bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of electrical stimulation used in the pulse trawl fishery for common sole on internal injuries in sandeels
Authors: Schram Edward , Molenaar Pieke , Soetaert Maarten , Burggraaf Dirk , Boute Pim G , Lankheet Martin J , Rijnsdorp Adriaan D 
Published: May 2022

Abstract
Electric stimulation was used in the North Sea beam trawl fishery for common sole to reduce its environmental impact. Because electrical stimulation may cause internal injuries in fish, a laboratory experiment was conducted to study the effect of pulse exposure on lesser sandeel (Ammodytes tobianus) and greater sandeel (Hyperoplus lanceolatus), important mid-trophic species in the North Sea ecosystem. We exposed 244 sandeels between two electrodes to a pulsed bipolar current for 2 s in an experimental cage with 5 cm sediment; 221 control fish were handled similarly but not exposed. The occurrence of spinal injuries and internal haemorrhages were scored using X-radiography and dissection. None of the sandeels exposed to a field strength of up to 600 V m–1 showed spinal injury or haemorrhage. Equal numbers of minor spinal abnormalities were found in exposed and control fish. In the absence of spinal injuries, we estimated by bootstrapping the field strength below which spinal injuries are unlikely to occur, i.e. the lower limit threshold, and the corresponding limit dose–response relationship between field strength and injury probability. We conclude that it is unlikely that pulse trawl fishery will have an ecologically significant adverse effect on the population abundance of sandeels, because of the low probabilities of exposure and injury.
Impact of Age on Clinical Outcomes and Efficacy of Adjuvant Dual Anti-HER2 Targeted Therapy
Authors: Lambertini Matteo , Fielding Shona , Loibl Sibylle , Janni Wolfgang , Clark Emma , Franzoi Maria Alice , Fumagalli Debora , Caballero Carmela , Arecco Luca , Salomoni Sharon , Ponde Noam F , Poggio Francesca , Kim Hee Jeong , Villarreal-Garza Cynthia , Pagani Olivia , Paluch-Shimon Shani , Ballestrero Alberto , Del Mastro Lucia , Piccart Martine , Bines Jose , Partridge Ann H , de Azambuja Evandro 
Published: May 2022

AbstractBackgroundYoung age at breast cancer (BC) diagnosis has historically been a rationale for overtreatment. Limited data with short follow-up exist on the prognostic value of age at diagnosis in HER2-positive BC and the benefit of anti-HER2 therapy in young patients.MethodsAPHINITY (NCT01358877) is an international, placebo-controlled, double-blind randomized phase III trial in HER2-positive early BC patients investigating the addition of pertuzumab to adjuvant chemotherapy plus trastuzumab. The prognostic and predictive value of age on invasive disease-free survival (IDFS) as continuous and dichotomous variable (aged 40 years or younger and older than 40 years) was assessed. A subpopulation treatment effect pattern plot analysis was conducted to illustrate possible treatment-effect heterogeneity based on age as a continuous factor.ResultsOf 4804 included patients, 768 (16.0%) were aged 40 years or younger at enrollment. Median follow-up was 74 (interquartile range = 62-75) months. Young age was not prognostic either as dichotomous (hazard ratio [HR] = 1.06, 95% confidence interval [CI] = 0.84 to 1.33) or continuous (HR = 1.00, 95% CI = 1.00 to 1.01) variable. Lack of prognostic effect of age was observed irrespective of hormone receptor status and treatment arm. No statistically significant interaction was observed between age and pertuzumab effect (Pinteraction = 0.61). Adding pertuzumab improved IDFS for patients in the young (HR = 0.86, 95% CI = 0.56 to 1.32) and older (HR = 0.75, 95% CI = 0.62 to 0.92) cohorts. Similar results were observed irrespective of hormone receptor status. Subpopulation treatment effect pattern plot analysis confirmed the benefit of pertuzumab in 6-year IDFS across age subpopulations.ConclusionsIn patients with HER2-positive early BC treated with modern anticancer therapies, young age did not demonstrate either prognostic or predictive value, irrespective of hormone receptor status.
The Sense and Nonsense of Antimicrobial Susceptibility Testing in Cystic Fibrosis
Authors: LiPuma John J 
Published: May 2022

