risk Factor for Thrombosis
Authors: Shigekiyo T , Uno Y , Tomonari A , Satoh K , Hondo H , Ueda S , Saito S 
Published: July 2018

SummaryThe risk of thrombosis in type I congenital plasminogen (PLG) deficiency has been suggested, but is still not confirmed. We studied 40 members of two unrelated families with this disease, and found that 21 were heterozygotes of type I congenital PLG deficiency. Three of them had thrombosis, but the other 18 had no thrombosis. The percentages of family members with no history of thrombosis up to a given age among subjects with type I congenital PLG deficiency and healthy controls were analyzed by the Kaplan-Meier method. No significant difference between the two groups was observed by the generalized Wilcoxon test (p = 0.23). These results suggest that there is no significant correlation between type I congenital PLG deficiency and thrombosis.
Extracorporeal Model for Study of Factors Affecting Thrombus Formation
Authors: Benis Anthony M , Nossel Hymie L , Aledort Louis M , Koffsky Robert M , Stevenson James F , Leonard Edward F , Shiang Howard , Litwak Robert S 
Published: July 2018

SummaryFactors determining thrombus formation on a foreign surface were studied with the use of plastic flow chambers introduced into extracorporeal shunts. Silicone rubber shunts, joining the carotid artery and jugular vein, were implanted in dogs and remained patent for several weeks. The flow chamber geometry consisted of a 4.8 mm diameter straight tube having a 3.2 × 3.2 mm circumferential cavity in the wall. Chambers were introduced sequentially into the shunts for exposure times of 10 to 30 minutes and regulated blood flow rates of 100 to 400 ml/min. The dry weight of thrombus accumulated in the chamber (5 to 50 mg) was found to increase with exposure time up to 20 minutes and to decrease with increasing flow rate. Various components of the process of thrombus formation were altered by the administration of acetylsalicylic acid, heparin and lysozyme, used alone and in pairs. Heparin was found to be the most effective antithrombotic agent, dry weights of accumulated thrombus being on the order of 50 percent lower when compared to control values. The efficacy of heparin was found to be unaffected by the presence of aspirin and lysozyme, which themselves were not effective antithrombotic agents under the conditions of these experiments. The technique described here may provide a useful animal model for studying the influence of blood flow and different biomaterials on thrombus formation.
The Effects of Infusion of Thrombin or Endotoxin in Rabbits Treated with Cortisone
Authors: Stafford Benjamin T , Rapaport Samuel I , Shen Stephen M.-C 
Published: July 2018

SummaryRabbits treated for 4 days with cortisone to prepare for the generalized Shwartzman reaction (GSR) were infused with thrombin or endotoxin. Whereas endotoxin induced the GSR, infusion of from 120-400 U/kg of thrombin over 1 to 2½ hr failed to induce the GSR. Mean values for fibrinogen consumption after thrombin or endotoxin, calculated from changes in plasma fibrinogen concentration and plasma 12 5I-fibrinogen radioactivity, were as follows: for rabbits infused with thrombin, from 43 to 61 mg/kg over a 3 hr period; for rabbits infused with endotoxin, 58.5 mg/kg over a 6 hr period. A small peak of non-clottable protein radioactivity, indicative of secondary fibrinolysis, was found in animals infused with thrombin but not in animals infused with endotoxin. A striking late rise in plasma fibrinogen levels was noted in animals infused with endotoxin. It was not noted in animals infused with thrombin. This observation provides further evidence that endotoxin stimulates fibrinogen synthesis by mechanisms independent of intravascular clotting or fibrinolysis. The failure to produce the GSR with thrombin in cortisone-treated rabbits leads us to conclude that depression of reticuloendothelial cell clearance of fibrin can not account for the preparatory effect of cortisone for the GSR after endotoxin.
Collagen-Induced Platelet Aggregation: The Role of Adenine Nucleotides and the Release Reaction
Authors: Kattlove Herman , Gomez M. Hugo 
Published: July 2018

SummaryCollagen-induced platelet aggregation is associated with the release of ADP and the catabolism of radioactive ATP. These studies demonstrate that the amount of human platelet ADP released and ATP catabolized increase with time of stirring of the collagen-platelet rich plasma (PRP) mixture and with increasing amounts of collagen. These changes in adenine nucleotides occurred simultaneously with the aggregation. No early changes preceding aggregation were noted. Stirring the collagen-PRP mixture maximized ADP release and ATP catabolism; some ADP release and ATP catabolism occurred with minimal agitation. Incubation of PRP with metabolic poisons (2-deoxyglucose with either KCN or oligomycin), which lowered platelet ATP content, also reduced collagen-induced release of ADP and aggregation. However, platelet adhesion to collagen was unaffected by metabolic poisons. These data suggest that collagen directly stimulates ADP release. The demonstration of release in EDTA–PRP further suggests that platelet aggregation is not required for collagen-induced ADP release.
Decision-Making Factors for Ulnar Nerve Transposition in Cubital Tunnel Surgery
Authors: DeGeorge Brent , Kakar Sanjeev 
Published: July 2018

