bluuebunny/crossref_metadata_2025_split huggingface dataset:
OPTN Vascularized Composite Allograft Waiting List: Current Status and Trends in the United States
Authors: Wainright Jennifer L. , Wholley Christopher L. , Cherikh Wida S. , Musick Jennifer M. , Klassen David K. 
Published: May 2018

Background
Vascularized composite allograft (VCA) transplantation is a developing area in the field of transplantation.

Methods
This study used Organ Procurement and Transplantation Network (OPTN) VCA waiting list and transplant data from July 3, 2014 through February 28, 2018, to characterize the OPTN VCA waiting list in terms of composition, removal patterns, waiting time, resulting transplants, and trends over time.

Results
Between implementation of the OPTN VCA waiting list on July 3, 2014 and February 28, 2018, 54 candidates—53.7% were male, 79.6% were white, and 70.4% aged 18 to 44 years—were added to the OPTN VCA waiting list. Of these, 22 received deceased donor VCA transplants (6 bilateral upper limb, 4 unilateral upper limb, 5 craniofacial, 1 scalp, 1 abdominal wall, 1 penile, and 4 uterine), and 6 received living donor uterine transplants. Registrations increased in 2016 after uterine and penile transplants were introduced in the United States, resulting in a large shift in the composition of the VCA waiting list. Waiting times for VCA candidates vary greatly, with some VCA candidates receiving deceased donor transplants quickly and others waiting more than 3 years before transplantation.

Conclusions
The field of VCA transplantation and the composition of the OPTN VCA waiting list are evolving rapidly. Additional research is needed to understand these changes and investigate whether differences in need or differences in access have resulted in the variation seen on the VCA waiting list.
Outcomes of Pediatric ABO-incompatible Living Kidney Transplantations From 2002 to 2015: An Analysis of the Japanese Kidney Transplant Registry
Authors: Hattori Motoshi , Mieno Makiko , Shishido Seiichiro , Aikawa Atsushi , Ushigome Hidetaka , Ohshima Shinichi , Takahashi Kota , Hasegawa Akira 
Published: May 2018

Background
Extensive data have been accumulated for adults who have undergone ABO-incompatible (ABOi)-living kidney transplantation (LKT). In contrast, available published data on pediatric recipients who underwent ABOi-LKT from the early to middle 2000s is very limited. Thus, pediatric ABOi-LKT has remained relatively rare, and there is a lack of large, multicenter data.

Methods
We analyzed data from the Japanese Kidney Transplant Registry to clarify the patient and graft outcomes of pediatric recipients who underwent ABOi-LKT from 2002 to 2015. A total of 102 ABOi and 788 ABO-compatible (ABOc) recipients were identified in this study. All recipients had received basiliximab and a triple immunosuppressive protocol comprising calcineurin inhibitors, mycophenolate mofetil, and steroids. The ABOi recipients also received preconditioning therapies including B-cell depletion by a splenectomy or rituximab treatment and therapeutic apheresis.

Results
Death rates for ABOi and ABOc recipients were 0.17 versus 0.17 deaths per 100 patient-years. Graft loss rates for ABOi and ABOc recipients were 1.58 versus 1.45 events per 100 patient-years. No particular causes of death or graft loss predominantly affected ABOi or ABOc recipients.

Conclusions
The results of this registry analysis suggest that pediatric ABOi-LKT can be performed efficiently. Although further studies are clearly required to perform pediatric ABOi-LKT more safely and less invasively, ABOi-LKT is now an acceptable treatment for pediatric patients with end-stage renal disease.
Donor-specific Antibodies, Immunoglobulin-free Light Chains, and BAFF Levels in Relation to Risk of Late-onset PTLD in Liver Recipients
Authors: Engels Eric A. , Jennings Linda W. , Everly Matthew J. , Landgren Ola , Murata Kazunori , Yanik Elizabeth L. , Pfeiffer Ruth M. , Onaca Nicholas , Klintmalm Goran B. 
Published: May 2018

Background
Posttransplant lymphoproliferative disorder (PTLD) is a neoplastic complication of transplantation, with early cases largely due to immunosuppression and primary Epstein-Barr virus infection. Etiology may differ for later-onset cases, but the contributions of immunosuppression, immune reactivity to the donor organ, and chronic B cell activation are uncertain.