Abstract
Antimicrobial susceptibility testing (AST) has been used to guide therapy of airway infection in persons with cystic fibrosis (CF) for decades. However, evidence that AST adds benefit to treatment outcomes in CF is lacking. In fact, the routine use of AST has potential to exacerbate inappropriate antibiotic use. Several features of airway infection in CF contribute to the limitations of AST in predicting treatment outcomes, providing rationale for abandoning this practice altogether. Other features of CF infection suggest, however, that select use of AST can provide worthwhile guidance to antibiotic selection.
Isolated echinococcal infection of the spleen: a rare case report
Authors: Sotirios Botaitis , Savas Deftereos , Maria-Eleni Zachou , Stauros Vasileiadis , Sempachedin Perente 
Published: May 2022

Abstract
Echinococciasis is a zoonotic infection observed in almost every anatomic location in the body. The liver and lungs are the most frequent sites of infection. However, spleen involvement is rare, and isolated splenic hydatid disease is even less common. Herein, we report a case of isolated splenic hydatid cyst without any tissue involvement that was treated with the classical surgical approach.
Evolutionary history of the grass gynoecium
Authors: Sokoloff Dmitry D , Fomichev Constantin I , Rudall Paula J , Macfarlane Terry D , Remizowa Margarita V 
Published: May 2022

AbstractThe grass family (Poaceae) includes cereal crops that provide a key food source for the human population. The food industry uses the starch deposited in the cereal grain, which develops directly from the gynoecium. Morphological interpretation of the grass gynoecium remains controversial. We re-examine earlier hypotheses and studies of morphology and development in the context of more recent analyses of grass phylogenetics and developmental genetics. Taken in isolation, data on gynoecium development in bistigmatic grasses do not contradict its interpretation as a solitary ascidiate carpel. Nevertheless, in the context of other data, this interpretation is untenable. Broad comparative analysis in a modern phylogenetic context clearly demonstrates that the grass gynoecium is pseudomonomerous. A bistigmatic grass gynoecium has two sterile carpels, each producing a stigma, and a fertile carpel that lacks a stigma. To date, studies of grass developmental genetics and developmental morphology have failed to fully demonstrate the composite nature of the grass gynoecium be­cause its complex evolutionary history is hidden by extreme organ integration. It is problematic to interpret the gynoecium of grasses in terms of normal angiosperm gynoecium typology. Even the concept of a carpel becomes misleading in grasses; instead, we recommend the term pistil for descriptive purposes.
The Gaia-ESO survey: Constraining evolutionary models and ages for young low mass stars with measurements of lithium depletion and rotation
Authors: Binks A S , Jeffries R D , Sacco G G , Jackson R J , Cao L , Bayo A , Bergemann M , Bonito R , Gilmore G , Gonneau A , Jiminéz-Esteban F , Morbidelli L , Randich S , Roccatagliata V , Smiljanic R , Zaggia S 
Published: May 2022

Abstract
A growing disquiet has emerged in recent years that standard stellar models are at odds with observations of the colour-magnitude diagrams (CMDs) and lithium depletion patterns of pre main sequence (PMS) stars in clusters. In this work we select 1,246 high probability K/M-type constituent members of 5 young open clusters (5–125 Myr) in the Gaia-ESO Survey to test a series of models that use standard input physics and others that incorporate surface magnetic fields or cool starspots. We find that: standard models provide systematically under-luminous isochrones for low-mass stars in the CMD and fail to predict Li-depletion of the right strength at the right colour; magnetic models provide better CMD fits with isochrones that are ∼1.5 − 2 times older, and provide better matches to Li depletion patterns. We investigate how rotation periods, most of which are determined here for the first time from Transiting Exoplanet Survey Satellite data, correlate with CMD position and Li. Among the K-stars in the older clusters we find the brightest and least Li-depleted are the fastest rotators, demonstrating the classic ‘Li-rotation connection’ for the first time at ∼35 Myr in NGC 2547, and finding some evidence that it exists in the early M-stars of NGC 2264 at &lt;10 Myr. However, the wide dispersion in Li depletion observed in fully-convective M-dwarfs in the γ Vel cluster at ∼20 Myr appears not to be correlated with rotation and is challenging to explain without a very large (&gt;10 Myr) age spread.
PhyloCloud: an online platform for making sense of phylogenomic data
Authors: Deng Ziqi , Botas Jorge , Cantalapiedra Carlos P , Hernández-Plaza Ana , Burguet-Castell Jordi , Huerta-Cepas Jaime 
Published: May 2022