Background We designed a survey to ascertain the current perspectives of hand surgeons on the evaluation and management of ulnar nerve instability at the elbow. The secondary aim was to assess the concordance of hand surgeons on definitions of the terms “subluxated” and “dislocated” for classification of ulnar nerve instability.
Methods A questionnaire, including demographic practice variables, cubital tunnel practice patterns, preoperative imaging and electrodiagnostic evaluation, and a series of standardized intraoperative photographs of ulnar nerve instability at the elbow were developed and distributed to the current American Society for Surgery of the Hand (ASSH) membership.
Results A total of 690 (26.8%) members completed the survey; 84.2% of respondents indicated that they evaluate for ulnar nerve instability preoperatively with clinical examination, whereas only 6.1% indicated they routinely obtained dynamic ultrasound. Respondents indicated that the factors most strongly influencing their decision to proceed with anterior transposition of the ulnar nerve were subluxation on physical examination (89.6%), history consistent with ulnar nerve subluxation (85.8%), and muscle atrophy (43.2%). On review of clinical photographs, respondents demonstrated varying degrees of agreement on the terms “subluxated” or “dislocated” and recommendations for ulnar nerve transposition at intermediate degrees of ulnar nerve instability.
Conclusion ASSH members routinely evaluate for ulnar nerve instability with history and clinical examination without uniform use of preoperative ultrasound, and nearly half of the time the decision to transpose the ulnar nerve is made intraoperatively. Definitions for the degree of ulnar nerve instability at the elbow are not uniformly agreed upon, and further development of a classification system may be warranted to standardize treatment.
Chromatin organization by an interplay of loop extrusion and compartmental segregation
Authors: Nuebler Johannes , Fudenberg Geoffrey , Imakaev Maxim , Abdennur Nezar , Mirny Leonid A. 
Published: July 2018

SignificanceHuman DNA is 2 m long and is folded into a 10-μm-sized cellular nucleus. Experiments have revealed two major features of genome organization: Segregation of alternating active and inactive regions into compartments, and formation of compacted local domains. These were hypothesized to be formed by different mechanisms: Compartments can be formed by microphase separation and domains by active, motor-driven, loop extrusion. Here, we integrate these mechanisms into a polymer model and show that their interplay coherently explains diverse experimental data for wild-type and mutant cells. Our results provide a framework for the interpretation of chromosome organization in cellular phenotypes and highlight that chromatin is a complex, active matter shaped by an interplay of phase segregation and loop extrusion.
Zyxin promotes colon cancer tumorigenesis in a mitotic phosphorylation-dependent manner and through CDK8-mediated YAP activation
Authors: Zhou Jiuli , Zeng Yongji , Cui Lian , Chen Xingcheng , Stauffer Seth , Wang Zhan , Yu Fang , Lele Subodh M. , Talmon Geoffrey A. , Black Adrian R. , Chen Yuanhong , Dong Jixin 
Published: July 2018

Significance
Zyxin is a member of the cell–cell adhesion complex and controls cell cytoskeleton and motility. Analysis from clinical samples revealed that Zyxin is highly expressed in colon cancer compared with normal tissue, suggesting an oncogenic role for Zyxin in cancer. Depletion of Zyxin resulted in significantly impaired colon cancer cell proliferation, migration, cellular transformation, and tumor formation in xenograft animal models. We also showed that Zyxin is phosphorylated by CDK1 during mitosis. Mitotic phosphorylation is required for Zyxin activity in promoting colon cancer growth. Zyxin regulates YAP activity through the colon cancer oncogene CDK8. We further showed that CDK8 directly phosphorylates YAP and promotes its activation. These observations identify the Zyxin–CDK8–YAP axis as a potential therapeutic target in cancer.
Folding artificial mucosa with cell-laden hydrogels guided by mechanics models
Authors: Chan Hon Fai , Zhao Ruike , Parada German A. , Meng Hu , Leong Kam W. , Griffith Linda G. , Zhao Xuanhe 
Published: July 2018

Significance
While mucosal folding is a ubiquitous phenomenon observed in many hollow or tubular human tissues/organs, recapitulating the process for tissue engineering has yet to be achieved. Here we fold a cell-laden hydrogel film to recapitulate the folding of a physiologically mimicking artificial mucosa. We attach the cell-laden hydrogel film onto a prestretched tough-hydrogel substrate, which after relaxation induces controlled patterns in the artificial mucosa. A combination of theory and numerical simulations predicts the folding conditions and the morphologies, thereby guiding the design of surface folding. This simple strategy can facilitate the understanding and engineering of mucosa for tissues/organs such as stomach, colon, and intestine. The work also demonstrates a paradigm in tissue engineering via harnessing mechanical instabilities guided by quantitative mechanics models.
Mangrove Mapping Using SPOT 6 at East Lombok Indonesia
Authors: Rudiastuti Aninda W , Yuwono Doddy M , Hartini Sri 
Published: July 2018

