bluuebunny/crossref_metadata_2025_split huggingface dataset:
Examining Causes and Prevention Strategies of Adverse Events in Deceased Hospital Patients: A Retrospective Patient Record Review Study in the Netherlands
Authors: Smits Marleen , Langelaan Maaike , de Groot Janke , Wagner Cordula 
Published: March 2019

Objective
To improve patient safety and possibly prevent mortality from adverse events (AEs) in hospitals, it is important to gain insight in their underlying causes. We aimed to examine root causes and potential prevention strategies of AEs in deceased hospital patients.

Methods
Data on 571 AEs were used from two retrospective patient record review studies of patients who died during hospitalization in the Netherlands. Trained reviewers assessed contributing factors and potential prevention strategies. The results were analyzed together with data on preventability of the AE and the relationship of the AE with the death of the patient.

Results
In 47% of the AEs, patient-related causes were identified, in 35% human causes, in 9% organizational causes, and in 3% technical causes. Preventable AEs were caused by technical, organizational, and human causes (78%, 74%, and 74%, respectively) more often than by patient-related causes (33%). In addition, technical factors caused AEs leading to preventable death (78%) relatively often. Recommended strategies to prevent AEs were quality assurance/peer review, evaluation of safety behavior, improving procedures, and improving information and communication structures.

Conclusions
Human failures played an important role in the causation of AEs in Dutch hospitals, because they occurred frequently and they were frequently the cause of preventable AEs. To a lesser extent, latent organizational and technical factors were identified. Patient-related factors were often identified, but the preventability of the AEs with these causes was low. For future research into causes of AEs, we recommend combining record review with interviewing.
Pathologic Response to Pretransplant Locoregional Therapy is Predictive of Patient Outcome After Liver Transplantation for Hepatocellular Carcinoma
Authors: DiNorcia Joseph , Florman Sander S. , Haydel Brandy , Tabrizian Parissa , Ruiz Richard M. , Klintmalm Goran B. , Senguttuvan Srinath , Lee David D. , Taner C. Burcin , Verna Elizabeth C. , Halazun Karim J. , Hoteit Maarouf , Levine Matthew H. , Chapman William C. , Vachharajani Neeta , Aucejo Federico , Nguyen Mindie H. , Melcher Marc L. , Tevar Amit D. , Humar Abhinav , Mobley Constance , Ghobrial Mark , Nydam Trevor L. , Amundsen Beth , Markmann James F. , Berumen Jennifer , Hemming Alan W. , Langnas Alan N. , Carney Carol A. , Sudan Debra L. , Hong Johnny C. , Kim Joohyun , Zimmerman Michael A. , Rana Abbas , Kueht Michael L. , Jones Christopher M. , Fishbein Thomas M. , Markovic Daniela , Busuttil Ronald W. , Agopian Vatche G. 
Published: March 2019

Objective:
The aim of the study was to determine the rate, predictors, and impact of complete pathologic response (cPR) to pretransplant locoregional therapy (LRT) in a large, multicenter cohort of hepatocellular carcinoma (HCC) patients undergoing liver transplantation (LT).

Background:
LRT is used to mitigate waitlist dropout for patients with HCC awaiting LT. Degree of tumor necrosis found on explant has been associated with recurrence and overall survival, but has not been evaluated in a large, multicenter study.

Methods:
Comparisons were made among patients receiving pre-LT LRT with (n = 802) and without (n = 2637) cPR from the United States Multicenter HCC Transplant Consortium (UMHTC), and multivariable predictors of cPR were identified using logistic regression.

Results:
Of 3439 patients, 802 (23%) had cPR on explant. Compared with patients without cPR, cPR patients were younger; had lower Model for End-stage Liver Disease (MELD) scores, AFP levels, and neutrophil–lymphocyte ratios (NLR); were more likely to have tumors within Milan criteria and fewer LRT treatments; and had significantly lower 1-, 3-, and 5-year incidence of post-LT recurrence (1.3%, 3.5%, and 5.2% vs 6.2%, 13.5%, and 16.4%; P < 0.001) and superior overall survival (92%, 84%, and 75% vs 90%, 78%, and 68%; P < 0.001). Multivariable predictors of cPR included age, sex, liver disease diagnosis, MELD, AFP, NLR, radiographic Milan status, and number of LRT treatments (C-statistic 0.67).

