bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid evolution of genome‐wide gene expression and plasticity during saline to freshwater invasions by the copepod Eurytemora affinis species complex
Authors: Posavi Marijan , Gulisija Davorka , Munro James B. , Silva Joana C. , Lee Carol Eunmi 
Published: October 2020

AbstractSaline migrants into freshwater habitats constitute among the most destructive invaders in aquatic ecosystems throughout the globe. However, the evolutionary and physiological mechanisms underlying such habitat transitions remain poorly understood. To explore the mechanisms of freshwater adaptation and distinguish between adaptive (evolutionary) and acclimatory (plastic) responses to salinity change, we examined genome‐wide patterns of gene expression between ancestral saline and derived freshwater populations of the Eurytemora affinis species complex, reared under two different common‐garden conditions (0 versus 15 PSU). We found that evolutionary shifts in gene expression (between saline and freshwater inbred lines) showed far greater changes and were more widespread than acclimatory responses to salinity (0 versus 15 PSU). Most notably, 30–40 genes showing evolutionary shifts in gene expression across the salinity boundary were associated with ion transport function, with inorganic cation transmembrane transport forming the largest Gene Ontology category. Of particular interest was the sodium transporter, the Na+/H+ antiporter (NHA) gene family, which was discovered in animals relatively recently. Thirty key ion regulatory genes, such as NHA paralogue #7, demonstrated concordant evolutionary and plastic shifts in gene expression, suggesting the evolution of ion transporter function and plasticity during rapid invasions into novel salinities. Moreover, freshwater invasions were associated with the evolution of reduced plasticity in the freshwater population, again for the same key ion transporters, consistent with the predicted evolution of canalization following adaptation to stressful conditions. Our results have important implications for understanding evolutionary and physiological mechanisms of range expansions by some of the most widespread invaders in aquatic habitats.
Movement of transposable elements contributes to cichlid diversity
Authors: Carleton Karen L. , Conte Matthew A. , Malinsky Milan , Nandamuri Sri Pratima , Sandkam Benjamin A. , Meier Joana I. , Mwaiko Salome , Seehausen Ole , Kocher Thomas D. 
Published: October 2020

AbstractAfrican cichlid fishes are a prime model for studying speciation mechanisms. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for cichlid phenotypic variation. One of their most variable phenotypes is visual sensitivity, with some of the largest spectral shifts among vertebrates. These shifts arise primarily from differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi cichlids, we previously identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or an opsin gene. In this comprehensive study, we show that these indels are the result of the movement of transposable elements (TEs) that correlate with opsin expression variation across the Malawi flock. In tracking the evolutionary history of these particular indels, we found they are endemic to Lake Malawi, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. However, an independent indel has arisen at a similar genomic location in one locus outside of the Malawi flock. The convergence in TE movement suggests these loci are primed for TE insertion and subsequent deletions. Increased TE mobility may be associated with interspecific hybridization, which disrupts mechanisms of TE suppression. This might provide a link between cichlid hybridization and accelerated regulatory variation. Overall, our study suggests that TEs may be an important driver of key regulatory changes, facilitating rapid phenotypic change and possibly speciation in African cichlids.
Genomic basis of the loss of diadromy inGalaxias maculatus: Insights from reciprocal transplant experiments
Authors: Delgado M. Lisette , Manosalva Aliro , Urbina Mauricio A. , Habit Evelyn , Link Oscar , Ruzzante Daniel E. 
Published: October 2020

AbstractDiadromy is known for having major effects on the distribution and richness of aquatic species, and so does its loss. The loss of diadromy has led to the diversification of many species, yet research focusing on understanding its molecular basis and consequences are limited. This is particularly true for amphidromous species despite being the most abundant group of diadromous species.Galaxias maculatus, an amphidromous species and one of the most widely distributed fishes in the Southern Hemisphere, exhibits many instances of nonmigratory or resident populations. The existence of naturally replicated resident populations in Patagonia can serve as an ideal system for the study of the mechanisms that lead to the loss of the diadromy and its ecological and evolutionary consequences. Here, we studied two adjacent river systems in which resident populations are genetically differentiated yet derived from the same diadromous population. By combining a reciprocal transplant experiment with genomic data, we showed that the two resident populations followed different evolutionary pathways by exhibiting a differential response in their capacity to survive in salt water. While one resident population was able to survive salt water, the other was not. Genomic analyses provided insights into the genes that distinguished (a) migratory from nonmigratory populations; (b) populations that can vs those that cannot survive a saltwater environment; and (c) between these resident populations. This study demonstrates that the loss of diadromy can be achieved by different pathways and that environmental (selection) and random (genetic drift) forces shape this dynamic evolutionary process.
Neural reading
Authors: Orekhov Boris , Fischer Frank 
Published: October 2020

