bluuebunny/crossref_metadata_2025_split huggingface dataset:
Depression of Collateral Blood Flow Following Arterial Thrombosis
Authors: Schaub Robert G. , Sande Ronald , Meyers Kenneth M. 
Published: July 2018

SummaryPermanent ligation of the feline aorta at the iliac bifurcation is followed by rapid opening of pre-existing collateral blood vessels. However, if ligation is combined with formation of a clot, these protective collateral vessels do not function. This study was undertaken to determine if drugs which alter serotonin function can improve collateral blood flow after arterial thrombosis. Permanent ligations were placed at the iliac bifurcation, circumflex iliac and sixth lumbar arteries in all cats. A clot was produced in the aorta of 27 cats by injection of 0.1 ml of thromboplastin. Ligated clot-occluded cats were untreated (10); had blood serotonin depleted using a single dose of reserpine (0.1 mg/kg i. m.) followed by para-chlorophenylanine (p-CPA) (100 mg/kg orally) every 3 days (9) ; or were treated prior to surgery with a serotonin antagonist cinanserin HC1 (4 mg/kg i. v.) (8). Control cats (18) were acutely ligated. 9 of these cats were untreated, 5 were cinanserin HC1-treated, and 4 were reserpine/p-CPA-treated. Extent of collateral development was assessed by aortograms 3 days after occlusion and by neurologic rating. Aortograms of acutely ligated cats indicated a significant collateral blood flow around the segment of ligated aorta, while ligated clot-occluded cats had a severely depressed hind-limb perfusion. Reserpine/p-CPA-treated ligation clot-occluded cats had aortograms similar to acutely ligated cats. The cinanserin HC1-treated ligation clot-occluded cats had aortograms which indicated hind-limb perfusion was not as adequate as the acutely ligated cats. However, the perfusion of these animals was improved over untreated ligation clot-occluded cats. Neurologic rating correlated with aortograms. These results suggest: 1) the clinical consequences of arterial thrombosis cannot be entirely attributed to mechanical occlusion of an artery, but may be due to depression of protective collateral blood flow induced by thrombosis, 2) serotonin is an important factor in this depression of collateral blood flow, and 3) isolation of the factors responsible for collateral inhibition could permit the development of therapeutic interventions.
Disseminated intravascular Coagulation in Status Epilepticus
Authors: Fischer Sharon P. , Lee Joseph , Zatuchni Jacob , Greenberg Jack 
Published: July 2018

SummaryDisseminated intravascular coagulation is here reported as a complication of status epilepticus. Other features of this case were rhabdomyolysis, hyperthermia, myoglobinuria and renal failure.
Adenylate Cyclase and Phosphodiesterase Activity in the Platelet Release Abnormality
Authors: Chesney Carolyn Mci. , Baker Ann S. , Carvalho Angelina Ca. , Ozer Asli , Meissner George F. , Colman Robert W. 
Published: July 2018

Summary11 patients with histories of clinical bleeding were selected as examples of platelet release abnormality. Mean bleeding time was 18 ± 2.6 min (normal ±SEM; 6 ±0.44); mean platelet adhesiveness was 9.9 ± 4.3% (normal ±SEM; 30 ±2.2). Clot retraction and platelet factor 3 were normal. Platelet aggregation with adenosine diphosphate (ADP), epinephrine and collagen was decreased, as was 14C-serotonin release. Electron microscopic studies of platelets exposed to epinephrine showed 2 subgroups: one which failed to aggregate or have centralization of organelles and a second which developed pseudopodia and centralization of organelles, but rarely aggregated or degranulated.Measurements of activity of adenylate cyclase and phosphodiesterase under basal conditions were performed on platelets from patients and control subjects. Adenylate cyclase activity was significantly lower and phosphodiesterase activity significantly higher in the patient group. Prostaglandin E1 was a potent stimulator of adenylate cyclase in both groups, as was NaF. It was concluded that the causative defects in patients with “platelet release abnormality” do not reside in either the activity of adenylate cyclase or of phosphodiesterase. Changes in formation and destruction of cyclic adenosinemonophosphate (AMP) may instead be regarded as a compensatory response to a defect in another effector system.
Molecular Cloning and Cell-Free Expression of Mouse Antithrombin III
Authors: Wu John K , Sheffield William P , Blajchman Morris A 
Published: July 2018