Conclusions:
For LT recipients with HCC receiving pretransplant LRT, achieving cPR portends significantly lower posttransplant recurrence and superior survival. Factors predicting cPR are identified, which may help prioritize patients and guide LRT strategies to optimize posttransplant cancer outcomes.
The First Report of Laparoscopic Pancreaticoduodenectomy for Primary Duodenal Carcinoma in a Patient With Situs Inversus Totalis: Report of a Rare Case
Authors: Guo Cheng-Xiang , Chen Wei , Yao Wei-Yun , Li Guo-Gang , Zhang Qi , Chen Yi-Wen , Pan Yao , Shen Yi-Nan , Liang Ting-Bo , Bai Xue-Li 
Published: March 2019

Background:
Situs inversus (SI) is a rare congenital anomaly characterized by the transposition of thoracic and abdominal viscera. Laparoscopic pancreaticoduodenectomy (LPD) is increasingly used in patients with periampullar and pancreatic carcinomas. For patients with SI, LPD can be more complicated because of reversed anatomy and possible other associated anomalies that have not been expected before surgery.

Case Presentation:
A female patient with SI totalis presented with inappetence, vomiting, and weight loss for 2 months. Imaging modalities and angiography revealed a mass in the periampullary region without obvious vascular abnormalities. The mass was successfully resected via LPD based on an elaborate preoperative plan. The surgical pathology report demonstrated adenocarcinoma of the duodenal papilla. The patient has been followed up for 4 months and no tumor recurrence or long-term complications were observed.

Conclusion:
LPD is technically difficult but feasible in patients with SI.
Evidence for the F200Y (TAC) mutation conferring benzimidazole resistance in a southern USA cattle population of Haemonchus placei spreading from a single emergence
Authors: Chaudhry Umer , Redman E. M. , Kaplan Ray , Yazwinski Thomas , Sargison Neil , Gilleard John S. 
Published: March 2019

AbstractThe benzimidazoles are one of the most important broad-spectrum anthelmintic drug classes for the control of parasitic nematodes of domestic animals and humans. They have been widely used in the livestock sector, particularly in small ruminants for over 40 years. This has resulted in the development and wide spread of resistance in small ruminant gastrointestinal nematode parasite species, including Haemonchus contortus. Recently, resistance to benzimidazole drugs has been reported in Haemonchus placei, but there is relatively little information on its prevalence. It is important to develop a molecular tools to identify resistance mutations in H. placei early in their development in order to understand the emergence and spread. Our previous study demonstrated the F200Y (TAC) mutation at their early stage in 6/9 H. placei populations derived from southern USA, albeit at low frequencies between 2 and 10%. The present study analysis the phylogenetics of the isotype-1 β-tubulin locus to suggest that F200Y (TAC) mutation has been spread from a single emergence in H. placei; likely by the anthroprogenic movement of ruminant livestock in southern USA. Population genetic data of H. placei using a panel of microsatellite markers revealed little genetic sub-structure, consistent with a high level of gene flow in this region. Overall, these results provide clear genetic evidence for the spread of F200Y (TAC) benzimidazoles resistance mutation to multiple different locations from a single emergence in H. placei.
Hierarchical representation of multi-step tasks in multiple-demand and default mode networks
Authors: Wen Tanya , Duncan John , Mitchell Daniel J 
Published: March 2019