Abstract
Accumulated biomass estimation in mangrove forest is important for assessing its productivity and sustainability. It is also important on revealing the potential amount of carbon that can be emitted in the form of carbon dioxide when deforestation took place. Mangrove as a part of the coastal ecosystem is related to Blue Carbon, especially in controlling climate change. This is due to its ability in utilizing carbon dioxide for photosynthesis and store it in stock biomass and sediment. This study addressed to estimate the mangrove extent at East Lombok as a part of One Map Mangrove Bali – Nusa Tenggara, and also trying to estimate its above ground biomass (AGB). Those are indispensable, especially for eastern part of Lombok which has the greatest mangroves area and mostly in good condition such as Gili Lawang and Gili Sulat. Forest biomass can be estimated through combination of field measurement and remote sensing - GIS methods. SPOT 6 and another high resolution-imagery were used as primary remotely sensed data. On screen digitation using RGB-NIR bands and Normalized Difference Vegetation Index (NDVI) image transformation are applied for the initial canopy density classification. For field measurement at 2016, plot sample sized 10 m x 10 m were used for mangrove parameter inventory. Non-destructive biomass estimation applied in this research which is applicable for mangrove ecosystems, using allometric equations. AGB estimation model also applied in mangrove area at two small islands. Bruguiera sp. and Rhizopora sp. dominated in East Lombok. While, Sonneratia sp., and Avicennia sp dominantly appeared in seaward zone of mangrove zonation. The spatial analysis resulted mangrove area in East Lombok is 1759.5778 ha. The estimation results of above ground biomass (trees and saplings) using 12 sample plots in East Lombok is 12,667.316 kg, while there are 881,677 kg of AGB of mangrove in Gili Lawang and Gili Sulat based on the AGBs model applied.
Modeling Deforestation and Green Houses Gas Emissions in Morowali Utara District, Central Sulawesi Province, Indonesia
Authors: Nahib Irmadi , Suwarno Yatin 
Published: July 2018

Abstract
Land use cover conversion from forest to another land was constributing for total green houses gas (GHS) emission, especially from forestry sector. The Central Sulawesi Province has forest area about 4.258 million ha. The deforestation in Central Sulawesi Province for period 2000-2009 reached 432,111.50 Ha (10.15 %). Morowali Utara District is one of district in Central Sulawesi Province, which contribution 15,20 % total deforestation in Central Sulawesi province. This study aims to calculate the rate of deforestation and simulation carbon emission in Morowali Utara District by using REDD+ model. The main data used in this study are land use or cover map (2003, 2009 and 2015), driver variable (distance from : forest edge, roads, streams, and slope) as the explanatory variables of deforestation. The results show that the deforestation on the period 2003-2015 reached 62,017.47 (9,19 %) or the rate of deforestation 5,168.12 ha year−1. Logistic regression model for prediction of deforestation is Y1 = −2.2649 + 0.001126 X1 − 0.000152 X2 − 0.000225 X3 + 0.010704 X4 (ROC = 0,7408), meanwhile the amount of carbon that the REDD project will protect given a departure from the business as usual deforestation scenario up to 18.868 million tCO2e.
Differential coexpression in human tissues and the confounding effect of mean expression levels
Authors: Farahbod Marjan , Pavlidis Paul 
Published: July 2018

Abstract

Motivation
Differential coexpression—the alteration of gene coexpression patterns observed in different biological conditions—has been proposed to be a mechanism for revealing rewiring of transcription regulatory networks. Despite wide use of methods for differential coexpression analysis, the phenomenon has not been well-studied. In particular, in many applications, differential coexpression is confounded with differential expression, that is, changes in average levels of expression across conditions. This confounding, despite affecting the interpretation of the differential coexpression, has rarely been studied.

Results
We constructed high-quality coexpression networks for five human tissues and identified coexpression links (gene pairs) that were specific to each tissue. Between 3 and 32% of coexpression links were tissue-specific (differentially coexpressed) and this specificity is reproducible in an external dataset. However, we show that up to 75% of the observed differential coexpression is substantially explained by average expression levels of the genes. ‘Pure’ differential coexpression independent from differential expression is a minority and is less reproducible in external datasets. We also investigated the functional relevance of pure differential coexpression. Our conclusion is that to a large extent, differential coexpression is more parsimoniously explained by changes in average expression levels and pure links have little impact on network-based functional analysis.