Abstract
Phylogenomics data have grown exponentially over the last decades. It is currently common for genome-wide projects to generate hundreds or even thousands of phylogenetic trees and multiple sequence alignments, which may also be very large in size. However, the analysis and interpretation of such data still depends on custom bioinformatic and visualisation workflows that are largely unattainable for non-expert users. Here, we present PhyloCloud, an online platform aimed at hosting, indexing and exploring large phylogenetic tree collections, providing also seamless access to common analyses and operations, such as node annotation, searching, topology editing, automatic tree rooting, orthology detection and more. In addition, PhyloCloud provides quick access to tools that allow users to build their own phylogenies using fast predefined workflows, graphically compare tree topologies, or query taxonomic databases such as NBCI or GTDB. Finally, PhyloCloud offers a novel tree visualisation system based on ETE Toolkit v4.0, which can be used to explore very large trees and enhance them with custom annotations and multiple sequence alignments. The platform allows for sharing tree collections and specific tree views via private links, or make them fully public, serving also as a repository of phylogenomic data. PhyloCloud is available at https://phylocloud.cgmlab.org
GEOexplorer: a webserver for gene expression analysis and visualisation
Authors: Hunt Guy P , Grassi Luigi , Henkin Rafael , Smeraldi Fabrizio , Spargo Thomas P , Kabiljo Renata , Koks Sulev , Ibrahim Zina , Dobson Richard J B , Al-Chalabi Ammar , Barnes Michael R , Iacoangeli Alfredo 
Published: May 2022

Abstract
Gene Expression Omnibus (GEO) is a database repository hosting a substantial proportion of publicly available high throughput gene expression data. Gene expression analysis is a powerful tool to gain insight into the mechanisms and processes underlying the biological and phenotypic differences between sample groups. Despite the wide availability of gene expression datasets, their access, analysis, and integration are not trivial and require specific expertise and programming proficiency. We developed the GEOexplorer webserver to allow scientists to access, integrate and analyse gene expression datasets without requiring programming proficiency. Via its user-friendly graphic interface, users can easily apply GEOexplorer to perform interactive and reproducible gene expression analysis of microarray and RNA-seq datasets, while producing a wealth of interactive visualisations to facilitate data exploration and interpretation, and generating a range of publication ready figures. The webserver allows users to search and retrieve datasets from GEO as well as to upload user-generated data and combine and harmonise two datasets to perform joint analyses. GEOexplorer, available at https://geoexplorer.rosalind.kcl.ac.uk, provides a solution for performing interactive and reproducible analyses of microarray and RNA-seq gene expression data, empowering life scientists to perform exploratory data analysis and differential gene expression analysis on-the-fly without informatics proficiency.
Behaviour within a Clinical Trial and Implications for Mammography Guidelines
Authors: Kowalski Amanda E 
Published: May 2022

Abstract
Mammography guidelines have weakened in response to evidence that mammograms diagnose breast cancers that would never eventually cause symptoms, a phenomenon called “overdiagnosis.” Given concerns about overdiagnosis, instead of recommending mammograms, US guidelines encourage women aged 40–49 to get them as they see fit. To assess whether these guidelines target women effectively, I propose an approach that examines mammography behaviour within an influential clinical trial that followed participants long enough to find overdiagnosis. I find that women who are more likely to receive mammograms are healthier and have higher socioeconomic status. More importantly, I find that the 20-year level of overdiagnosis is at least 3.5 times higher among women who are most likely to receive mammograms. At least 36$\%$ of their cancers are overdiagnosed. These findings imply that US guidelines encourage mammograms among healthier women who are more likely to be overdiagnosed by them. Guidelines in other countries do not.
Can transparency undermine peer review? A simulation model of scientist behavior under open peer review
Authors: Bianchi Federico , Squazzoni Flaminio 
Published: May 2022

Abstract
Transparency and accountability are keywords in corporate business, politics, and science. As part of the open science movement, many journals have started to adopt forms of open peer review beyond the closed (single- or double-blind) standard model. However, there is contrasting evidence on the impact of these innovations on the quality of peer review. Furthermore, their long-term consequences on scientists’ cooperation and competition are difficult to assess empirically. This paper aims to fill this gap by presenting an agent-based model that simulates competition and status dynamics between scholars in an artificial academic system. The results would suggest that if referees are sensitive to competition and status, the transparency achieved by open peer review could backfire on the quality of the process. Although only abstract and hypothetical, our findings suggest the importance of multidimensional values of peer review and the anonymity and confidentiality of the process.
Distribution and Diversity of Prunus Necrotic Ringspot Virus, Prune Dwarf Virus, and Peach Latent Mosaic Viroid in Wild Prunus spp. in South Carolina and Georgia
Authors: Rodriguez Bonilla Fabian , Cieniewicz Elizabeth 
Published: May 2022