AbstractThe creation of poems via neural networks is relatively easy nowadays and the internet is replete with corresponding examples. However, it largely lacks interpretive concepts. What should be done with the results generated in this way? How can we draw scientific conclusions from them? This is all the more difficult to answer as it still remains unclear where to position deep‐learning approaches in the canon of digital‐humanities methods. But it is clear that humanities scholars must reckon with machines being responsible for, or at least involved in, the creation of their objects of study. After a historical introduction to automated poetry generation, we try to conceptualize neural‐net poetry and argue that its interpretation, i.e. the close reading of texts generated that way, based on large source corpora, can be an insightful addition to the toolbox of computational literary studies, an approach in development that we suggest calling “neural reading.” Our main argument is that artificial neural networks are able to reproduce parts of the stylistic features of a training sample, in our case poetic corpora, acting as a kind of digital echo chamber of literary history. These features are mainly observed in smaller language units, at the level of morphology, vocabulary, syntax, and prosody. Our findings open new directions for the study of style in larger corpora. We will illustrate this with three Russian corpora (a selection of translated hexameters from the eighteenth to the twentieth century and the poetry of Natalia Azarova and Vladimir Vysotsky) and one German corpus (collected poems of Friedrich Hölderlin).
Prophylactic Closed Suction Drainage Is Irrelevant to Accelerated Rehabilitation after Open Reduction and Internal Fixation for Closed Distal Femur Fractures
Authors: Zhang Jun‐zhe , Zhao Kuo , Li Jun‐yong , Meng Hong‐yu , Zhu Yan‐bin , Zhang Ying‐ze 
Published: October 2020

ObjectiveTo investigate whether closed suction drainage (CSD) is related to accelerated rehabilitation of patients after open reduction and internal fixation (ORIF) for closed distal femur fractures.MethodsThis study was a prospective, randomized controlled clinical trial. Between October 2018 and June 2020, 160 closed distal femur fracture patients who were prepared for ORIF were prospectively randomized into two groups: a CSD group with the mean age of 57.91 ± 14.38 years (32 [40%] men and 48 [60%] women) and a non‐CSD group with the mean age of 59.73 ± 17.55 years (27 [34%] men and 54 [66%] women). Wound visual analogue scale (VAS) pain scores, peri‐wound skin temperature, hematocrit (Hct), hemoglobin (Hb) concentrations, hidden blood loss (HBL), dressing change, period of wound oozing, postoperative blood transfusion, and length of postoperative hospital stay were recorded. Postoperative wound complications, namely wound infections, wound haematoma, wound dehiscence, erythema of wound, and lower limb deep vein thrombosis (DVT) were collected. All the patients were administrated by a single surgical team and followed up for 1 month after the ORIF.ResultsThe patients without CSD were identified with lower peri‐wound skin temperature and wound VAS pain scores during the first three postoperative days (36.69 ± 0.33 vs 36.86 ± 0.38 °C, P = 0.002; 1.88 ± 0.82 vs 3.15 ± 1.15, P = 0.000). However, both the peri‐wound skin temperature and wound VAS pain scores did not differ significantly between the two groups on the fifth postoperative day. In addition, patients with CSD had a longer length of postoperative hospitalization time (11.45 ± 5.95 vs 9.78 ± 4.64 days, P = 0.049). There was no statistically significant difference between CSD and non‐CSD groups within 1 month after the ORIF regarding blood loss, period of wound oozing, and postoperative complications, such as incidence of wound infection, haematoma, erythema, dehiscence, and lower limb DVT.ConclusionProphylactic CSD after primary ORIF for closed distal femur fractures not only had no significant advantage to minimize blood loss and wound complications, but increased local inflammation and postoperative hospital stay, and thus we suggest that prophylactic CSD after primary ORIF for closed distal femur fractures is not recommended for optimized clinical pathways and accelerated recovery.
Comparative efficacy between localized 308‐nm excimer light and targeted 311‐nm narrowband ultraviolet B phototherapy in vitiligo: A randomized, single‐blind comparison study
Authors: Poolsuwan Pimsiri , Churee Chutima , Pattamadilok Bensachee 
Published: October 2020