AbstractTask episodes consist of sequences of steps that are performed to achieve a goal. We used fMRI to examine neural representation of task identity, component items, and sequential position, focusing on two major cortical systems – the multiple-demand (MD) and default mode networks (DMN). Human participants (20 male, 22 female) learned six tasks each consisting of four steps. Inside the scanner, participants were cued which task to perform and then sequentially identified the target item of each step in the correct order. Univariate time-course analyses indicated that intra-episode progress was tracked by a tonically increasing global response, plus an increasing phasic step response specific to MD regions. Inter-episode boundaries evoked a widespread response at episode onset, plus a marked offset response specific to DMN regions. Representational similarity analysis was used to examine encoding of task identity and component steps. Both networks represented the content and position of individual steps, but the DMN preferentially represented task identity while the MD network preferentially represented step-level information. Thus, although both DMN and MD networks are sensitive to step-level and episode-level information in the context of hierarchical task performance, they exhibit dissociable profiles in terms of both temporal dynamics and representational content. The results suggest collaboration of multiple brain regions in control of multi-step behavior, with MD regions particularly involved in processing the detail of individual steps, and DMN adding representation of broad task context.Significance StatementAchieving one’s goals requires knowing what to do and when. Tasks are typically hierarchical, with smaller steps nested within overarching goals. For effective, flexible behavior, the brain must represent both levels. We contrast response time-courses and information content of two major cortical systems – the multiple-demand (MD) and default mode networks (DMN) – during multi-step task episodes. Both networks are sensitive to step-level and episode-level information, but with dissociable profiles. Intra-episode progress is tracked by tonically increasing global responses, plus MD-specific increasing phasic step responses. Inter-episode boundaries evoke widespread responses at episode onset, plus DMN-specific offset responses. Both networks encode content and position of individual steps, but the DMN and MD networks favor task identity and step-level information respectively.
Neuro-genetic plasticity ofCaenorhabditis elegansbehavioral thermal tolerance
Authors: Stegeman Gregory W. , Medina Denise , Cutter Asher D. , Ryu William S. 
Published: March 2019

AbstractBackgroundAnimal responses to thermal stimuli involve intricate contributions of genetics, neurobiology and physiology, with temperature variation providing a pervasive environmental factor for natural selection. Thermal behavior thus exemplifies a dynamic trait that requires non-trivial phenotypic summaries to appropriately capture the trait in response to a changing environment. To characterize the deterministic and plastic components of thermal responses, we developed a novel micro-droplet assay of nematode behavior that permits information-dense summaries of dynamic behavioral phenotypes as reaction norms in response to increasing temperature (thermal tolerance curves, TTC).ResultsWe found thatC. elegansTTCs shift predictably with rearing conditions and developmental stage, with significant differences between distinct wildtype genetic backgrounds. Moreover, after screening TTCs for 58C. elegansgenetic mutant strains, we determined that genes affecting thermosensation, includingcmk-1andtax-4, potentially play important roles in the behavioral control of locomotion at high temperature, implicating neural decision-making in TTC shape rather than just generalized physiological limits. However, expression of the transient receptor potential ion channel TRPA-1 in the nervous system is not sufficient to rescue rearing-dependent plasticity in TTCs conferred by normal expression of this gene, indicating instead a role for intestinal signaling involving TRPA-1 in the adaptive plasticity of thermal performance.ConclusionsThese results implicate nervous system and non-nervous system contributions to behavior, in addition to basic cellular physiology, as key mediators of evolutionary responses to selection from temperature variation in nature.
Live-cell Imaging Analysis of Antimycin-Type Depsipeptides via Bioorthogonal Stimulated Raman Scattering Microscopy
Authors: Seidel Jeremy , Miao Yupeng , Porterfield William , Cai Wenlong , Zhu Xuejun , Kim Seong-Jong , Hu Fanghao , Bhattarai-Kline Santi , Min Wei , Zhang Wenjun 
Published: March 2019

AbstractSmall-molecule natural products have been an essential source of pharmaceuticals to treat human diseases, but very little is known about their behavior inside dynamic, living human cells. Here, we demonstrate the first structure-activity-distribution study of complex natural products, the anti-cancer antimycin-type depsipeptides, using the emerging bioorthogonal Stimulated Raman Scattering (SRS) Microscopy. Our results show that the intracellular enrichment and distribution of these compounds are driven by their potency and specific protein targets, as well as the lipophilic nature of compounds.
Improving the accuracy of single turnover active fluorometry (STAF) for the estimation of phytoplankton primary productivity (PhytoPP)
Authors: Boatman Tobias G. , Geider Richard J. , Oxborough Kevin 
Published: March 2019

