bluuebunny/crossref_metadata_2025_split huggingface dataset:
Historical Roots of Modern Plastic Surgery
Authors: Chopan Mustafa , Sayadi Lohrasb , Buchanan Patrick J. , Katz Adam J. , Mast Bruce A. 
Published: November 2018

BackgroundHighly cited publications are referred to as citation classics and can signify important contributions to a discipline. Although citation classics in plastic surgery have been identified, none were published before 1960. Citation classics in earlier periods may contain the historical roots or intellectual origins of the field. We set out to identify such scholarly works and analyze their characteristics.MethodsA novel technique of citation analysis, referred to as reference publication year spectroscopy, was used to analyze the literature. The spectrogram revealed distinct peaks before 1960, which corresponded to 20 citation classics. These 20 references were then analyzed with respect to historical context, topic of interest, anatomical region, originality, and if authors were named for their findings (eponyms).ResultsTwenty distinct citation classics (published from 1851 to 1959) were identified, accounting for 430 literature citations. Salmon’s “Arteres de la Peau” was the most cited reference, followed by Gillies’ “Principles of Plastic Surgery” and Neuber’s “Fat Grafting.” The theme of angiosomes was highly represented. Most citation classics dealt with reconstruction of acquired defects (37%) and primarily focused on the head and neck regions (45%). Thirty-five percent of clinical studies were noted for their originality, and 5 studies earned their authors’ eponymous distinctions.ConclusionThe roots of modern plastic surgery began in the late 19th century with early efforts to describe cutaneous vasculature. Historical studies that either establish principles or lead to an advancement in our reconstructive methods have the best chance of achieving classical status.
Current Management of Self-Inflicted Wounds in Surgery
Authors: David Joshua A. , Rifkin William J. , Chiu Ernest S. 
Published: November 2018

Objective
Despite the presence of self-inflicted wounds (SIWs) across all of medicine, our current understanding of SIWs in surgery is limited. Here, we detail the pertinent aspects of the history, diagnosis, decision making, and management of SIWs as they relate to the field of surgery. In addition, we present the first comprehensive review of SIWs across the surgical literature.

Summary Background Data
Self-inflicted wounds have been recognized for much of recorded human history and span a wide spectrum of patient behaviors, motivations, and underlying psychiatric illnesses.

Methods
We performed a comprehensive literature review of SIWs in the surgical literature. In total, 189 articles were identified.

Results
The most common site of primary SIW was the upper extremity (36.2%), and the most common presenting injuries were lacerations (22.7%). Forty-two percent of patients had received prior surgical procedures for their SIWs, and the average length of time preceding treatment or diagnosis of an injury as an SIW was 2.29 years. Self-inflicted wounds resulting from foreign body insertions were most common (25.9%). Psychiatric factors accounted for most SIW production (35%), of which factitious disorder was the most common (12.7%). Other motivations for SIW production included autoeroticism (8.6%), substance related (6.6%), organic brain disease (5.0%), and self-therapy/surgery by patients (1.7%). Surgical management was ultimately required for nearly 75% of SIWs and was successful in most cases.

Conclusions
Self-inflicted wounds are frequently encountered in all surgical specialties and encompass many anatomic locations, presentations, and patient-motivating factors. Surgical intervention is common, and successful outcomes are often achieved.
Plasma miR-181a-5p Downregulation Predicts Response and Improved Survival After FOLFIRINOX in Pancreatic Ductal Adenocarcinoma
Authors: Meijer Laura L. , Garajová Ingrid , Caparello Chiara , Le Large Tessa Y. S. , Frampton Adam E. , Vasile Enrico , Funel Niccola , Kazemier Geert , Giovannetti Elisa 
Published: November 2018

Objective:
The aim of the study was to identify plasma microRNA (miRNA) biomarkers for stratifying and monitoring patients with locally advanced or metastatic pancreatic ductal adenocarcinoma (PDAC) treated with FOLFIRINOX, and to investigate their functional roles.