AbstractBackgroundThere are limited data to compare efficacy between recent 308‐nm excimer and conventional 311‐nm narrowband ultraviolet B (NB‐UVB) light in the treatment of vitiligo.ObjectiveTo compare efficacy between 308‐nm excimer light and 311‐nm NB‐UVB in patients with symmetrical vitiligo lesions.MethodsThirty‐six symmetrically paired vitiligo lesions on the same anatomical area were enrolled. One side of the symmetrical lesions was treated with localized 308‐nm excimer light, and the opposite side was treated with targeted 311‐nm NB‐UVB assigned randomly by computer. All lesions were treated with the same protocol, for 48 sessions. Repigmentation was evaluated using Vitiligo Area Scoring Index (VASI) and grading the repigmentation was carried out with three independent investigators.ResultsThirty‐six symmetrically vitiligo lesions were randomly treated, one side with 308‐nm excimer light and the opposite side with 311‐nm NB‐UVB. After 48 sessions, a significantly lower VASI score and a higher grade of repigmentation were observed in 308‐nm excimer light–treated side (P < .001). Nine lesions (25%) treated with 308‐nm excimer light and only five lesions (13.89%) treated with 311‐nm NB‐UVB achieved excellent repigmentation. The 308‐nm excimer light and 311‐nm NB‐UVB–treated sides rapidly obtained 25% repigmentation within a mean of 19.42 sessions and 26.25 sessions, respectively (P = .002). There was no significant difference in mean cumulative UV dosage (P = .065). Side effect as phototoxicity was similar in both sides (P = .08).ConclusionLocalized 308‐nm excimer light appears to be more effective and also more rapidly induces repigmentation than targeted 311‐nm NB‐UVB for treatment of vitiligo.
Accommodation and new hurdles: The increasing importance of politics for immigrants' access to social programmes in Western democracies
Authors: Koning Edward A. 
Published: October 2020

AbstractAlthough immigrants' place in welfare state systems is of large relevance to academics and policymakers alike, there have been few attempts to compare immigrants' social rights in different countries at different moments in time systematically. This article presents the results from a comparative policy analysis that maps immigrants' access to seven different social programmes, in 20 different Western democracies, at four different points in time. The main findings are threefold. First, there are large differences in the extent to which different welfare states differentiate in benefit extension between immigrants and native‐born citizens. Second, over the last two decades, many countries have adjusted their welfare systems with the specific aim to accommodate immigrants, whereas many have also introduced punitive barriers that require immigrants to satisfy additional requirements. Third, these developments seem largely driven by politics: in particular, the adoption of punitive barriers has been more common in places where the political climate is more hostile to immigrants. These findings raise important questions about the future of social protection in an era of cross‐border mobility.
Risk factors for intra‐abdominal fungal infection after simultaneous pancreas‐kidney transplantation: A single‐center retrospective experience
Authors: Flateau Clara , Aït‐Ammar Nawel , Angebault Cécile , Salomon Laurent , Matignon Marie , Lepeule Raphaël , Melica Giovanna , Grimbert Philippe , Lelièvre Jean‐Daniel , Gallien Sébastien , Botterel Françoise 
Published: October 2020