Methods
We conducted a case-control study of late-onset PTLD (diagnosed >1 year posttransplant) in a cohort of liver recipients. We assessed serum samples (obtained >6 months before diagnosis in cases) from N = 60 cases and N = 166 matched controls for donor-specific antibodies (DSAs, evaluable for N = 221 subjects), immunoglobulin kappa and lambda free light chains (FLCs, N = 137), and B cell activating factor (BAFF, N = 226). Conditional or unconditional logistic regression was used to calculate adjusted odds ratios (aORs).

Results
Circulating DSAs were less common in PTLD cases than controls (18% vs 30%), although this difference was borderline significant (aOR, 0.51; 95% confidence interval [CI], 0.24-1.10; P = 0.09). Donor-specific antibodies against class II HLA antigens predominated and likewise showed a borderline inverse association with PTLD (aOR, 0.58; 95% CI, 0.27-1.24). The FLC levels were less frequently abnormal in cases than controls, but measurements were available for only a subset and confidence intervals were wide (elevated kappa: aOR, 0.57; 95% CI, 0.15-2.12; P = 0.40; elevated lambda: aOR, 0.68; 95% CI, 0.30-1.50; P = 0.34). B cell–activating factor levels were not associated with PTLD.

Conclusions
Our results suggest that circulating DSAs are associated with decreased risk of late-onset PTLD. Because DSAs may develop in the setting of underimmunosuppression, the inverse association with DSAs supports a role for immunosuppression in the etiology of late-onset PTLD.
Early Steroid Withdrawal Compared With Standard Immunosuppression in Kidney Transplantation - Interim Analysis of the Amsterdam-Leiden-Groningen Randomized Controlled Trial
Authors: van Sandwijk Marit S. , de Vries Aiko P.J. , Bakker Stephan J.L. , ten Berge Ineke J.M. , Berger Stefan P. , Bouatou Yassine R. , de Fijter Johan W. , Florquin Sandrine , Homan van der Heide Jaap J. , Idu Mirza M. , Krikke Christina , van der Pant Karlijn A.M.I. , Reinders Marlies E. , Ringers Jan , van der Weerd Neelke C. , Bemelman Frederike J. , Sanders Jan-Stephan S. 
Published: May 2018

BACKGROUND
The optimal immunosuppressive regimen in kidney transplant recipients, delivering maximum efficacy with minimal toxicity, is unknown.

METHODS
The Amsterdam, LEiden, GROningen trial is a randomized, multicenter, investigator-driven, noninferiority, open-label trial in 305 kidney transplant recipients, in which 2 immunosuppression minimization strategies—one consisting of early steroid withdrawal, the other of tacrolimus minimization 6 months after transplantation—were compared with standard immunosuppression with basiliximab, corticosteroids, tacrolimus, and mycophenolic acid. The primary endpoint was kidney function. Secondary endpoints included death, primary nonfunction, graft failure, rejection, discontinuation of study medication, and a combined endpoint of treatment failure. An interim analysis was scheduled at 6 months, that is, just before tacrolimus minimization.

RESULTS
This interim analysis revealed no significant differences in Modification of Diet in Renal Disease between the early steroid withdrawal group and the standard immunosuppression groups (43.2 mL/min per 1.73 m2 vs 45.0 mL/min per 1.73 m2, P = 0.408). There were also no significant differences in the secondary endpoints of death (1.0% vs 1.5%; P = 0.737), primary nonfunction (4.1% vs 1.5%, P = 0.159), graft failure (3.1% vs 1.5%, P = 0.370), rejection (18.6% vs 13.6%, P = 0.289), and discontinuation of study medication (19.6% vs 12.6%, P = 0.348). Treatment failure, defined as a composite endpoint of these individual secondary endpoints, was more common in the early steroid withdrawal group (P = 0.027), but this group had fewer serious adverse events and a more favorable cardiovascular risk profile.

