bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pan-European Data Harmonization for Biobanks in ADOPT BBMRI-ERIC
Authors: Mate Sebastian , Kampf Marvin , Rödle Wolfgang , Kraus Stefan , Proynova Rumyana , Silander Kaisa , Ebert Lars , Lablans Martin , Schüttler Christina , Knell Christian , Eklund Niina , Hummel Michael , Holub Petr , Prokosch Hans-Ulrich 
Published: September 2019

Abstract
Background High-quality clinical data and biological specimens are key for medical research and personalized medicine. The Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium (BBMRI-ERIC) aims to facilitate access to such biological resources. The accompanying ADOPT BBMRI-ERIC project kick-started BBMRI-ERIC by collecting colorectal cancer data from European biobanks.
Objectives To transform these data into a common representation, a uniform approach for data integration and harmonization had to be developed. This article describes the design and the implementation of a toolset for this task.
Methods Based on the semantics of a metadata repository, we developed a lexical bag-of-words matcher, capable of semiautomatically mapping local biobank terms to the central ADOPT BBMRI-ERIC terminology. Its algorithm supports fuzzy matching, utilization of synonyms, and sentiment tagging. To process the anonymized instance data based on these mappings, we also developed a data transformation application.
Results The implementation was used to process the data from 10 European biobanks. The lexical matcher automatically and correctly mapped 78.48% of the 1,492 local biobank terms, and human experts were able to complete the remaining mappings. We used the expert-curated mappings to successfully process 147,608 data records from 3,415 patients.
Conclusion A generic harmonization approach was created and successfully used for cross-institutional data harmonization across 10 European biobanks. The software tools were made available as open source.
Mechanism of activation of the human cysteine desulfurase complex by frataxin
Authors: Patra Shachin , Barondeau David P. 
Published: September 2019

Significance
In humans, essential iron-sulfur (Fe-S) cluster cofactors are synthesized using an assembly complex that depends on the protein frataxin (FXN). The physiological function of FXN, which is linked to the fatal neurodegenerative disease Friedreich’s ataxia (FRDA), is still under debate. Here, we show that FXN accelerates Fe-S cluster formation by positioning a mobile loop cysteine of the assembly complex to interact with the substrate and function as an acid, nucleophile, and sulfur carrier during the reaction. Our architectural switch model suggests that FXN controls Fe-S cluster biosynthesis by inducing an unusual rearrangement of protein subunits in the assembly complex. These results provide mechanistic insights into this critical biological process and establish a foundation for the design of new FRDA treatments.
La variación lingüística del vocativo en el lenguaje juvenil madrileño
Authors: De Latte Fien , Enghels Renata 
Published: September 2019

AbstractThis paper investigates the formal and functional variation of the vocative in contemporary Spanish teenage talk. For this purpose, all vocative occurrences found in conversations between teenagers in theCorpus Oral de Madrid-2016are analyzed. The vocative is known to be highly productive in Spanish teenage talk, on both formal and functional levels. First, we provide the inventory of vocative forms used by Madrilenian teenagers, examine their origin and describe their semantic-pragmatic features, with special attention for the nominal vocative expressions used as symbols of in-group identity. The second part disentangles the pragmatic-discursive functions assumed by these forms, by taking into account the vocative’s multifunctionality. Teenagers tend to use vocatives as a phatic mechanism which allows them to control the contact with their interlocutor(s).
Improved iterative tomographic reconstruction for x-ray imaging with edge-illumination
Authors: Modregger Peter , Meganck Jeff , Hagen Charlotte K , Massimi Lorenzo , Olivo Alessandro , Endrizzi Marco 
Published: September 2019