AbstractBackgroundData on the risk factors and outcome of intra‐abdominal fungal infections (IAFI) following simultaneous pancreas‐kidney transplantation (PKT) are scarce.Materials/methodsA retrospective monocentric study was conducted on all patients who underwent simultaneous PKT from January 2007 to December 2016. Deep sites positive cultures for fungi during the first post‐transplantation year were collected. Clinical, radiological, and microbiological data of proven and probable invasive fungal infections were analysed.ResultsAmong sixteen PKT patients, 15 were included. Seven patients (47%) developed an invasive fungal infection, exclusively IAFI (six proven, one probable). The proven IAFI included four peritonitis, one pancreatic necrosis with infected hematoma, and one patient with positive preservation fluid only (PF).Candida albicans(n = 4) was the most prevalent species (associated withGalactomyces candidusin one case),C glabrata,C dubliniensis,andC kruseiwere found in one case each. Three patients had either a positive direct examination and/or culture for renal or pancreatic PF and the culture of PF was positive for the same species that caused IAFI. IAFIs were significantly associated with pancreatic graft arterial thrombosis (5/7 vs 0/8,P = .007) and fungal contamination of PF (3/7 vs 0/8,P = .008). Among patients with IAFI, all required an early surgical revision post‐transplantation [1‐18 days] and six had early or delayed pancreatic graft removal. One patient died in the first post‐transplant year.ConclusionIAFI is a common complication in PKT, associated with pancreatic graft thrombosis or fungal contamination of the graft PF, and can sometimes lead to pancreatic detransplantation.
Sequence analysis of the Petunia inflata S‐locus region containing 17 S‐Locus F‐Box genes and the S‐RNase gene involved in self‐incompatibility
Authors: Wu Lihua , Williams Justin S. , Sun Linhan , Kao Teh‐Hui 
Published: October 2020

SUMMARYSelf‐incompatibility in Petunia is controlled by the polymorphic S‐locus, which contains S‐RNase encoding the pistil determinant and 16–20 S‐locus F‐box (SLF) genes collectively encoding the pollen determinant. Here we sequenced and assembled approximately 3.1 Mb of the S2‐haplotype of the S‐locus in Petunia inflata using bacterial artificial chromosome clones collectively containing all 17 SLF genes, SLFLike1, and S‐RNase. Two SLF pseudogenes and 28 potential protein‐coding genes were identified, 20 of which were also found at the S‐loci of both the S6a‐haplotype of P. inflata and the SN‐haplotype of self‐compatible Petunia axillaris, but not in the S‐locus remnants of self‐compatible potato (Solanum tuberosum) and tomato (Solanum lycopersicum). Comparative analyses of S‐locus sequences of these three S‐haplotypes revealed potential genetic exchange in the flanking regions of SLF genes, resulting in highly similar flanking regions between different types of SLF and between alleles of the same type of SLF of different S‐haplotypes. The high degree of sequence similarity in the flanking regions could often be explained by the presence of similar long terminal repeat retroelements, which were enriched at the S‐loci of all three S‐haplotypes and in the flanking regions of all S‐locus genes examined. We also found evidence of the association of transposable elements with SLF pseudogenes. Based on the hypothesis that SLF genes were derived by retrotransposition, we identified 10 F‐box genes as putative SLF parent genes. Our results shed light on the importance of non‐coding sequences in the evolution of the S‐locus, and on possible evolutionary mechanisms of generation, proliferation, and deletion of SLF genes.
Transarticular elastic external skeletal fixator correction of a stifle rotational deformity and patellar luxation in a dog
Authors: Chen Tiffany , Bosscher Georgia , Fox Derek , Arnoldy Courtney , Bleedorn Jason 
Published: October 2020

AbstractObjectiveTo report the preoperative evaluation, treatment with transarticular elastic external skeletal fixation (ESF), and outcome of a dog with bilateral medial patellar luxation (MPL) and stifle rotational deformity.AnimalOne nonambulatory, 2.5‐month‐old, 7.5‐kg mixed‐breed intact female dog.Study designCase reportMethodsComplex pelvic limb deformities were assessed with physical examination and computed tomography (CT) and characterized as bilateral grade 4 MPL and 90° internal rotation of the tibia in relation to the femur. Three‐dimensional imaging and bone models were used to quantify the deformity and rehearse surgical correction. Transarticular elastic chains between ESF pins in the femur and tibia were used to gradually correct stifle rotational malalignment on each pelvic limb. Soft tissue releases, imbrication, and a transphyseal staple were used to correct the patellar luxation (PL) and femoral varus. The dog was reevaluated for 1 year postoperatively.ResultsShort‐ and long‐term management included intensive physical rehabilitation to increase pelvic limb strength and function. Surgical treatment resulted in resolution of the PL and neutral stifle alignment. The dog was able to ambulate with persistent decreased range of motion of the stifle.ConclusionTransarticular elastic chains and femoral physeal stapling improved the function of a dog with severe bone deformities and PL in a growing dog.
A review of applications of animal‐inspired evolutionary algorithms in reservoir operation modelling
Authors: Jahandideh‐Tehrani Mahsa , Bozorg‐Haddad Omid , Loáiciga Hugo A. 
Published: October 2020

