bluuebunny/crossref_metadata_2025 huggingface dataset:
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

Platelet 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

The 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

Eine 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

Chemotherapy-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

The 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.
Room temperature continuous frequency tuning InGaAs/InP single-photon detector
Authors: Chen Huan , Jiang Musheng , Sun Shihai , Tang Guangzhao , Liang Linmei
Published: July 2018

The available high speed InGaAs/InP-based single-photon avalanche detectors (SPAD) are normally worked at fixed gate or narrow tunable gate frequency. However, a wide tunable gate frequency or even free running single photon detectors at high speed would be very useful in quantum key distribution, quantum entanglement distribution and so on. Here, we present a high speed InGaAs/InP-based single photon avalanche detector (SPAD) with tunable gate frequency from 900MHz to 1000MHz which also can work under the room temperature without any cooling setups. Instead of restricting the spike noise by self-differencing or filtering method, we use an Analog to Digital Converter(ADC) to sample the output voltage of the APD. Through the sampled voltage we can discriminate an avalanche signal from the noise. Based on the sampling method, a room temperature SPAD is implemented with a dark count rate of 2.5 × 10−5 per gate and afterpulse probability of 1.3%, given the condition that detection efficiency of 10.6%, dead time of 1ns, and clock frequency of 1GHz. The wide tunable gate frequency makes the SPAD very suitable for practical use and commercial producing.
Free vibration of biopolymer spherical shells of high structural heterogeneity
Authors: Zhang Lei , Ru C. Q.
Published: July 2018

A refined elastic shell model is used to study the effect of high structural heterogeneity on natural frequencies and vibration modes of biopolymer spherical shells. With this model, the structural heterogeneity of a biopolymer spherical shell is characterized by an effective bending thickness (which can be quite different from the average thickness) and the transverse shear modulus (which can be much lower than the in-plane shear modulus). Our results show that actual natural frequencies of axisymmetric spheroidal modes of a biopolymer spherical shell can be much lower than those predicted by the classical homogeneous shell model based on the average thickness, although natural frequencies of axisymmetric torsional modes are close to those predicted by the classical model. For example, with physically realistic parameters for virus capsid STMV, the natural frequencies of spheroidal modes predicted by the present model are about 30-50% lower than those predicted by the classical model, in better agreement with known simulation results. In addition, in the low frequency range of several viral capsids, the number of independent non-axisymmetric vibration modes predicted by the present model is considerably larger than that predicted by the classical homogeneous shell model, in qualitative agreement with known atomistic simulations. These results suggest that the refined shell model could offer a relatively simple model to simulate mechanical behavior of biopolymer spherical shells of high structural heterogeneity.
The role of molecular genetics in livestock production
Authors: Ferreira de Camargo Gregório Miguel
Published: July 2018

Genetic variations that lead to easy-to-identify phenotypic changes have always been of interest to livestock breeders since domestication. Molecular genetics has opened up possibilities for identifying these variations and understanding their biological and population effects. Moreover, molecular genetics is part of the most diverse approaches and applications in animal production nowadays, including paternity testing, selection based on genetic variants, diagnostic of genetic diseases, reproductive biotechniques, fraud identification, differentiation of hybrids, parasite identification, genetic evaluation, diversity studies, and genome editing, among others. Therefore, the objective of this review was to describe the different applications of molecular genetics in livestock production, contextualising them with examples and highlighting the importance of the study of these topics and their applications.
New populations of the rare subterranean blind cave eel Ophisternon candidum (Synbranchidae) reveal recent historical connections throughout north-western Australia
Authors: Moore Glenn I. , Humphreys William F. , Foster Ralph
Published: July 2018