AbstractPhotosystem II (PSII) photochemistry is the ultimate source of reducing power for phytoplankton primary productivity (PhytoPP). Single turnover active chlorophyll fluorometry (STAF) provides a non-intrusive method that has the potential to measure PhytoPP on much wider spatiotemporal scales than is possible with more direct methods such as 14C fixation and O2 evolved through water oxidation. Application of a STAF-derived absorption coefficient for PSII light-harvesting (aLHII) provides a method for estimating PSII photochemical flux on a unit volume basis (JVPII). Within this study, we assess potential errors in the calculation of JVPII arising from sources other than photochemically active PSII complexes (baseline fluorescence) and the package effect. Although our data show that such errors can be significant, we identify fluorescence-based correction procedures that can be used to minimize their impact. For baseline fluorescence, the correction incorporates an assumed consensus PSII photochemical efficiency for dark-adapted material. The error generated by the package effect can be minimized through the ratio of variable fluorescence measured within narrow wavebands centered at 730 nm, where the re-absorption of PSII fluorescence emission is minimal, and at 680 nm, where re-absorption of PSII fluorescence emission is maximal. We conclude that, with incorporation of these corrective steps, STAF can provide a reliable estimate of JVPII and, if used in conjunction with simultaneous satellite measurements of ocean color, could take us significantly closer to achieving the objective of obtaining reliable autonomous estimates of PhytoPP.
Immune and environment-driven gene expression during invasion: An eco-immunological application of RNA-Seq
Authors: Selechnik D , Richardson MF , Shine R , Brown GP , Rollins LA 
Published: March 2019

AbstractHost-pathogen dynamics change rapidly during a biological invasion and are predicted to impose strong selection on immune function. The invader may experience an abrupt reduction in pathogen-mediated selection (‘enemy release’), thereby favoring decreased investment into ‘costly’ immune responses, and the extent of this reduction may depend on factors such as propagule size. Across plants and animals, there is mixed support for this prediction. Pathogens are not the only form of selection imposed on invaders; differences in abiotic environmental conditions between native and introduced ranges are also expected to drive rapid evolution. Here, we assess the expression patterns of immune and environmentally-associated genes in the cane toad (Rhinella marina) across its invasive Australian range. Transcripts encoding mediators of costly immune responses (inflammation, cytotoxicity) showed a curvilinear relationship with invasion history, with highest expression in toads from oldest and newest colonized areas. This pattern is surprising given theoretical expectations of density dynamics in invasive species, and may be because density influences both intraspecific competition and parasite transmission, generating conflicting effects on the strength of immune responses. Alternatively, this expression pattern may be the result of other evolutionary forces, such as spatial sorting and genetic drift, working simultaneously with natural selection. Our findings do not support predictions about immune function based on the enemy release hypothesis, and suggest instead that the effects of enemy release are difficult to isolate in wild populations. Additionally, expression patterns of genes underlying putatively environmentally-associated traits are consistent with previous genetic studies, providing further support that Australian cane toads have adapted to novel abiotic challenges.
Superlets: time-frequency super-resolution using wavelet sets
Authors: Moca Vasile V. , Nagy-Dăbâcan Adriana , Bârzan Harald , Mureşan Raul C. 
Published: March 2019

AbstractTime-frequency analysis is ubiquitous in many fields of science. Due to the Heisenberg-Gabor uncertainty principle, a single measurement cannot estimate precisely the location of a finite oscillation in both time and frequency. Classical spectral estimators, like the short-time Fourier transform (STFT) or the continuous-wavelet transform (CWT) optimize either temporal or frequency resolution, or find a tradeoff that is suboptimal in both dimensions. Following concepts from optical super-resolution, we introduce a new spectral estimator enabling time-frequency super-resolution. Sets of wavelets with increasing bandwidth are combined geometrically in asuperletto maintain the good temporal resolution of wavelets and gain frequency resolution in the upper bands.Superletsoutperform the STFT, CWT, and other super-resolution methods on synthetic data and brain signals recorded in humans and rodents, resolving time-frequency details with unprecedented precision. Importantly,superletscan reveal transient oscillation events that are hidden in the averaged time-frequency spectrum by other methods.
Confidence reports in decision-making with multiple alternatives violate the Bayesian confidence hypothesis
Authors: Li Hsin-Hung , Ma Wei Ji 
Published: March 2019