SummaryThe homology between antithrombin III (AT-III) of mouse, of man, and that of other species was investigated. Preliminary experiments showed that mouse AT-III inhibited human α-thrombin efficiently (second order rate constant [K
2nd] 5.8 × 103 M–1 s–1) as compared to human AT-III (K
2nd 6.7 × 103 M–1), but was not recognized on immunoblots by antibodies that recognized both human and rabbit AT-III. In order to compare AT-III from different species at the molecular level, a cDNA clone for murine AT-III was isolated from a λZAP mouse liver cDNA library on the basis of hybridization to a rabbit AT-III cDNA probe. The 1509 bp murine AT-III cDNA consists of a 1398 bp open reading frame, preceded by a 15 bp 5’ untranslated region, followed by a 75 bp 3’ untranslated region. The deduced primary protein structure consists of a 32 amino acid signal sequence, with a mature portion of 433 residues. Mature murine AT-III is 89% identical to its human counterpart, 86% identical to bovine AT-III, and 82% identical to that of the rabbit. Constructs lacking the nucleotides encoding the signal sequence were engineered and expressed in a cell-free system. The resulting 47 kDa non-glycosylated translation product was capable of being cleaved by human α-thrombin, of forming SDS-stable complexes with the protease, and of binding to immobilized heparin. Isolation of the murine AT-III cDNA will make feasible molecularly defined experiments with murine AT-III in the mouse system.
Effect of DDAVP on Endotoxin-Induced Intravascular Coagulation in Rabbits
Authors: Paloma M J , Páramo J A , Rocha E 
Published: July 2018

SummaryWe have evaluated the effect of l-Deamino-8D-arginine vasopressin (DDAVP) on an experimental model of intravascular coagulation (DIC) induced in rabbits by injection of 20 µg kg–1 h–1 during 6 h of E. coli lipopolysaccharide. DDAVP significantly ameliorated the platelet drop and fibrinogen decrease (p <0.01) induced by endotoxin in control animals. A significant reduction in factor XII consumption (p <0.01) and a decrease in the generation of endotoxin induced PAI-1 activity in rabbits circulation was also observed (p <0.005). Moreover, fibrin deposition in kidneys of rabbits receiving DDAVP was significantly reduced as compared to control animals. Finally, the mortality rate in the control group was significantly higher than in DDAVP-treated rabbits (p <0.01). The hemostatic changes induced by DDAVP correlated with lower fibrin deposition and reduction in mortality rates.
Platelet Factor XIII Increases the Fibrinolytic Resistance of Platelet-Rich Clots by Accelerating the Crosslinking of α2-Antiplasmin to Fibrin
Authors: Reed Guy L , Matsueda Gary R , Haber Edgar 
Published: July 2018

SummaryPlatelet clots resist fibrinolysis by plasminogen activators. We hypothesized that platelet factor XIII may enhance the fibrinolytic resistance of platelet-rich clots by catalyzing the crosslinking of α2-antiplasmin (α2AP) to fibrin. Analysis of plasma clot structure by polyacrylamide gel electrophoresis and immunoblotting revealed accelerated α2AP-fibrin crosslinking in platelet-rich compared with platelet-depleted plasma clots. A similar study of clots formed with purified fibrinogen (depleted of factor XIII activity), isolated platelets, and specific factor XIII inhibitors indicated that this accelerated crosslinking was due to the catalytic activity of platelet factor XIII. Moreover, when washed platelets were aggregated by thrombin, there was evidence of platelet factor XIII-mediated crosslinking between platelet α2AP and platelet fibrin(ogen). Specific inhibition (by a monoclonal antibody) of the α2AP associated with washed platelet aggregates accelerated the fibrinolysis of the platelet aggregate. Thus in platelet-rich plasma clots, and in thrombin-induced platelet aggregates, platelet factor XIII actively formed α2AP-fibrin crosslinks, which appeared to enhance the resistance of platelet-rich clots to fibrinolysis.
Thrombolytic Activity of Two Chimeric Recombinant Plasminogen Activators (FK2tu-PA and K2tu-PA) in Rabbits
Authors: Agnelli Giancarlo , Pascucci Claudia , Colucci Mario , Nenci Giuseppe G , Mele Antonio , Bürgi Rolf , Heim Jutta 
Published: July 2018