The enigmatic blind cave eel Ophisternon candidum is one of Australia’s least known fishes and is one of only three vertebrates in Australia with an entirely subterranean existence. For more than half a century, O. candidum was thought to be restricted to some 100km of coastal cave systems in north-western Australia. Herein we report on two new populations, each separated by hundreds of kilometres, and provide the first complete list of all known records of subterranean Ophisternon in Western Australia. Using morphological and molecular data, we show that these populations are conspecific, with one population showing evidence of genetic differentiation. Geological and biogeographic explanations are explored, along with conservation considerations. All populations face actual and potential threats, especially from mining activities, and there is a need for management and conservation strategies specific to each population.
Friend and foe
Authors: Pięta Hanna
Published: July 2018

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.
Single block 3D numerical model for linear friction welding of titanium alloy
Authors: Baffari Dario , Buffa Gianluca , Campanella Davide , Fratini Livan , Micari Fabrizio
Published: July 2018

A two-stage approach for the simulation of Linear Friction Welding is presented. The proposed model, developed using the commercial simulation package DEFORM, is 3D Lagrangian, thermo-mechanically coupled. The first phase of the process was modelled with two distinct workpieces, while the remaining phases were simulated using a single-block model. The Piwnik–Plata criterion was set up and used to determine the shifting from the dual object to the single-block model. The model, validated against experimental temperature measurements, is able to predict the main field variables distributions with varying process parameters. Titanium alpha and beta phases evolution during the whole process has been predicted and the obtained results have been correlated to the experimentally measured micro-mechanical properties of the joints.
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

Policies 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

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

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

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.
Dynamic Reorganization of Motor Networks During Recovery from Partial Spinal Cord Injury in Monkeys
Authors: Chao Zenas C , Sawada Masahiro , Isa Tadashi , Nishimura Yukio
Published: July 2018

After spinal cord injury (SCI), the motor-related cortical areas can be a potential substrate for functional recovery in addition to the spinal cord. However, a dynamic description of how motor cortical circuits reorganize after SCI is lacking. Here, we captured the comprehensive dynamics of motor networks across SCI in a nonhuman primate model. Using electrocorticography over the sensorimotor areas in monkeys, we collected broadband neuronal signals during a reaching-and-grasping task at different stages of recovery of dexterous finger movements after a partial SCI at the cervical levels. We identified two distinct network dynamics: grasping-related intrahemispheric interactions from the contralesional premotor cortex (PM) to the contralesional primary motor cortex (M1) in the high-γ band (>70 Hz), and motor-preparation-related interhemispheric interactions from the contralesional to ipsilesional PM in the α and low-β bands (10–15 Hz). The strengths of these networks correlated to the time course of behavioral recovery. The grasping-related network showed enhanced activation immediately after the injury, but gradually returned to normal while the strength of the motor-preparation-related network gradually increased. Our findings suggest a cortical compensatory mechanism after SCI, where two interdependent motor networks redirect activity from the contralesional hemisphere to the other hemisphere to facilitate functional recovery.
ACC Sulcal Patterns and Their Modulation on Cognitive Control Efficiency Across Lifespan: A Neuroanatomical Study on Bilinguals and Monolinguals
Authors: Del Maschio Nicola , Sulpizio Simone , Fedeli Davide , Ramanujan Keerthi , Ding Guosheng , Weekes Brendan S , Cachia Arnaud , Abutalebi Jubin
Published: July 2018

The anterior cingulate cortex (ACC) is a key structure implicated in the regulation of cognitive control (CC). Previous studies suggest that variability in the ACC sulcal pattern—a neurodevelopmental marker unaffected by maturation or plasticity after birth—is associated with intersubject differences in CC performance. Here, we investigated whether bilingual experience modulates the effects of ACC sulcal variability on CC performance across the lifespan. Using structural MRI, we first established the distribution of the ACC sulcal patterns in a large sample of healthy individuals (N = 270) differing on gender and ethnicity. Second, a participants’ subsample (N = 157) was selected to test whether CC performance was differentially affected by ACC sulcation in bilinguals and monolinguals across age. A prevalent leftward asymmetry unaffected by gender or ethnicity was reported. Sulcal variability in the ACC predicted CC performance differently in bilinguals and monolinguals, with a reversed pattern of structure–function relationship: asymmetrical versus symmetrical ACC sulcal patterns were associated with a performance advantage in monolinguals and a performance detriment to bilinguals and vice versa. Altogether, these findings provide novel insights on the dynamic interplay between early neurodevelopment, environmental background and cognitive efficiency across age.
Endoscopic therapy of colorectal anastomotic hematoma with hypertonic dextrose
Authors: Shashi Preeti , Kochhar Gursimran , Shen Bo
Published: July 2018