Abstract
Iterative tomographic reconstruction has been established as a viable alternative for data analysis in phase-sensitive x-ray imaging based on the edge-illumination principle. However, previously published approaches did not account for drifts of optical elements during a scan, which can lead to artefacts. Up to now, the strategy to reduce these artefacts was to acquire additional intermediate flat field images, which were used to correct the sinograms. Here, we expand the theoretical model to take these effects into account and demonstrate a significant reduction of (ring)-artefacts in the final reconstructions, while allowing for a significant reduction of scan time and dose. We further improve the model by including the capability to reconstruct combined absorption and phase contrast slices, which we experimentally demonstrate to deliver improved contrast to noise ratios compared to previously employed single shot approaches.
Helicity transport and dynamo sustainment for helical plasma states
Authors: Paccagnella R 
Published: September 2019

Abstract
Plasma states dominated by single helical modes are often observed in the Reverse Field Pinch (RFP) plasma confinement devices. In this paper the properties of these states are studied on the basis of a relaxation model that assumes the existence of several topological invariants related to the dominant mode. It is hypothesized that the value of the first invariant in this chain, is determined by the existence of a plasma dynamo mechanism that transport helicity. This hypothesis enables us to determine the steady state properties of the plasma equilibrium and some other interesting physical consequences. Further, by considering the properties of the transfer of helicity from the mesoscale (fluctuations) to the macroscale (equilibrium), through the dynamo field, a nonlinear dynamical model can be constructed, that evolves in time to a steady state with a non-vanishing dynamo field, when helicity is injected in the system, as in the case of the ohmic sustained RFP, while the dynamo oscillates initially, but is damped later in time, for vanishing helicity input.
Two-axis cavity optomechanical torque characterization of magnetic microstructures
Authors: Hajisalem G , Losby J E , de Oliveira Luiz G , Sauer V T K , Barclay P E , Freeman M R 
Published: September 2019

Abstract
Significant new functionality is reported for torsion mechanical tools aimed at full magnetic characterizations of both spin statics and dynamics in micro- and nanostructures. Specifically, two orthogonal torque directions are monitored and the results co-analyzed to separate magnetic moment and magnetic susceptibility contributions to torque, as is desired for characterization of anisotropic three-dimensional structures. The approach is demonstrated through application to shape and microstructural disorder-induced magnetic anisotropies in lithographically patterned permalloy, and will have utility for the determination of important magnetic thin-film and multilayer properties including interface anisotropy and exchange bias. The results reflect remarkable sensitivity of the out-of-plane magnetic torque to the nature of small edge domains perpendicular to the applied field direction, and also contain tantalizing indications of direct coupling to spin dynamics at the frequency of the mechanics.
Spin-valley filter effect and Seebeck effect in a silicene based antiferromagnetic/ferromagnetic junction
Authors: Niu Zhi Ping 
Published: September 2019

Abstract
The presence of the coupled spin and valley degrees of freedom makes silicene an important material for spintronics and valleytronics. Here we report a spin-valley filter effect in a silicene based antiferromagnetic/ferromagnetic junction. It is found that at zero Fermi level a valley locked bipolar spin filter effect is observed, where in a broad gate voltage range in one valley one spin (the other spin) electrons contribute to the current under the positive (negative) bias, but in the other valley the transport is forbidden. At the finite Fermi level a valley locked fully spin-polarized current can exist under both the positive and negative biases. Furthermore, at the high Fermi level by reversing the bias direction, the spin filter effect can switch to the valley filter effect. In addition, by changing the sign of the Fermi level, the spin polarization direction of the current can be reversed. If a temperature bias is applied, the spin-dependent Seebeck effect (SSE) always exists. With increasing the temperature bias, the system undergoes three regions: valley locked SSE, normal SSE and valley Seebeck effect. Moreover, by tuning the interlayer electric field, three phases: thermally induced valley locked spin filter effect, valley Seebeck effect and valley mixed Seebeck effect are observed.
Numerical simulation of critical dissipative non-equilibrium quantum systems with an absorbing state
Authors: Gillman Edward , Carollo Federico , Lesanovsky Igor 
Published: September 2019