Summary Background Data:
FOLFIRINOX has become a standard therapy for patients with advanced PDAC and can be used to potentially downstage disease. However, only a subset of patients respond, and biomarkers to guide decision-making are urgently needed.

Methods:
We used microarray-based profiling to discover deregulated miRNAs in pre- and postchemotherapy plasma samples from patients based on their progression-free survival (PFS) after FOLFIRINOX. Nine candidate plasma miRNAs were validated in an independent cohort (n = 43). The most discriminative plasma miRNA was correlated with clinicopathological factors and survival, and also investigated in an additional cohort treated with gemcitabine plus nab-paclitaxel. Expression patterns were further evaluated in matched tumor tissues. In vitro studies explored its function, key downstream gene-targets, and interaction with 5-fluorouracil, irinotecan, and oxaliplatin.

Results:
Plasma miR-181a-5p was significantly downregulated in non-progressive patients after FOLFIRINOX. In multivariate analysis, this decline correlated with improved PFS and overall survival, especially when combined with CA19-9 decline [hazard ratio (HR) = 0.153, 95% confidence interval (CI), 0.067–0.347 and HR = 0.201, 95% CI, 0.070–0.576, respectively]. This combination did not correlate with survival in patients treated with gemcitabine plus nab-paclitaxel. Tissue expression of miR-181a-5p reflected plasma levels. Inhibition of miR-181a-5p coupled with oxaliplatin exposure in pancreatic cell lines decreased cell viability.

Conclusions:
Plasma miR-181a-5p is a specific biomarker for monitoring FOLFIRINOX response. Decline in plasma miR-181a-5p and CA19-9 levels is associated with better prognosis after FOLFIRINOX and may be useful for guiding therapeutic choices and surgical exploration.
Novel 3,6-Dihydroxypicolinic Acid Decarboxylase Mediated Picolinic Acid Catabolism inAlcaligenes faecalisJQ135
Authors: Jiguo Qiu , Yanting Zhang , Shigang Yao , Hao Ren , Meng Qian , Qing Hong , Zhenmei Lu , Jian He 
Published: November 2018

AbstractAlcaligenesfaecalisstrain JQ135 utilizes picolinic acid (PA) as sole carbon and nitrogen source for growth. In this study, we screened a 6-hydroxypicolinic acid (6HPA) degradation-deficient mutant through random transposon mutagenesis. The mutant hydroxylated 6HPA into an intermediate, identified as 3,6-dihydroxypicolinic acid (3,6DHPA) with no further degradation. A novel decarboxylase PicC was identified that was found to be responsible for the decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. Although, PicC belonged to amidohydrolase_2 family, it shows low similarity (<45%) when compared to other reported amidohydrolase_2 family decarboxylases. Moreover, PicC was found to form a monophyletic group in the phylogenetic tree constructed using PicC and related proteins. Further, the genetic deletion and complementation results demonstrated thatpicCwas essential for PA degradation. The PicC was Zn2+-dependent non-oxidative decarboxylase that can specifically catalyze the irreversible decarboxylation of 3,6DHPA to 2.5-dihydroxypyridine. TheKmandkcattowards 3,6DHPA were observed to be 13.44 μM and 4.77 s-1, respectively. Site-directed mutagenesis showed that His163 and His216 were essential for PicC activity.ImportancePicolinic acid is a natural toxic pyridine derived from L-tryptophan metabolism and some aromatic compounds in mammalian and microbial cells. Microorganisms can degrade and utilize picolinic acid for their growth, and thus, a microbial degradation pathway of picolinic acid has been proposed. Picolinic acid is converted into 6-hydroxypicolinic acid, 3,6-dihydroxypicolinic acid, and 2,5-dihydroxypyridine in turn. However, there was no physiological and genetic validation for this pathway. This study demonstrated that 3,6DHPA was an intermediate in PA catabolism process and further identified and characterized a novel amidohydrolase_2 family decarboxylase PicC. It was also shown that PicC could catalyze the decarboxylation process of 3,6-dihydroxypicolinic acid into 2,5-dihydroxypyridine. This study provides a basis for understanding PA degradation pathway and the underlying molecular mechanism.
The complete plastid genomes of four species from Brassicales
Authors: Mu Weixue , Yang Ting , Liu Xin 
Published: November 2018