Anastomotic dehiscence and leak are dreaded complications after a colorectal resection and can often present with rectal bleeding and pelvic abscess or sepsis. Although most cases of bleeding after gastrointestinal anastomoses are minor and self-limited, major bleeding, as defined by hemodynamic instability or the need for blood transfusions, poses a significant challenge for management. Here we report a case in which a patient presenting with profuse rectal bleeding and pelvic hematoma secondary to a colorectal anastomotic leak was treated endoscopically with 50% dextrose spray then enema.
Marine sublittoral benthos fails to track temperature in response to climate change in a biogeographical transition zone
Authors: Gaudin François , Desroy Nicolas , Dubois Stanislas F , Broudin Caroline , Cabioch Louis , Fournier Jérôme , Gentil Franck , Grall Jacques , Houbin Céline , Le Mao Patrick , Thiébaut Éric
Published: July 2018

Species ranges are shifting globally to track temperature changes in response to climate warming, with substantial variability among taxa. In the English Channel, a biogeographical transition zone between the cold temperate and warm temperate provinces of the North-East Atlantic, distribution shifts have been relatively well documented for plankton, fish and intertidal benthic organisms, but little information is available on sublittoral benthos. Following a description of the magnitude of the sea bottom temperature (SBT) rise, the changes in the distribution and occupancy of 65 benthic invertebrate species were analysed by comparing data collected throughout the English Channel at more than 200 stations sampled during a cool period in the 1960s–1970s and at present in 2012–2014. A non-uniform rise in SBT for the last three decades was observed at the regional scale, varying from 0.07 to 0.54°C per decade. This rise differs from that reported for sea surface temperature (SST) in stratified areas suggesting that SBT should be used rather than SST to analyse responses of subtidal organisms to climate change. Despite shifts in both minimum and maximum sea bottom isotherms (2.5 and 3.2 km.year−1, respectively), the distribution centroid shift of most species remained <1.0 km.year−1, regardless of the average temperatures they usually experience. Conversely, decreases were observed in the occurrence of most cold-water species and increases were found in the occurrence of most warm-water species. These results suggest that ongoing climate change could lead to a decrease in benthic biodiversity at range limits, especially where connection routes are lacking for new migrants.
An efficient algorithm for compression-based compressed sensing
Authors: Beygi Sajjad , Jalali Shirin , Maleki Arian , Mitra Urbashi
Published: July 2018

Modern image and video compression codes employ elaborate structures in an effort to encode them using a small number of bits. Compressed sensing (CS) recovery algorithms, on the other hand, use such structures to recover the signals from a few linear observations. Despite the steady progress in the field of CS, the structures that are often used for signal recovery are still much simpler than those employed by state-of-the-art compression codes. The main goal of this paper is to bridge this gap by answering the following question: can one employ a compression code to build an efficient (polynomial time) CS recovery algorithm? In response to this question, the compression-based gradient descent (C-GD) algorithm is proposed. C-GD, which is a low-complexity iterative algorithm, is able to employ a generic compression code for CS and therefore enlarges the set of structures used in CS to those used by compression codes. Three theoretical contributions are provided: a convergence analysis of C-GD, a characterization of the required number of samples as a function of the rate-distortion function of the compression code and a robustness analysis of C-GD to additive white Gaussian noise and other non-idealities in the measurement process. Finally, the presented simulation results show that, in image CS, using compression codes such as JPEG2000, C-GD outperforms state-of-the-art methods, on average, by about $2$–$3$ dB in peak signal-to-noise ratio.
Controllability of a one-dimensional fractional heat equation: theoretical and numerical aspects
Authors: Biccari Umberto , Hernández-Santamaría Víctor
Published: July 2018