SummaryThe aim of this study was to evaluate the thrombolytic activity of two hybrid plasminogen activators (HPAs) in a rabbit jugular vein thrombosis model. In the two HPAs the kringle-2 domain (K2tu-PA) or the finger and the kringle-2 domains (FK2tu-PA) of tissue-type plasminogen activator (t-PA) are linked to the catalytic protease domain of single chain urokinase type plasminogen activator (scu-PA). The two HPAs were compared with rt-PA and scu-PA on a weight/weight basis. K2tu-PA, FK2tu-PA, rt-PA and scu-PA were infused at doses of 0.4, 0.8 and 1.2 mg/kg over 3 h. Saline served as control. Saline produced 11 ± 2% thrombolysis. The three doses of K2tu-PA led to 38 ± 4%, 66 ± 5% and 89 ± 7% thrombolysis, respectively; the three doses of FK2tu-PA: 18 ± 3%, 29 ± 5% and 33 ± 6%, respectively; the three doses of rt-PA 32 ± 2%, 49 ± 3% and 68 ± 6%, respectively; the three doses of scu-PA 16 ± 2%, 24 ± 3% and 32 ± 4%, respectively. K2tu-PA and rt-PA showed a statistically significant higher thrombolytic activity than FK2tu-PA and scu-PA at the three tested doses (p <0.01). The thrombolytic activity of K2tu-PA was significantly higher than rt-PA at the two higher doses (p <0.01). Both K2tu-PA and rt-PA produced a statistically significant reduction of fibrinogen, α2-antiplasmin and plasminogen 3 h after the start of the infusions of the two higher doses. No statistically significant differences between K2tu-Pa and rt-PA were observed. Concomitant with the lower thrombolytic activity, the systemic proteolytic effects of FK2tu-PA and scu-PA were less pronounced. We conclude that the two HPAs we tested are effective thrombolytic agents. K2tu-PA deserves particular attention in future experiments.
Pharmakodynamik von chemisch modifizierten niedermolekularen Heparinen
Authors: Malsch R. , Harenberg J. , Heene D. L. , Piazolo L. 
Published: July 2018

ZusammenfassungEine Verbesserung der pharmakologischen Eigenschaften von Heparinoiden und Heparinen kann durch gezielte chemische Modifikation erreicht werden. Ziel der vorliegenden Arbeit war es, durch die Kopplung von lipophilen Substanzen an niedermolekulares Heparin die intravenöse Pharmakodynamik zu verbessern. Die pharmakodynamischen Daten dieser Heparine wurden in vitro und ex vivo bestimmt. Cholesterinhemisuccinyl-LMM-Heparin hat eine In-vitro-Anti-Throm-binaktivität von 70 E/mg und eine Anti-Faktor-Xa-Aktivität von 140 E/mg. L-Ascor-binsäure-6-Palmitat-LMM-Heparin hat eine In-vitro-Anti-Thrombinaktivität von 34 E/mg und eine Anti-Faktor-Xa-Aktivität von 72 E/mg. Die modifizierten Heparine wurden mit der Pharmakodynamik von Fragmin® verglichen. Durch die Kopplung von Heparin an lipophile Substanzen wie Cholesterin und L-Ascorbinsäure-6-Palmitat wurden sowohl die Anti-Thrombin- als auch die Anti-Faktor-Xa-Halbwertszeiten signifikant verlängert, die totale Plasmaclearance war für die Anti-Faktor-Xa-Aktivität erniedrigt.
Major Changes of von Willebrand Factor Multimer Distribution in Cirrhotic Patients with Stable Disease or Acute Decompensation
Authors: Palyu Eszter , Harsfalvi Jolan , Tornai Tamas , Papp Maria , Udvardy Miklos , Szekeres-Csiki Katalin , Pataki Lajos , Vanhoorelbeke Karen , Feys Hendrik , Deckmyn Hans , Tornai Istvan 
Published: July 2018