AbstractBrassicales is a diverse angiosperm order with about 4,700 recognized species. Here, we assembled and described the complete plastid genomes from four species of Brassicales: Capparis urophylla F.Chun (Capparaceae), Carica papaya L. (Caricaceae), Cleome rutidosperma DC. (Cleomaceae), and Moringa oleifera Lam. (Moringaceae), including two plastid genomes newly assembled for two families (Capparaceae and Moringaceae). The four plastid genomes are 159,680 base pairs on average in length and encode 78 protein-coding genes. The genomes each contains a typical structure of a Large Single-Copy (LSC) region and a Small Single-Copy (SSC) region separated by two Inverted Repeat (IR) regions. We performed the maximum-likelihood (ML) phylogenetic analysis using three different data sets of 66 protein-coding genes (ntAll, ntNo3rd and AA). Our phylogenetic results from different dataset are congruent, and are consistent with previous phylogenetic studies of Brassiales.
Cities of the future, visualizing climate change to inspire actions
Authors: Bastin Jean-Francois , Clark Emily , Elliott Thomas , Hart Simon , den Hoogen Johan van , Hordijk Iris , Ma Haozhi , Majumder Sabiha , Manoli Gabriele , Maschler Julia , Mo Lidong , Routh Devin , Yu Kailiang , Zohner Constantin , Crowther Thomas, W. 
Published: November 2018

AbstractCombating against climate change requires unified action across all sectors of society. However, this collective action is precluded by the ‘consensus gap’ between scientific knowledge and public opinion. A growing body of evidence suggests that facts do not persuade people to act. Instead, it is visualization - the ability to simulate relatable scenarios - is the most effective approach for motivating behavior change. Here, we exemplify this approach, using current climate projections to enable people to visualize cities of the future, rather than describing intangible climate variables. Analyzing city pairs for 520 major cities of the world, we characterize which cities will most closely resemble the climate conditions of which other major cities by 2050. On average, most cities will resemble cities that are over 1000km south, and 22% of cities will experience climate conditions that are not currently experienced by any existing major cities. We predict that London’s climate in 2050 will resemble Barcelona’s climate today, Madrid will resemble to Marrakesh, Moscow to Sofia, Seattle to San Francisco, Stockholm to Budapest, Tokyo to Changsha, etc. Our approach illustrates how complex climate data can be packaged to provide tangible information. By allowing people to visualize their own climate futures, we hope to empower citizens, policy makers and scientists to visualize expected climate impacts and adapt decision making accordingly.
Sprouting and anastomosis in the Drosophila trachea and the vertebrate vasculature: similarities and differences in cell behaviour
Authors: Kotini Maria Paraskevi , Andaloussi Mäe Maarja , Belting Heinz-Georg , Betsholtz Christer , Affolter Markus 
Published: November 2018

AbstractBranching morphogenesis is a fascinating process whereby a simple network of biological tubes increases its complexity by adding new branches to existing ones, generating an enlarged structure of interconnected tubes. Branching morphogenesis has been studied extensively in animals and much has been learned about the regulation of branching at the cellular and molecular level. Here, we discuss studies of the Drosophila trachea and of the vertebrate vasculature, which have revealed how new branches are formed and connect (anastomose), leading to the establishment of complex tubular networks. We briefly describe the cell behaviour underlying tracheal and vascular branching. Although similar at many levels, the branching and anastomosis processes characterized thus far show a number of differences in cell behaviour, resulting in somewhat different tube architectures in these two organs. We describe the similarities and the differences and discuss them in the context of their possible developmental significance. We finish by highlighting some old and new data, which suggest that live imaging of the development of capillary beds in adult animals might reveal yet unexplored endothelial behaviour of endothelial cells.
Multicolor fluorescent imaging by space-constrained computational hyperspectral imaging
Authors: Wang Yina , Yang Bin , Feng Siyu , Pessino Veronica , Huang Bo 
Published: November 2018