We analyse the controllability problem for a one-dimensional heat equation involving the fractional Laplacian $(-d_x^{\,2})^{s}$ on the interval $(-1,1)$. Using classical results and techniques, we show that, acting from an open subset $\omega \subset (-1,1)$, the problem is null-controllable for $s>1/2$ and that for $s\leqslant 1/2$ we only have approximate controllability. Moreover, we deal with the numerical computation of the control employing the penalized Hilbert Uniqueness Method and a finite element scheme for the approximation of the solution to the corresponding elliptic equation. We present several experiments confirming the expected controllability properties.
A priori error for unilateral contact problems with Lagrange multipliers and isogeometric analysis
Authors: Antolin Pablo , Buffa Annalisa , Fabre Mathieu
Published: July 2018

In this paper we consider a unilateral contact problem without friction between a rigid body and a deformable one in the framework of isogeometric analysis. We present the theoretical analysis of the mixed problem. For the displacement, we use the pushforward of a nonuniform rational B-spline space of degree $p$ and for the Lagrange multiplier, the pushforward of a B-spline space of degree $p-2$. These choices of space ensure the proof of an inf–sup condition and so on, the stability of the method. We distinguish between contact and noncontact sets to avoid the classical geometrical hypothesis of the contact set. An optimal a priori error estimate is demonstrated without assumption on the unknown contact set. Several numerical examples in two and three dimensions and in small and large deformation frameworks demonstrate the accuracy of the proposed method.
Effects of Different Doses of GEN-003, a Therapeutic Vaccine for Genital Herpes Simplex Virus-2, on Viral Shedding and Lesions: Results of a Randomized Placebo-Controlled Trial
Authors: Van Wagoner Nicholas , Fife Kenneth , Leone Peter A , Bernstein David I , Warren Terri , Panther Lori , Novak Richard M , Beigi Richard , Kriesel John , Tyring Stephen , Koltun William , Lucksinger Gregg , Morris Amy , Zhang Bin , McNeil Lisa K , Tasker Sybil , Hetherington Seth , Wald Anna
Published: July 2018

Background

GEN-003 is a candidate therapeutic vaccine for genital herpes simplex virus type 2 (HSV-2). We compared virologic and clinical impact of varying GEN-003 doses.

Methods

Adults with symptomatic HSV-2 received placebo or GEN-003 (30 or 60 µg antigen with 25, 50, or 75 µg adjuvant). Viral shedding and lesion rates before vaccination were compared with those measured immediately after vaccination, then at weeks 29–33 and 53–57 after last dose.

Results

Compared with baseline shedding rates, the rate ratios for viral shedding immediately after treatment were as follows: 0.82 (95% confidence interval [CI], 0.49–1.36), 30 µg antigen/25 µg adjuvant (30/25) dose; 0.64 (95% CI, 0.45–0.92), 30/50 dose; 0.63 (95% CI, 0.37–1.10), 30/75 dose; 0.56 (95% CI, 0.36–0.88), 60/25 dose; 0.58 (95% CI, 0.38–0.89), 60/50 dose; 0.45 (95% CI, 0.16–0.79), 60/75 dose; and 0.98 (95% CI, 0.76–1.26), placebo. Lesion rate reductions by GEN-003 ranged from 31% to 69%, but lesion rates also decreased among placebo recipients (62%). Reductions in shedding and lesion rate were durable for 12 months for the 60 µg antigen plus 50 or 75 µg adjuvant groups. No serious adverse events occurred with vaccination.