Prunus-infecting ilarviruses and viroids are important pathogens in southeastern U.S. peach production. To identify potential sources of inoculum, we conducted a survey for two ilarviruses, Prunus necrotic ringspot virus (PNRSV) and prune dwarf virus (PDV), and a viroid, peach latent mosaic viroid (PLMVd), all suggested to be pollen transmissible, in wild Prunus spp . in South Carolina and Georgia. PNRSV was detected in 12% (14/117) of wild Prunus spp., mostly in wild black cherry ( Prunus serotina), with one PNRSV isolate detected in Carolina cherry laurel ( P. caroliniana). PDV and PLMVd were not detected in wild Prunus spp. in this survey. No significant relationship was observed between virus/viroid infection and tree age in P. serotina. Sequence analysis of the gene encoding the PNRSV coat protein from isolates recovered from wild Prunus spp. revealed clustering of South Carolina and Georgia isolates with reference isolate ‘PE5’, an isolate obtained from peach ( P. persica) in the United States. Together, these results suggest that wild Prunus spp. have the potential to serve as inoculum sources for pollen transmissible viruses near orchards. However, the extent of actual virus ingress into orchards from wild Prunus spp. requires further investigation. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Novel Polyanionic Tracts Improve Expression of a TPP1:K16ApoE Chimera
Authors: Modak Anurag , Banach‐Petrosky Whitney , Sleat David E. , Lobel Peter 
Published: May 2022

BackgroundLow expression of highly‐charged recombinant proteins remains a critical challenge in developing protein‐based therapeutics. It has been shown that inclusion of a polyanionic tract (PAT) may improve expression through inter‐ and intramolecular interactions. We previously developed a chimeric construct consisting of tripeptidyl‐peptidase 1 (TPP1), a glycine‐serine linker ([GS]5), a glycine‐aspartate PAT ([GD3]3), and a basic cell‐penetrating peptide K16ApoE as a potential therapeutic agent for late‐infantile neuronal ceroid lipofuscinosis. While TPP1‐(GS)5‐(GD3)3‐(GS)5‐K16ApoE was expressed efficiently, it was cleaved at the PAT. We therefore sought to design novel PATs that improve expression of the full‐length chimera.MethodsTPP1:K16ApoE chimeric proteins were synthesized to contain tri‐glutamate sequences instead of tri‐aspartate sequences in the original (GD3)3PAT. All seven possible combinations of substitutions were engineered: (GE3)3, (GE3)‐(GD3)2, (GD3)‐(GE3)‐(GD3), (GD3)2‐(GE3), (GE3)2‐(GD3), (GE3)‐(GD3)‐(GE3), or (GD3)‐(GE3)2. Chimeric proteins were expressed in Chinese hamster ovary (CHO) cells and media samples were assayed for TPP1 activity. Activity was normalized to a wild‐type (unmodified) TPP1 positive control expressed in CHO cells. The identity of each construct was verified using SDS‐PAGE and mass spectrometry. Welch’s ANOVA test was used to determine expressional differences between TPP1‐(GS)5‐K16ApoE and PAT‐modified chimeras and the resulting p‐values were adjusted for multiple comparisons using Dunnett’s T3 multiple comparison test.ResultsSeven constructs were synthesized, corresponding to each of the aforementioned tri‐glutamate‐substituted PATs, following the general format of TPP1‐(GS)5‐(PAT)‐(GS)5‐K16ApoE. All chimeras expressed successfully as full‐length constructs (Figure 1). No TPP1 activity was detected in the media of untransfected CHO cells. TPP1‐(GS)5‐K16ApoE was previously determined to express at 1.4±1.0% of unmodified TPP1. Of these chimeras with novel PATs, TPP1‐(GS)5‐(GE3)‐(GD3)2‐(GS)5‐K16ApoE [mean ± standard error: 7.3±1.7%, p=0.0040] and TPP1‐(GS)5‐(GE3)2‐(GD3)‐(GS)5‐K16ApoE [5.8±3.1%, p=0.0397] exhibited significantly increased expression relative to TPP1‐(GS)5‐K16ApoE at the 0.05 level of significance.ConclusionAlteration of the a priori (GD3)3 PAT sequence by varying the aspartate and glutamate content was sufficient to prevent cleavage of the resulting TPP1:K16ApoE chimeras. However, only the (GE3)‐(GD3)2 and (GE3)2‐(GD3) PATs yielded a 5‐fold and a 4‐fold, respectively, improvement in expression over the original TPP1‐(GS)5‐K16ApoE construct. Further investigation is required to understand the electrostatic and/or structural basis of these findings.
Morphological characterization of Mast cells in the cochlea during postnatal rodent development
Authors: Smorodchenko Alina , Dudnik Tatyana , Karayay Betül , Sergeeva Valentina , Olze Heidi , Szczepek Agnieszka J. 
Published: May 2022