Supplementary information
Supplementary data are available at Bioinformatics online.
The indirect influence of quasars on reionization
Authors: Seiler Jacob , Hutter Anne , Sinha Manodeep , Croton Darren 
Published: July 2018

ABSTRACT
The exact role of quasars during the Epoch of Reionization remains uncertain. With consensus leaning towards quasars producing a negligible amount of ionizing photons, we pose an alternate question: Can quasars indirectly contribute to reionization by allowing ionizing photons from stars to escape more easily? Using the semi-analytic galaxy evolution model to evolve a galaxy population through cosmic time, we construct an idealized scenario in which the escape fraction of stellar ionizing photons (fesc) is boosted following quasar wind events, potentially for several dynamical times. We find that under this scenario, the mean value of fesc as a function of galaxy stellar mass peaks for intermediate mass galaxies. This mass dependence will have consequences for the 21-cm power spectrum, enhancing power at small scales and suppressing it at large scales. This hints that whilst quasars may not directly contribute to the ionizing photon budget, they could influence reionization indirectly by altering the topology of ionized regions.
Characteristics of Adult Cigarette Smokers Who “Relight” and the Effects of Exposure to Tobacco Smoke Constituents
Authors: Allen Sophia I , Wasserman Emily , Veldheer Susan , Yingst Jessica , Hrabovsky Shari , Liao Jason , Krebs Nicolle M , Horn Kimberly , Reinhart Lisa , Modesto Jennifer , Putt Kayla , Evins A Eden , Muscat Joshua E , Richie John P , Foulds Jonathan 
Published: July 2018

AbstractIntroductionAbout half of smokers relight their cigarette, a habit that is a risk factor for chronic bronchitis and possibly lung cancer. Little is known about the characteristics of smokers who relight and their dependence on nicotine. It is unknown whether relighting affects exposure to tobacco smoke constituents. This study examined the characteristics of relighters of usual brand cigarettes and whether relighting affects exposure to selected tobacco smoke constituents.MethodsWe explored relighting status and frequency, using baseline data from 248 adult smokers participating in studies of reduced nicotine cigarettes in relation to demographic and cigarette characteristics, smoking behaviors, nicotine dependence, biomarkers of exposure (exhaled carbon monoxide, blood cotinine), and biomarkers of oxidative stress (ratio of oxidized/reduced glutathione).Results69.4% (n = 172) of subjects reported relighting, and they relit an average of five cigarettes out of 20. Both relighters and non-relighters smoked a mean of 20 cigarettes per day (p = .6). Relighting was significantly associated with higher nicotine dependence, use of longer rod cigarettes, older age, lower income, and unemployment. There were no significant associations between relighting and blood cotinine, exhaled carbon monoxide or measures of oxidized/reduced blood glutathione.ConclusionsThe majority of subjects were relighters, who had higher levels of nicotine dependence than non-relighters. Relighters had similar levels of plasma cotinine and exhaled carbon monoxide to non-relighters.ImplicationsNo study has compared the cigarette characteristics and biomarkers of exposure of adult cigarette smokers who relight with those who do not. Relighting behavior was common in our sample and was associated with low income, not currently working, higher nicotine dependence, cigarette rod length, daily cigarette use years, and a lifetime history of depressed mood.
Management After Percutaneous Cholecystostomy: What Should We do With the Catheter?
Authors: Charrier Thibaut , Kepenekian Vahan , Muller Arnaud , Valette Pierre-Jean , Glehen Olivier , Cotte Eddy , Passot Guillaume 
Published: July 2018

Background:
Percutaneous cholecystostomy (PC) is an alternative to cholecystectomy for acute calculous cholecystitis (ACC) in patients with high mortality risk, but the catheters’ and patients’ management remains unclear. This study aimed to determine outcomes after PC and to define surgical strategy.

Methods:
All patients who underwent PC between 2009 and 2014 for ACC in a single institution were reviewed for outcomes and postdrainage management.

Results:
Forty-one patients underwent PC with a median age of 77 years. Twenty patients (45%) presented American Society of Anesthesiologists (ASA) score 3-4, and all had cholecystitis grade II or III. The 6-month mortality was 17% (7/41 patients). Twelve patients (29%) presented PC-related complications. Catheters were removed, clamped, left open, and dislodged for 17, 9, 5, and 5 patients, respectively. Three patients died after PC, and data were missing for 2 patients. Twenty-five (61%) patients underwent cholecystectomy after PC, and were significantly younger (median age, 70 vs. 83; P<0.010), and presented with higher ASA score (ASA: 3-4, 36% vs. 68%; P=0.041) and more grade III cholecystitis (16% vs. 44%; P=0.050). Among 16 patients who did not undergo cholecystectomy, none presented recurrent gallstone disease (median survival, 7 mo; range, 0 to 55).

Conclusions:
The risk of complications associated with the catheter is high. To prevent morbidity related to PC, we suggest removing the catheter when ACC is controlled.