Conclusions

The most efficacious vaccine combinations for GEN-003 were the 60 µg/50 µg and 60 µg/75 µg doses.
The stroke navigator: meaningful use of the electronic health record to efficiently report inpatient stroke care quality
Authors: Nathan Jay K , Foley Jenevra , Hoang Tiffany , Hiner Jim , Brooks Stephanie , Gendreau Julian L , Meurer William J , Pandey Aditya S , Adelman Eric E
Published: July 2018

To facilitate high-quality inpatient care for stroke patients, we built a system within our electronic health record (EHR) to identify stroke patients while they are in the hospital; capture necessary data in the EHR to minimize the burden of manual abstraction for stroke performance measures, decreasing daily time requirement from 2 hours to 15 minutes; generate reports using an automated process; and electronically transmit data to third parties. Provider champions and support from the EHR development team ensured that we balanced the needs of the hospital with those of frontline providers. This work summarizes the development and implementation of our stroke quality system.
Does Time of Day Affect Variety-Seeking?
Authors: Gullo Kelley , Berger Jonah , Etkin Jordan , Bollinger Bryan
Published: July 2018

Variety-seeking is a fundamental aspect of choice. But given circadian rhythms in chronobiology, might variety-seeking vary by time of day? Four studies, including an empirical analysis of millions of purchases, demonstrate diurnal variation in variety-seeking. Variety-seeking is lower in the morning than other times of day. People pick less varied flavors of yogurt, for example, when choosing in the morning. Further, the results demonstrate the underlying role of circadian changes in physiological stimulation and arousal. The effect is mediated by a physiological measure of arousal (i.e., body temperature) and moderated by factors that shape physiological arousal (i.e., sunlight and individual differences in circadian preferences). These findings shed light on drivers of variety-seeking and the biological basis of consumer behavior more generally.
The First Procedural Order
Authors: Commission Jeffery , Moloo Rahim
Published: July 2018

This chapter considers the supplementary procedural rules that are typically decided at the outset of an investment arbitration and the process through which those rules come to be. It begins by discussing the procedural issues that parties and arbitral tribunals often see fit to address at the outset, including the procedural timetable, bifurcation, seat (if applicable), location, fees and costs, language, pleadings, discovery, witnesses, expert witnesses, amicus curiae, and confidentiality/transparency. The chapter also examines the process for deciding these procedural issues, noting that the procedure is most often a hybrid of communicating to the tribunal issues agreed by the parties and debating before the tribunal controverted procedural issues, which the tribunal then resolves. The First Procedural Order is the result of the First Procedural Conference.
Prologue
Authors: Orentlicher Diane
Published: July 2018

In this prologue, the author reflects on the process of updating in 2005 the United Nations Set of Principles for the Protection and Promotion of Human Rights Through Action to Combat Impunity (‘The Principles’). The author, who drafted the report that accompanied the Updated Principles, discusses the challenges involved in her work as well as the factors that were taken into consideration in the preparation of the report. The Principles, first conceived in 1997, serve two fundamentally different functions: first, as a classic soft law instrument and second, as ‘standards drawn from experience’ that could serve ‘as a broad strategic framework for action against impunity’. As a source of practical guidance derived from ‘best practices’, the Principles seek to honor local agency, reflecting in particular the perspectives of victims. They also recognize the elemental importance of clarifying where local discretion ends and legal obligation begins.
Preamble
Authors: Boven Theo van
Published: July 2018

The Preamble of the Principles is based on the premise that the Principles will provide guidance to States and other entities in developing effective measures for combating impunity. A leading normative component of the Preamble is the trilogy of the core rights to know, to justice and to reparation, including guarantees of non-recurrence. This chapter first describes the functions and characteristics of a Preamble and provides an overview of the report of Special Rapporteur Louis Joinet before discussing the Updated Set of Principles and the evolving notion of ‘transitional justice’; the campaign against impunity; and the orientation and scope of the Principles, including the Preamble, in the broader settings of restoring peace and democracy. Issues concerning broad participatory involvement of victims, human rights defenders and other sectors of civil society are also considered.
Definition of a Commission’s Terms of Reference
Authors: Bisset Alison
Published: July 2018