Mast cells (MC) are immune cells of hematopoietic origin widely distributed in the mammalian body's connective tissue. Their activity plays a potential immunoregulatory role associated with allergic reactions, autoimmune, cardiovascular, and neuronal diseases. Previously, the inner ear‐related MCs were described in the endolymphatic sac. However, the presence of MCs in the mammalian cochlea was not yet investigated.Here, we demonstrate for the first time that the MCs are present in the healthy cochlea of C57BL/6 mice and Wistar rats. Using histochemistry and immunohistochemistry on the cryo‐/paraffine sections of the whole cochlea and cochlea explants, we detected MCs in the modiolus, spiral ligament, scala vestibuli, and occasionally in scala tympani. The identified MCs expressed various MC‐specific markers: cKit/CD117, chymase, tryptase, and FcεRIa. Quantitative analysis demonstrated a significant decrease in the number of MCs during the postnatal development, resulting in only a few MCs present in the cochlea of rats and mice. In addition, 24h incubation of the cochlear explant with 40 µM of cisplatin lead to a significant reduction of MC numbers.The presence of MCs in the cochlea may shed new light on postnatal maturation of the auditory periphery and possible involvement in cisplatin ototoxicity. Currently, our findings expand the knowledge about the physiology and pathology of the auditory periphery.Considering the pivotal role of MCs in inflammation, future functional studies should explain this new basic knowledge and translate it into clinical application.
Enzymatic removal of cell surface antigens as a route towards universal O type blood and organs
Authors: Withers Stephen G. 
Published: May 2022

Mammalian cell surfaces are coated in specific sugar structures, many of which function as antigens and are involved in cellular recognition. Important examples are the oligosaccharide A, B, and H antigens present on red blood cells that differentiate the A, B and O blood types. Enzymatic cleavage of the GalNAc and Gal residues from the cell surface would allow conversion of A and B red blood cells, respectively, to O type. Since Type O blood can be universally donated to patients with the same Rh factor, access to efficient enzymes would greatly broaden and simplify blood supply. We have sought such enzymes in metagenomic libraries derived from the human gut microbiome.Total DNA was extracted from feces samples, fragmented into pieces containing ~30‐40 genes (40‐50 kB) and transformed into E. coli. After picking colonies into 384 well plates we screened them for enzymes that can be used to remove the Gal or GalNAc residues that function as the antigenic determinants from A and B type red blood cells, thereby generating “universal” O type blood. A set of efficient enzymes of a new class has been identified and characterized and used to convert whole units of A blood to O. These enzymes work approximately 30 times faster than any previously characterized and with high specificity. Further, they function well in whole blood thus can be hopefully integrated into the current blood processing process.1These enzymes also function well on tissue surfaces and, when perfused through donated human A‐type lungs successfully cleared A‐antigen from surfaces exposed to the blood. Subsequent perfusion of the lungs with O‐type plasma to mimic an ABO‐incompatible transplant showed that antigen removal minimized antibody binding and antibody‐mediated injury relative to the control lung, thus may greatly temper the acute rejection phase.2 This could allow expansion of ABO‐incompatible lung transplantations, leading to significant improvements in logistics and fairness of organ allocation.

Rahfeld, P. et al. “An enzymatic pathway in the human gut microbiome that converts A to universal O‐type blood” (2019) Nature Microbiology 4, 1475‐1485.
Wang et al Conversion of blood type A donor lungs into universal blood type lungs using ex vivo ABO enzymatic treatment” (2022) Science Translational Medicine In Press, Scheduled Feb 2022