Abstract
The simulation of out-of-equilibrium dissipative quantum many body systems is a problem of fundamental interest to a number of fields in physics, ranging from condensed matter to cosmology. For unitary systems, tensor network methods have proved successful and extending these to open systems is a natural avenue for study. In particular, an important question concerns the possibility of approximating the critical dynamics of non-equilibrium systems with tensor networks. Here, we investigate this by performing numerical simulations of a paradigmatic quantum non-equilibrium system with an absorbing state: the quantum contact process. We consider the application of matrix product states and the time-evolving block decimation algorithm to simulate the time-evolution of the quantum contact process at criticality. In the Lindblad formalism, we find that the Heisenberg picture can be used to improve the accuracy of simulations over the Schrödinger approach, which can be understood by considering the evolution of operator-space entanglement. Furthermore, we also consider a quantum trajectories approach, which we find can reproduce the expected universal behaviour of key observables for a significantly longer time than direct simulation of the average state. These improved results provide further evidence that the universality class of the quantum contact process is not directed percolation, which is the class of the classical contact process.
Fibre-optic based particle sensing via deep learning
Authors: Grant-Jacob James A , Jain Saurabh , Xie Yunhui , Mackay Benita S , McDonnell Michael D T , Praeger Matthew , Loxham Matthew , Richardson David J , Eason Robert W , Mills Ben 
Published: September 2019

Abstract
We demonstrate the capability for the identification of single particles, via a neural network, directly from the backscattered light collected by a 30-core optical fibre, when particles are illuminated using a single mode fibre-coupled laser light source. The neural network was shown to be able to determine the specific species of pollen with ∼97% accuracy, along with the distance between the end of the 30-core sensing fibre and the particles, with an associated error of ±6 μm. The ability to be able to classify particles directly from backscattered light using an optical fibre has potential in environments in which transmission imaging is neither possible nor suitable, such as sensing over opaque media, in the deep sea or outer space.
Altered Collection Interfaces in Hematopoietic Progenitor Collection of Sickle Cell Patients
Authors: Tsai Jonathan , Manis John , Ching Kimberly 
Published: September 2019

Abstract
Sickle cell disease (SCD) results from a point mutation in the beta globin gene leading to abnormal hemoglobin production and, correspondingly, abnormal sickling of erythrocytes that result in chronic anemia and vaso-occlusive crises. Patients with sickle cell are commonly treated with lifelong transfusions or hydroxyurea to increase fetal hemoglobin to ameliorate sickling. Evolving therapies are aimed at correcting known mutations with gene therapy on autologous hematopoietic stem and progenitor cells (HSCs), indicating a growing need for optimal stem cell collections from SCD patients. Recent studies have shown the safety and efficacy of plerixafor to increase peripheral CD34+ cells, enhancing collection. Here we show that standard apheresis collection procedures from sickle cell patients are inefficient when compared to healthy donors. Eleven patients with SCD were recruited to receive plerixafor and followed by peripheral CD34+ cell monitoring and apheresis collection. Overall, efficiency ranged from 2% to 55% with no correlation to total peripheral CD34+ cell count. To better understand where the CD34+ cells sedimented in the apheresis instrument, we collected different layers of the interface ranging from 3% to 10% estimated Hct and found that deeper layers with higher hematocrit (7.5%-10%) are enriched for CD34+ cells when compared to historical donors with healthy red cells. All patients had undergone red cell exchange prior to collection, yet this intervention did not prevent the altered sedimentation of CD34+ cells. These findings indicate that CD34+ cells from SCD patients sediment at a deeper, higher Hct interface layer during apheresis and support the altered collection practices for the efficient collection of HSCs for cellular therapies.
Thromboelastography in Trauma: A 1-Year Institutional Experience
Authors: Wells David , Hess John R , Sabath Daniel E 
Published: September 2019