Principle 8 provides for the creation of strong commissions with clear terms of reference that ensure delineation between their role and that of courts. However, it offers no guidance on how to coordinate the proceedings of commissions. Indeed, the Principle’s stipulations that commissions should possess quasi-judicial powers and the abilities to investigate all violations increases the likelihood of overlap in investigations and, therefore, the potential for operational tension. This chapter first provides a contextual and historical background on Principle 8 before discussing its theoretical framework and how the requirements of Principle 8 are reflected in modern practice. It highlights the practical difficulties associated with endowing commissions with wide mandates and truth-seeking powers, where there are also efforts to pursue criminal justice, by citing the experiences of South Africa, East Timor and Sierra Leone.
Guarantees for Victims and Witnesses Testifying on Their Behalf
Authors: Bisset Alison
Published: July 2018

Principle 10 provides guarantees for victims and witnesses testifying on their behalf. The participation of victims and witnesses in truth seeking processes is important in efforts to uncover the truth about the past. Many commissions have been mandated to gather victim testimony as a key objective and to provide victims with a forum in which to give account of the abuses suffered and to restore their dignity. When there is no testimony, commissions are unlikely to fulfill their broader mandates of establishing a historical record of past violations. After giving a contextual and historical background on Principle 10, this chapter discusses its theoretical framework and how commissions operate in practice in terms of witness protection.
Measures for the Preservation of Archives
Authors: Cadelo Valentina , Peterson Trudy Huskamp
Published: July 2018

Principle 14 outlines measures for the preservation of archives, a fundamental corollary to the right to know the truth. In order to preserve governmental and nongovernmental archives, their destruction must be prevented and active steps need to be taken to prolong the life of the materials. Technical measures and penalties must prevent any removal, destruction, concealment or falsification of archives to ensure that there will be no impunity for perpetrators of violations of human rights and/or humanitarian law. Preserving archives is particularly important during periods of governmental transition and regime change. After providing a contextual and historical background on Principle 14, this chapter discusses its theoretical framework as well as state practice on public records and archives.
Cooperation Between Archive Departments and the Courts and Non-Judicial Commissions of Inquiry
Authors: Ciorciari John D
Published: July 2018

Principle 16 stresses the need for cooperation between archive departments and the courts and non-judicial commissions of inquiry. This principle highlights two key challenges of managing archival access: respecting legitimate national security needs and protecting privacy. With respect to national security, the Principle’s requirement of independent judicial review renders it more demanding than the International Covenant on Civil and Political Rights and other major human rights instruments, which merely require that restrictions be prescribed by law are necessary to protect national security or public order. Principle 16’s forward-leaning position draws attention to the fact that national security and public order exemptions are easily abused by states keen to avoid embarrassment or self-incrimination. This chapter first provides a contextual and historical background on Principle 16 before discussing its theoretical framework as well as archival access in practice.
Specific Measures Related to the Restoration of or Transition to Democracy and/or Peace
Authors: Ciorciari John D
Published: July 2018

Principle 18 outlines specific measures related to the restoration of or transition to democracy and/or peace. Transitional states emerging from repressive rule face a host of serious archival challenges. Outgoing officials sometimes burn or destroy incriminating documents to cover their tracks, as occurred in East Germany, South Korea, South Africa, Egypt, and the Soviet Union. Principle 18 emphasizes the importance of protecting and preserving, inventorying, and analyzing archives of the old regime. It reflects an understanding that archives are keys to advancing accountability, the right to truth, and other elements of a successful transition to peace and/or democracy. After providing a contextual and historical background on Principle 18, this chapter discusses its theoretical framework as well as the ways in which states and third countries have managed archives related to past human rights abuses. It also highlights some areas for improvement in terms of archival practice in transitional periods.
Restrictions on Prescription
Authors: Pinzauti Giulia
Published: July 2018