AbstractDecision confidence reflects our ability to evaluate the quality of decisions and guides subsequent behaviors. Experiments on confidence reports have almost exclusively focused on two-alternative decision-making. In this realm, the leading theory is that confidence reflects the probability that a decision is correct (the posterior probability of the chosen option). There is, however, another possibility, namely that people are less confident if thebest twooptions are closer to each other in posterior probability, regardless of how probable they are inabsoluteterms. This possibility has not previously been considered because in two-alternative decisions, it reduces to the leading theory. Here, we test this alternative theory in a three alternative visual categorization task. We found that confidence reports are best explained by the difference between the posterior probabilities of the best and the next-best options, rather than by the posterior probability of the chosen (best) option alone, or by the overall uncertainty (entropy) of the posterior distribution. Our results upend the leading notion of decision confidence and instead suggest that confidence reflects the observer’s subjective probability that they made the best possible decision.
Transcriptomics supports that pleuropodia of insect embryos function in degradation of the serosal cuticle to enable hatching
Authors: Konopová Barbora , Buchberger Elisa , Crisp Alastair 
Published: March 2019

ABSTRACTPleuropodia are limb-derived vesicular organs that transiently appear on the first abdominal segment of embryos from the majority of insect “orders”. They are missing in the modelDrosophilaand little is known about them. Experiments carried out on orthopteran insects eighty years ago indicated that the pleuropodia secrete a “hatching enzyme” that at the end of embryogenesis digests the serosal cuticle to enable the larva to hatch. This hypothesis contradicts the view that insect cuticle is digested by enzymes produced by the tissue that deposited it. We studied the development of the pleuropodia in embryos of the locustSchistocerca gregaria(Orthoptera) using transmission electron microscopy. RNA-seq was applied to generate a comprehensive embryonic reference transcriptome that was used to study genome-wide gene expression of ten stages of pleuropodia development. We show that the mature and secretion releasing pleuropodia are primarily enriched in transcripts associated with transport functions. They express genes encoding enzymes capable of digesting cuticular protein and chitin. These include the potent cuticulo-lytic Chitinase 5, whose transcript rises just before hatching. The pleuropodia are also enriched in transcripts for immunity-related enzymes, including the Toll signaling pathway, melanization cascade and lysozymes. These data provide transcriptomic evidence that the pleuropodia of orthopterans produce the “hatching enzyme”, whose important component is the Chitinase 5. They also indicate that the organs facilitate epithelial immunity and may function in embryonic immune defense. Based on their gene expression the pleuropodia appear to be an essential part of insect physiology.
Characterization of genes and alleles involved in the control of flowering time in grapevine
Authors: Kamal Nadia , Ochßner Iris , Schwandner Anna , Viehöver Prisca , Hausmann Ludger , Töpfer Reinhard , Weisshaar Bernd , Holtgräwe Daniela 
Published: March 2019

AbstractGrapevine (Vitis vinifera) is one of the most important perennial crop plants in worldwide. Understanding of developmental processes like flowering, which impact quality and quantity of yield in this species is therefore of high interest. This gets even more important when considering some of the expected consequences of climate change. Earlier bud burst and flowering, for example, may result in yield loss due to spring frost. Berry ripening under higher temperatures will impact wine quality. Knowledge of interactions between a genotype or allele combination and the environment can be used for the breeding of genotypes that are better adapted to new climatic conditions. To this end, we have generated a list of more than 500 candidate genes that may play a role in the timing of flowering. The grapevine genome was exploited for flowering time control gene homologs on the basis of functional data from model organisms likeA. thaliana. In a previous study, a mapping population derived from early flowering GF.GA-47-42 and late flowering ‘Villard Blanc’ was analyzed for flowering time QTLs. In a second step we have now established a workflow combining amplicon sequencing and bioinformatics to follow alleles of selected candidate genes in the F1individuals and the parental genotypes. Allele combinations of these genes in individuals of the mapping population were correlated with early or late flowering phenotypes. Specific allele combinations of flowering time candidate genes within and outside of the QTL regions for flowering time on chromosome 1, 4, 14, 17, and 18 were found to be associated with an early flowering phenotype. In addition, expression of many of the flowering candidate genes was analyzed over consecutive stages of bud and inflorescence development indicating functional roles of these genes in the flowering control network.