Background There is an unstable balance between pro- and anti-haemostatic processes in patients with cirrhosis. We hypothesized, that in patients with acute decompensation (AD) the major alterations of von Willebrand factor (VWF) could contribute to the pro-thrombotic situation as compared to patients with stable (ST) cirrhosis.
Patients and Methods We analysed different parameters of VWF, including detailed multimer distribution by densitometry and platelet adhesion, together with a disintegrin-like and metalloproteinase with thrombospondin type-1 motifs 13 (ADAMTS13) activity and antigen and C-reactive protein (CRP) levels in patients with ST cirrhosis (n = 99), with AD (n = 54) and controls (n = 92).
Results VWF antigen, ristocetin co-factor as well as collagen-binding activities were elevated in both cirrhotic groups in a stepwise manner. There was a decrease in high and an increase in low molecular weight multimer ratios in the majority of ST cirrhosis. However, in 24 out of 54 AD patients, ultra-large VWF multimers (ultra-large molecular weight multimers [ULMWM]) were found. ADAMTS13 activity in ST and AD patients without ULMWM was similar to controls (median [interquartile range; IQR]%: 98 [67–132] and 91 [60–110] vs. 106 [88–117], respectively). The presence of ULMWM in AD patients was associated with low ADAMTS13 activity [33 (24–49)%] and high CRP level [23 (7.1–83.6) mg/L]. Adhesion of normal platelets showed a stepwise increase in the presence of cirrhotic plasmas, reaching the highest level in AD patients with ULMWM.
Conclusion Characteristic changes of VWF parameters are seen in ST cirrhosis. In AD patients, highly increased VWF and reduced ADAMTS13 activity could be found, along with the presence of ULMWM, which are possible markers and contributors of the disease progression.
Chemotherapie-induzierte periphere Neuropathie
Authors: Gießen-Jung Clemens , von Baumgarten Louisa 
Published: July 2018

AbstractChemotherapy-induced peripheral neuropathy (CIPN) is a severe and common side effect induced by a variety of anticancer drugs. CIPN presents as a sensory, motor, and sometimes autonomic dysfunction with a large variability, from a mild tingling sensation and hyperesthesia, to severe neuropathic pain. Up to 40 % of patients will develop CIPN which may lead to dose-reduction or discontinuation of their current treatment and largely affects their quality of life (QoL). This review presents specific clinical features and pathomechanisms and discusses current preventive strategies and therapeutic options.
Knowledge management for policy impact: the case of the European Commission’s Joint Research Centre
Authors: Topp Lene , Mair David , Smillie Laura , Cairney Paul 
Published: July 2018

AbstractThe European Commission’s Joint Research Centre (JRC) employs over 2000 scientists and seeks to maximise the value and impact of research in the EU policy process. To that end, its Knowledge management for policy (KMP) initiative synthesised the insights of a large amount of interdisciplinary work on the ‘evidence-policy interface’ to promote a new skills and training agenda. It developed this training initially for Commission staff, but many of its insights are relevant to organisations which try to combine research, policymaking, management, and communication skills to improve the value and use of research in policy. We recommend that such organisations should develop teams of researchers, policymakers, and ‘knowledge brokers’ to produce eight key practices: (1) research synthesis, to generate ‘state of the art’ knowledge on a policy problem; (2) management of expert communities, to maximise collaboration; (3) understanding policymaking, to know when and how to present evidence; (4) interpersonal skills, to focus on relationships and interaction; (5) engagement, to include citizens and stakeholders; (6) effective communication of knowledge; (7) monitoring and evaluation, to identify the impact of evidence on policy; and (8) policy advice, to know how to present knowledge effectively and ethically. No one possesses all skills relevant to all these practices. Rather, we recommend that organisations at the evidence-policy interface produce teams of people with different backgrounds, perspectives, and complementary skills.
Friend and foe
Authors: Pięta Hanna 
Published: July 2018

Abstract
Previous research suggests that in Salazar’s Portugal, Soviet Poland was portrayed as both a friend and a foe. This article argues
that these conflicting images are partly due to distinct discourses that reached Portugal through translations of Polish
literature. Ultimately, it aims to give insights into the role of literary translation in the construction of a national image
abroad. Since all the translations in the corpus are indirect, special attention is paid to the way the mediating texts impacted
the image encoded in the target text. The article considers five channels via which texts were imported, presenting the results of
a textual analysis of one translation in each of these channels, including its indirect trajectory. The findings confirm the
importance of the analysed translations in the construction of the discussed images and show that the mediating texts had a
crucial filtering role as regards the transfer of these images.
Measuring the Affordability of Nutritious Diets in Africa: Price Indexes for Diet Diversity and the Cost of Nutrient Adequacy
Authors: Masters William A. , Bai Yan , Herforth Anna , Sarpong Daniel B. , Mishili Fulgence , Kinabo Joyce , Coates Jennifer C. 
Published: July 2018