Abstract
Viscoelastic testing to assess the overall clotting ability of a patient’s whole blood, such as thromboelastography (TEG), has risen in popularity over the past several years due its holistic assessment and rapid turnaround time, most notably in the realm of liver transplants and complex cardiac surgery. In the setting of trauma and assessing the concomitant coagulopathy, the rapid turnaround time and ability to assess for hyperfibrinolytic states had led to it being requested at our institution despite variable result interpretation and lack of reproducibility in previous studies. In response, our institution’s laboratory made this available at our hospital, which includes a large level 1 trauma center serving multiple states, with the aim of reassessing its utility after a 1-year period. Following the first year of use, data that were evaluated included TEG values and conventional laboratory testing temporally associated with the TEG order, including platelet count and fibrinogen level. Retrospective chart review was also performed to determine indication and context of testing, as well as for assessment of resulting interventions. Seventy-three samples from 58 patients were tested during the 1-year period, 30 of whom were admitted for trauma and 20 of whom were evaluated during the critical initial acute resuscitation period. Among the trauma patients, the majority of TEG samples (75.6%) did not demonstrate any abnormality. A primary reason cited by trauma surgeons for the need for TEG was its ability to accurately identify states of hyperfibrinolysis to determine the need for therapeutic agents such as tranexamic acid. In this regard, no evidence of hyperfibrinolysis was identified in any of the trauma patients. In fact, only a single hyperfibrinolytic sample was identified, corresponding to a nontrauma patient who had received a thrombolytic agent (alteplase) prior to TEG testing. Additionally, 75% of acute trauma patients received tranexamic acid, which was nearly always administered prior to the TEG sample being drawn. No evidence of TEG results affecting patient management was identified. As a result of the retrospective review of the data, use of TEG in the trauma population at our institution dramatically declined. We present this institutional review as an example of performing data review to influence test utilization practices.
Pending Log Monitors: Implementation for Improved Lab Efficiency
Authors: Perrone Marie , Behrens Caitlin , Lee Arthur , Pac Lincoln , Hoffman Noah 
Published: September 2019

Abstract
Hospital labs are increasingly consolidating into larger hospital systems with centralized testing locations. Specimens collected at disparate sites need to be transported to different locations for testing. Our LIS (Sunquest FlexiLab) does not provide a real-time display of specimens in need of transport to other locations. The current system lists pending specimens in paper printouts. The printouts have a difficult-to-read format, fail to account for certain add-on tests, and leave room for human error. In addition, IT staff must maintain test groups that are specific to each sending and receiving facility pair. This is a costly use of IT resources and is error prone due to test menu differences at each facility. In the current study, we evaluated the current system of batching specimens for transport and then designed a web-based application to provide a dynamic display of transport batches. The web-based application that we developed is called a “transport batch monitor” (TBM). The TBM displays specimens that need to be sent to another location for testing. This application was implemented in Python using the Flask microframework. Data are transferred in JSON format from Sunquest every 3 minutes using custom Caché ObjectScript routines. The application can be accessed with a secure login from any computer with Internet access and is displayed on large, fixed monitors in locations where transport batches are assembled. The display shows pertinent information for lab techs to be able to locate specimens that need to be sent out and is color-coded for ease of use. Metrics used to evaluate the current system included timing studies, surveys of lab staff performing the task, and paper usage. The process of collecting and batching specimens for transport to another facility took on average 24 minutes and required on approximately 22 sheets of paper. Anecdotally, specimens had historically been missed, especially when clinicians ordered add-on tests on specimens from days prior due to the way the LIS generated the printouts. Although 74% of techs surveyed reported that the task was somewhat easy or very easy, 32% were somewhat dissatisfied with the current system, and 40% said that the current paper printouts were either very unclear or somewhat unclear. Postimplementation metrics will be collected once the TBM has been implemented. We hypothesize that the transport batch monitor is a simple, inexpensive web-based tool that can greatly improve the day-to-day functioning of the lab. We hope it will improve efficiency and tech satisfaction, and reduce errors.
Genetic Testing to Resolve the Source of Hemolytic Antibody in Solid Organ Transplantation
Authors: Samraj Annie N , Morse Ryan , Krumm Niklas , Pagano Monica B , Hess John R , Tsang Hamilton 
Published: September 2019