CONCLUSIONS
Based on these interim results, early steroid withdrawal is a safe short-term immunosuppressive strategy. Long-term outcomes, including a comparison with tacrolimus minimization after 6 months, will be reported in the final 2-year analysis.
Attentional Bias Modification is associated with fMRI Response towards Negative Stimuli in Residual Depression: A Randomized Controlled Trial
Authors: Hilland E. , Landrø N.I. , Harmer C. J. , Browning M. , Maglanoc L. A. , Jonassen R. 
Published: May 2018

AbstractBackgroundModification of attentional biases (ABM) may lead to more adaptive emotion perception and emotion regulation. Understanding the neural basis of these effects may lead to greater precision for future treatment development. Task-related fMRI following ABM training has so far not been investigated in depression. The main aim of the RCT was to explore differences in brain activity after ABM training in response to emotional stimuli.MethodsA total of 134 previously depressed individuals were randomized into 14 days of ABM- or a placebo training followed by an fMRI emotion regulation task. Depression symptoms and subjective ratings of perceived negativity during fMRI was examined between the training groups. Brain activation was explored within predefined areas (SVC) and across the whole brain. Activation in areas associated with changes in attentional biases (AB) and degree of depression was explored.ResultsThe ABM group showed reduced activation within the amygdala and within the anterior cingulate cortex (ACC) when passively viewing negative images compared to the placebo group. No group differences were found within predefined SVC’s associated with emotion regulation strategies. Response within the temporal cortices was associated with degree of change in AB and with degree of depressive symptoms in ABM versus placebo.LimitationsThe findings should be replicated in other samples of depressed patients and in studies using designs that allow analyses of within-group variability from baseline to follow-up.ConclusionsABM training has an effect on brain function within circuitry associated with emotional appraisal and the generation of affective states.Clinicaltrials.gov identifier: NCT02931487
Cold Shock Fail to Restrain Pre-formed Bacterial Biofilm
Authors: Yu Wenying , Han Qiao , Song Xueying , Fu Jiaojiao , Liu Haiquan , Guo Zhuoran , Malakar Pradeep K , Pan Yingjie , Zhao Yong 
Published: May 2018

ABSTRACTEnvironmental temperature fluctuation has great impact on the formation of bacterial biofilm, while little information is available for assessing the influence of sharp temperature shifts on the fate of pre-formed biofilm. In this study, experimental evidence is firstly explored on the response ofVibrio parahaemolyticuspre-formed biofilm under cold shock (4 °C and 10 °C). Surprisingly, biofilm biomass ofV. parahaemolyticussignificantly increased during the period of cold shock as revealed by crystal violet staining. Polysaccharides and proteins contents in extracellular polymeric substances were gradually enhanced after cold shocks and exhibited high consistency. RT-qPCR demonstrated the expression of flagella and virulence-related genes were up-regulated. Most of QS and T3SS genes were slightly up-regulated, and three T3SS genes (vcrD1,vcrD2βandvopD1) were down-regulated. Furthermore, the biofilm structure ofV parahaemolyticushave been analyzed by Confocal laser scanning microscopy (CLSM), which sharply changed under cold shocks. The correlation analysis further displayed the significant correlation (P < 0.01) among biofilm structure parameters, and weak correlation (P < 0.05) between biofilm related genes and biofilm structure parameters. In conclusion, our results novel discovered thatV. parahaemolyticusbiofilm related genes were actively expressed and biofilm biomass was continuously increased, biofilm structure was tremendously changed after cold shock. This study underscored the risk that biofilm cells had the ability to adapt to low temperature shift.IMPORTANCEBiofilms are widespread in natural environments, especially on the surface of food and medical biomaterials, which threaten human safety from persistent infections. Previous studies simply focused on biofilm formation of microorganisms under steady state, however, the actual environment frequently fluctuated.V. parahaemolyticusis a widely distributed foodborne pathogen, temperature play a great role in its survival. Researchers generally assume that cold environment can restrain biofilm formation and bacterial activity. This study explored the effects ofV. parahaemolyticusbiofilm upon a shift from 37 °C to 4 °C or 10 °C from two aspects. On the one hand, the changes of biofilm biomass and EPS contents, the expression of biofilm related genes directly described that pre-formed bacterial biofilm could not be controlled efficiently in cold environment. On the other hand, the CLSM images revealed biofilm morphological structure change, the correlation analysis showed inner relationship among biofilm structure parameters and biofilm related genes. These results suggested that cold shock fail to restrain pre-formed bacterial biofilm, therefore be a potential risk in nature environment.
zetadiv: an R package for computing compositional change across multiple sites, assemblages or cases
Authors: Latombe Guillaume , McGeoch Melodie A. , Nipperess David A. , Hui Cang 
Published: May 2018