Principle 23 deals with statutory limitations (prescription, in French) aimed at protecting defendants from stale claims that might be difficult to counter. Statutory limitations refer to legal norms that regulate the effects of the passage of time in domestic systems. In criminal law, they provide for a maximum timeframe, or prescription period, within which criminal proceedings can be instituted or sentences enforced. The passage of time makes the gathering of evidence more difficult and may also reduce the effectiveness of criminal prosecution. Significant delays in criminal action may thus impair the accused’s right to a fair trial. Furthermore, criminal proceedings tend to lose legitimacy as time passes. After providing a contextual and historical background on Principle 23, this chapter discusses its theoretical framework and how the statutory limitations have been applied in practice under multilateral treaties, domestic legislation and case-law. It also examines the practice of United Nations organs.
Restrictions on the Effects of Legislation on Disclosure or Repentance
Authors: Gosnell Christopher
Published: July 2018

Principle 28 deals with restrictions on the effects of legislation on disclosure or repentance. According to this Principle, a person’s formal confession of a crime may, pursuant to ‘provisions of legislation on disclosure and repentance’, justify a ‘reduction of sentence’ but not ‘exempt[ion]’ from ‘criminal or other responsibility’. Such a person may be granted asylum, presumably by another State, where such a confession ‘may subject the perpetrator to persecution’. Principle 28 thus highlights the maximum benefit that may be accorded to a confession under an amnesty program: a reduction of sentence but not ‘exemption’ from responsibility altogether. However, this distinction does not reflect any established practice or norms of international law. This chapter first provides a contextual and historical background on Principle 28 before discussing its theoretical framework and how exemption from criminal responsibility in return for confession has been applied in practice.
Restrictions on the Principle of the Irremovability of Judges
Authors: Gosnell Christopher
Published: July 2018

Principle 30 deals with restrictions on the principle of the irremovability of judges. Judicial independence, both institutional and individual, is essential in any justice system and must be respected in a trans-regime setting. At the same time, it is necessary for the judiciary to adjudicate the crimes of a past regime with adequate vigour. This can present a major dilemma between necessary continuity and necessary reform, one that Principle 30 is designed to address. According to Principle 30, judges may not be removed if they were appointed ‘in conformity with the requirements of the rule of law’, but may be removed if they were ‘unlawfully appointed’ or ‘derive their judicial power from an act of allegiance’. This chapter first provides a contextual and historical background on Principle 30 before discussing its theoretical framework and how judges are treated in a trans-regime setting.
Equity and Debt Securities
Authors: Smith Marcus , Leslie Nico
Published: July 2018

This chapter discusses securities. Securities are an important and complex category of intangible. A ‘security’ is defined as a fungible financial instrument, offered for sale on identical terms to multiple investors on first issue, and thereafter generally traded in a market that facilitates its free transfer. Securities can broadly be classified into shares, debt securities, and hybrid securities. The chapter then looks at the legal incidents of securities, and how securities are allotted and held. Allotment describes the process whereby the issuer of securities agrees to issue those securities to a particular person and that person agrees to buy those securities. Meanwhile, the question of how securities are held has become an increasing complex area. Originally, securities were held in paper form. Such paper-based systems are increasingly becoming redundant but their operation remains important because they are relevant to the electronic systems by which securities are held today.
Promises to Assign or Create a trust
Authors: Smith Marcus , Leslie Nico
Published: July 2018

This chapter examines promises to assign or create a trust. It is possible to promise to assign a chose, rather than to assign a chose. At common law, such an agreement has no propriety implications. According to the common law, a contract operates in personam and breach of a promise to assign will give rise to the remedy of damages only. In equity, however, the effect of such a contract is very different. Equity treats a contract to do a thing as if the thing were already done and thus treats an agreement for value as if it had been performed at the time when it ought to have been performed. This doctrine applies as much as to trusts as it does to assignments, and equity will similarly give effect to a promise to create a trust.