Abstract

Introduction
Antibody-mediated hemolysis arising in the face of solid organ transplant can be devastating. Some degree of passenger lymphocyte syndrome is said to occur in up to 10% of ABO mismatched renal transplants, 40% of ABO mismatched liver transplants, and 70% of ABO mismatched heart-lung transplants, a reflection of the number of memory B-cells transplanted with the organ. Passenger lymphocyte syndrome is less common with minor antigens but can still be severe.

Materials and Methods
A series of patients developed immune hemolytic anemia after solid organ transplantation. Conventional serologic testing was performed using tube and solid-phase testing. Molecular testing was performed using gene-chip array.

Results
In patients receiving a minor antigen mismatched organ transplant and multiple allogenic red cell transfusions, serologic methods proved insufficient to resolve the source of minor blood group antibodies that arose in the aftermath of transplant. Genetic testing was able to clearly resolve donor and recipient types.

Conclusions
Passenger lymphocyte syndrome after mismatched organ transplantation is not rare. The mixtures of organ donor, recipient, and other transfused RBCs profoundly limit the usefulness of serologic testing. Genetic assignment of minor blood types to donor and recipient can guide therapy and inform prognosis.
Accuracy of Nanosphere Verigene Gram-Negative Blood Culture (BC-GN) Test for Rapid Detection of Extended-Spectrum Beta-Lactamases (ESBLs) From Positive Blood Cultures
Authors: Otero Dennise , Patros Clay , McElvania Erin , Singh Kamaljit 
Published: September 2019

Abstract

Background
The rapid and accurate detection of ESBL production in Gram-negative rod (GNR) bacteremia is critical as recent data suggest that carbapenem treatment decreases mortality. At the same time, avoiding widespread empiric carbapenem prescribing is an important goal of antimicrobial stewardship teams. The aim of this retrospective review was to determine the accuracy of a nucleic acid–based test, Luminex Verigene BC-GN panel, to detect ESBL-positive GNRs direct from blood cultures.

Methods
The Verigene BC-GN was performed on all first positive GNR blood cultures. In addition, routine antibiotic susceptibility testing was performed on all isolates by the disk-diffusion method and included phenotypic ESBL testing using cefotaxime and ceftazidime with and without clavulanate. Escherichia coli, Klebsiella spp., and Proteus mirabilis–positive blood cultures were identified as ESBL producers through either Verigene or phenotypic disk testing. Positive GNR blood cultures from February 2016 to July 2017 were included for review. The primary objective was to determine the sensitivity and specificity of Verigene for detection of ESBLs. The secondary objective was assessing the percent of community-onset and hospital-acquired ESBL-positive blood cultures.

Results
There were 83 positive blood cultures with ESBL producing GNR included in the primary review. A total of 82 of 83 positive GNR blood cultures were CTX-M gene positive via Verigene (sensitivity 98.8%). All 83 cultures were confirmed as ESBL producers via phenotypic tests. There were no positive Verigene cases with negative phenotypic results. All 68 ESBL E coli–positive cultures were detected by Verigene (100%), 10 ESBL K pneumoniae (100%), and four of the five ESBL P mirabilis–positive cultures (80%). Of the 73 results available for review in the secondary objectives, 68 were community onset (93%) and five were hospital acquired (7%).

Conclusion
The majority of ESBL-positive blood cultures in a low-prevalence setting were due to CTX-M producers. The Luminex Verigene BC-GN was accurate in detecting ESBL-producing Enterobacteriaceae from blood cultures and can be reliably used to guide antimicrobial therapy.