AbstractSpatial variation in compositional diversity, or species turnover, is necessary for capturing the components of heterogeneity that constitute biodiversity. However, no incidence-based metric of pairwise species turnover can calculate all components of diversity partitioning. Zeta (ζ) diversity, the mean number of species shared by any given number of sites or assemblages, captures all diversity components produced by assemblage partitioning. zetadiv is an R package for analysing and measuring compositional change for occurrence data using zeta diversity. Four types of analyses are performed on bird composition data in Australia: (i) decline in zeta diversity; (ii) distance decay; (iii) multi-site generalised dissimilarity modelling; and (iv) hierarchical scaling. Some analyses, such as the zeta decline, are specific to zeta diversity, whereas others, such as distance decay, are commonly applied to beta diversity, and have been adapted using zeta diversity to differentiate the contribution of common and rare species to compositional change.HighlightsAn R package to analyse compositional change using zeta diversity is presented.Zeta diversity is the mean number of species shared by any number of assemblagesZeta diversity captures all diversity components produced by assemblage partitioningAnalyses relate zeta diversity to space, environment and spatial scaleAnalyses differentiate the contribution of rare and common species to biodiversity
Radiographic evaluation of subcutaneously injected, water-soluble, iodinated contrast for lymphography
Authors: Lee Christopher E. , Matz Brad M. , Cole Robert C. , Boothe Harry W. , Tillson D Michael 
Published: May 2018

AbstractSentinel lymph node (SLN) mapping is common in many types of human cancers, and is gaining utility in veterinary medicine. There are currently many different methods described in veterinary medicine for pre-operative SLN mapping, however, most of these are restricted to referral institutions due to cost and need for specialized equipment. The purpose of this prospective, pilot study was to evaluate the feasibility of radiographic evaluation of water-soluble, iodinated contrast (WIC) injected subcutaneously for lymphography in dogs. Eight dogs were injected with 1-2 milliliters of WIC into the subcutaneous tissues overlying the tarsus in 4 separate locations mimicking a circumferential, peri-tumoral injection. Radiographs were taken at select time points up to 50 minutes. Image sequences were evaluated by a single, board-certified radiologist. All 8 dogs had visible contrast-enhancing lymphatic channels. Median time to lymphatic enhancement was immediately post-injection. Seven dogs (88%) had 8 contrast enhancing lymph nodes (7 popliteal and 1 superficial inguinal). Median time to lymph node enhancement was 20 minutes. In this study, the plantar aspect of the pes drained to the superficial inguinal lymph node, and the dorsal aspect of the pes drained to the popliteal lymph node. Subcutaneously-injected WIC was readily identifiable in the lymphatic channels and draining lymph node(s). Subcutaneously injected WIC may offer a practical alternative to previously described pre-operative methods of SLN mapping. Additionally, one cannot assume that the popliteal lymph node alone, drains the distal pelvic limb.
Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy
Authors: Venkatesan Aravind , Tagny Gildas , El Hassouni Nordine , Chentli Imene , Guignon Valentin , Jonquet Clement , Ruiz Manuel , Larmande Pierre 
Published: May 2018