AbstractSuccessful operation of reservoir systems to guarantee the optimal use of available water resources has been the subject of many studies. The advent and applications of evolutionary algorithms (EAs) in the field of reservoir operation have led to significant advances in our capacity to improve the planning and management of complex reservoir systems. This study reports a review of the applications of animal‐inspired EAs to reservoir operation optimization selected among a large number of available papers in this area of research. The animal‐inspired EAs herein identified concern algorithms that mimic biologic traits of animal (wild) species. Among the animal‐inspired EAs ant colony optimization (ACO), particle swarm optimization (PSO), shuffled frog leaping algorithm (SFLA), artificial bee colony (ABC), honey bee mating optimization (HBMO), firefly algorithm (FA), cuckoo search (CS) and the bat algorithm (BA) are the best‐known ones selected for this review. This paper presents a brief description of the algorithmic characteristics and various employed improved versions or varieties thereof of each of the stated EAs. Furthermore, the differences between the proposed animal‐inspired EAs and their improved versions are identified by comparing the performance of the implemented animal‐inspired EAs in the reviewed literature. PSO and its varieties have the largest number of reported applications. Our comparison results revealed that constrained, discrete and randomized varieties of the animal‐inspired EAs outperformed unconstrained, continuous and deterministic varieties, respectively because of larger feasible search space, better solution quality and shorter computational time. Moreover, all the animal‐inspired EAs outperformed traditional methods of reservoir optimization, such as nonlinear programming (NLP) and dynamic programming (DP).
Efficiency of a pilot hybrid wastewater treatment system comprising activated sludge and constructed wetlands planted with Canna lily and Cyperus papyrus
Authors: Hidayah Euis Nurul , Cahyonugroho Okik Hendriyanto , Pachwarya Ram Babu , Ramanathan A. L. 
Published: October 2020

AbstractCombination of constructed wetland with activated sludge (AS) is one of the application of sustainable development for dealing with environmental pollution. The objective of this study was to compare the performance of three system of domestic wastewater treatment, namely AS, combination AS with constructed wetland containing Canna lily (AS‐CWC), combination AS with constructed wetland containing Cyperus papyrus (AS‐CWP) for treating domestic wastewater. Mini pilot scale of treatment system was built under continuous flow. Samples were taken at outlet in each unit for measuring water quality parameters, such as BOD, TSS, , ‐N and ‐N. The results indicated that AS‐CWC performed a higher removal of BOD, and TSS than AS‐CWP and AS. AS‐CWC and AS‐CWP showed a statistically insignificant difference removal of ‐N and ‐N, though the former performed a higher removal than the later. This study revealed that TOC increased in the highest percentage in AS and the lowest increasing in AS‐CWP. Constructed wetlands should be integrated with primary treatment to enhancing effluent quality and reduce organic matter, a precursors of carcinogenic compound.
Bacterial chatter in chronic wound infections
Authors: Buch Pranali J. , Chai Yunrong , Goluch Edgar D. 
Published: October 2020

AbstractOne of the hallmark characteristics of chronic diabetic wounds is the presence of biofilm‐forming bacteria. Bacteria encapsulated in a biofilm may coexist as a polymicrobial community and communicate with each other through a phenomenon termed quorum sensing (QS). Here, we describe the QS circuits of bacterial species commonly found in chronic diabetic wounds. QS relies on diffusion of signaling molecules and the local concentration changes of these molecules that bacteria experience in wounds. These biochemical signaling pathways play a role not only in biofilm formation and virulence but also in wound healing. They are, therefore, key to understanding the distinctive nature of these infections. While several in vivo and in vitro models exist to study QS in wounds, there has been limited progress in understanding the interplay between QS molecules and host factors that contribute to wound healing. Lastly, we examine the potential of targeting QS for both diagnosis and therapeutic intervention purposes.