AbstractPolicies and programs often aim to improve the affordability of nutritious diets, but existing food price indexes are based on observed quantities that may not meet nutritional goals. To measure changes in the cost of reaching international standards of diet quality, we introduce a new cost of diet diversity index based on the lowest‐cost way to include at least five different food groups as defined by the widely used minimum dietary diversity for women (MDD‐W) indicator and compare that to a Cost of Nutrient Adequacy indicator for the lowest‐cost way to meet estimated average requirements of essential nutrients and dietary energy. We demonstrate application of both indexes using national average monthly prices from two very different sources: an agricultural market information system in Ghana (2009–14) and the data used for national consumer price indexes in Tanzania (2011–15). We find that the cost of diet diversity index for Ghana fluctuated seasonally and since mid‐2010 rose about 10% per year faster than national inflation, due to rising relative prices for fruit, which also drove up the cost of nutrient adequacy. In Tanzania there were much smaller changes in total daily costs, but more adjustment in the mix of food groups used for the least‐cost diet. These methods can show where and when nutritious diets are increasingly (un)affordable, and which nutritional criteria account for the change. These results are based on monthly national average prices, but the method is generalizable to other contexts for monitoring, evaluation, and assessment of changing food environments.
GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts
Authors: Walker Mark A , Pedamallu Chandra Sekhar , Ojesina Akinyemi I , Bullman Susan , Sharpe Ted , Whelan Christopher W , Meyerson Matthew 
Published: July 2018

Abstract

Summary
We present an updated version of our computational pipeline, PathSeq, for the discovery and identification of microbial sequences in genomic and transcriptomic libraries from eukaryotic hosts. This pipeline is available in the Genome Analysis Toolkit (GATK) as a suite of configurable tools that can report the microbial composition of DNA or RNA short-read sequencing samples and identify unknown sequences for downstream assembly of novel organisms. GATK PathSeq enables sample analysis in minutes at low cost. In addition, these tools are built with the GATK engine and Apache Spark framework, providing robust, rapid parallelization of read quality filtering, host subtraction and microbial alignment in workstation, cluster and cloud environments.

Availability and implementation
These tools are available as a part of the GATK at https://github.com/broadinstitute/gatk.

Supplementary information
Supplementary data are available at Bioinformatics online.
PepBDB: a comprehensive structural database of biological peptide–protein interactions
Authors: Wen Zeyu , He Jiahua , Tao Huanyu , Huang Sheng-You 
Published: July 2018

Abstract

Summary
A structural database of peptide–protein interactions is important for drug discovery targeting peptide-mediated interactions. Although some peptide databases, especially for special types of peptides, have been developed, a comprehensive database of cleaned peptide–protein complex structures is still not available. Such cleaned structures are valuable for docking and scoring studies in structure-based drug design. Here, we have developed PepBDB—a curated Peptide Binding DataBase of biological complex structures from the Protein Data Bank (PDB). PepBDB presents not only cleaned structures but also extensive information about biological peptide–protein interactions, and allows users to search the database with a variety of options and interactively visualize the search results.

Availability and implementation
PepBDB is available at http://huanglab.phys.hust.edu.cn/pepbdb/.
LigVoxel: inpainting binding pockets using 3D-convolutional neural networks
Authors: Skalic Miha , Varela-Rial Alejandro , Jiménez José , Martínez-Rosell Gerard , De Fabritiis Gianni 
Published: July 2018

Abstract

Motivation
Structure-based drug discovery methods exploit protein structural information to design small molecules binding to given protein pockets. This work proposes a purely data driven, structure-based approach for imaging ligands as spatial fields in target protein pockets. We use an end-to-end deep learning framework trained on experimental protein–ligand complexes with the intention of mimicking a chemist’s intuition at manually placing atoms when designing a new compound. We show that these models can generate spatial images of ligand chemical properties like occupancy, aromaticity and donor–acceptor matching the protein pocket.

Results
The predicted fields considerably overlap with those of unseen ligands bound to the target pocket. Maximization of the overlap between the predicted fields and a given ligand on the Astex diverse set recovers the original ligand crystal poses in 70 out of 85 cases within a threshold of 2 Å RMSD. We expect that these models can be used for guiding structure-based drug discovery approaches.

Availability and implementation
LigVoxel is available as part of the PlayMolecule.org molecular web application suite.

Supplementary information
Supplementary data are available at Bioinformatics online.