AbstractRecent advances in high-throughput technologies have resulted in a tremendous increase in the amount of omics data produced in plant science. This increase, in conjunction with the heterogeneity and variability of the data, presents a major challenge to adopt an integrative research approach. We are facing an urgent need to effectively integrate and assimilate complementary datasets to understand the biological system as a whole. The Semantic Web offers technologies for the integration of heterogeneous data and their transformation into explicit knowledge thanks to ontologies. We have developed the Agronomic Linked Data (AgroLD – www.agrold.org), a knowledge-based system relying on Semantic Web technologies and exploiting standard domain ontologies, to integrate data about plant species of high interest for the plant science community e.g., rice, wheat, arabidopsis. We present some integration results of the project, which initially focused on genomics, proteomics and phenomics. AgroLD is now an RDF (Resource Description Format) knowledge base of 100M triples created by annotating and integrating more than 50 datasets coming from 10 data sources –such as Gramene.org and TropGeneDB– with 10 ontologies –such as the Gene Ontology and Plant Trait Ontology. Our evaluation results show users appreciate the multiple query modes which support different use cases. AgroLD’s objective is to offer a domain specific knowledge platform to solve complex biological and agronomical questions related to the implication of genes/proteins in, for instances, plant disease resistance or high yield traits. We expect the resolution of these questions to facilitate the formulation of new scientific hypotheses to be validated with a knowledge-oriented approach.
Carbonic anhydrase II microcrystals suitable for XFEL studies
Authors: Lomelino Carrie L. , Kim Jin Kyun , Lee Cheol , Lim Seon Woo , Andring Jacob T. , Mahon Brian P. , Chung Moses , Kim Chae Un , McKenna Robert 
Published: May 2018

Recent advances in X-ray free-electron laser (XFEL) sources have permitted the study of protein dynamics. Femtosecond X-ray pulses have allowed the visualization of intermediate states in enzyme catalysis. In this study, the growth of carbonic anhydrase II microcrystals (40–80 µm in length) suitable for the collection of XFEL diffraction data at the Pohang Accelerator Laboratory is demonstrated. The crystals diffracted to 1.7 Å resolution and were indexed in space group P21, with unit-cell parameters a = 42.2, b = 41.2, c = 72.0 Å, β = 104.2°. These preliminary results provide the necessary framework for time-resolved experiments to study carbonic anhydrase catalysis at XFEL beamlines.
Initiating and maintaining a recovery process – experiences of persons with dual diagnosis
Authors: Skogens Lisa , von Greiff Ninive , Topor Alain 
Published: May 2018

Purpose
The purpose of this paper is to investigate the internal and social factors that persons with experience from severe mental illness and alcohol and other drugs problems, and who have received treatment for these problems, describe as important for initiating and maintaining a recovery process.

Design/methodology/approach
In total, 40 persons were interviewed and asked to describe factors they perceived as important for initiating and maintaining recovery. The software Nvivo was used to categorise data in internal and social factors with subcategories.

Findings
There is significant variation in how recovery emerged but involved in general having a proper social situation and finding meaning in life. Initially, the majority had a marginalised situation with need of assistance with housing, employment, financial and social support.

Research limitations/implications
The change process in the investigated group is interpreted as related to individual resources rather than belonging to a group defined as having “double trouble”.

Practical implications
The study implies that in addition to professional help to handle diagnosed problems, the group in focus also need support and interventions that address individual complex needs.

Social implications
Supporting activities/peer support seem to be important for those lacking support from family. At the same time, it is important to recognise the risk of being forced into a recovery identity which might lead to worsening the situation for those who do not fit into this.

Originality/value
By using the same design as in previous studies, comparisons with other groups are possible while still keeping the qualitative meaning of the investigated factors.
Thirty years of the Academic Journal (ARLA)
Authors: Ogliastri Enrique , Pombo Carlos , Salgado Elvira 
Published: May 2018

Purpose
The purpose of this paper is to introduce the anniversary issue marking 30 years of academic publication.

Design/methodology/approach
This anniversary issue contains 12 articles from 11 countries and 17 academic institutions which present literature reviews, meta-analyses, and novel studies. It also contains testimonials about the history of the journal from Enrique Ogliastri (Editor and/or Director between 1998 and 2018), Elvira Salgado (Editor between 2002 and 2013), and Carlos Pombo (Chief Editor, 2013 to the present).

Findings
The history of the journal may be divided into five stages: first, the foundation at the Universidad de Chile (1988-1998); second, the move to the Universidad de los Andes (Bogotá) and the preparation of a proposal to the Institute of Scientific Information (ISI) for inclusion among the scientific journals of the world (1999-2004); third, a period of consolidation in Latin America (2004-2007); fourth, the acceptance of the journal in ISI and the development of an electronic platform with free access to the journal (2008-2013); and fifth, the entry of the Emerald group as editorial partner (2013-2018).

Originality/value
The 12 articles present literature reviews, meta-analyzes, and novel studies.