AbstractHyperspectral imaging is a powerful technique to simultaneously study multiple fluorophore labels with overlapping emissions. Here we present a computational hyperspectral imaging method, which uses the sample spatial fluorescence information as a reconstruction constraint. Our method addresses both the under-sampling issue of compressive hyperspectral imaging and the low throughput issue of scanning hyperspectral imaging. With simulated and experimental data, we have demonstrated the superior reconstruction precision of our method in two and three-color imaging. We have experimentally validated this method in differentiating cellular structures labeled with two red-colored fluorescent proteins, tdTomato and mCherry, which have highly overlapping emission spectra. Our method has the advantage of totally free wavelength choice and can also be combined with conventional filter-based sequential multi-color imaging to further expand the choices of probes.
Efficient reverse breeding by VIGS-mediated transient crossover reduction
Authors: Calvo-Baltanas Vanesa , Wijnen Cris L. , Lukhovitskaya Nina , de Snoo C. Bastiaan , Hohenwarter Linus , de jong Hans , Schnittger Arp , Wijnker Erik 
Published: November 2018

AbstractF1 heterozygotes are traditionally generated by crossing homozygous parental lines. The opposite is achieved through reverse breeding, in which parental lines are generated from a heterozygote. Reverse breeding can be used to develop new F1 hybrid varieties without having prior access to homozygous breeding lines. For successful reverse breeding, the heterozygotes’ homologous chromosomes must be divided over two haploid complements, which is achieved by suppression of meiotic crossover (CO) recombination. We here show two innovations that facilitate efficient reverse breeding. Firstly, we demonstrate that downregulation of CO rates can be accomplished using virus-induced gene silencing (VIGS). We obtain transgene-free parental lines for a heterozygote in just two generations. Secondly, we show that incomplete CO suppression opens up several alternative strategies for the preservation of hybrid phenotypes through reverse breeding.
Adenosine Deaminase Acting on RNA 1 Associates with Orf Virus OV20.0 and Enhances Viral Replication
Authors: Liao Guan-Ru , Tseng Yeu-Yang , Tseng Jing-Yu , Lin Fong-Yuan , Yamada Yumiko , Liu Hao-Ping , Kuan Chih-Ying , Hsu Wei-Li 
Published: November 2018

AbstractOrf virus (ORFV) infects sheep and goats and is also an important zoonotic pathogen. The viral protein OV20.0 has been shown to suppress innate immunity by targeting the double-stranded RNA (dsRNA)-activated protein kinase (PKR) by multiple mechanisms. These mechanisms include a direct interaction with PKR and binding with two PKR activators, dsRNA and the cellular PKR activator (PACT), which ultimately leads to the inhibition of PKR activation. In the present study, we identified a novel association between OV20.0 and adenosine deaminase acting on RNA 1 (ADAR1). OV20.0 bound directly to the dsRNA binding domains (RBDs) of ADAR1 in the absence of dsRNA. Additionally, OV20.0 preferentially interacted with RBD1 of ADAR1, which was essential for its dsRNA binding ability and for the homodimerization that is critical for intact adenosine (A)-to-inosine (I) editing activity. Finally, the association with OV20.0 suppressed the A-to-I editing ability of ADAR1, while ADAR1 played a proviral role during ORFV infection by inhibiting PKR phosphorylation. These observations revealed a new strategy used by OV20.0 to evade antiviral responses via PKR.ImportanceViruses evolve specific strategies to counteract host innate immunity. ORFV, an important zoonotic pathogen, encodes OV20.0 to suppress PKR activation via multiple mechanisms, including interactions with PKR and two PKR activators. In this study, we demonstrated that OV20.0 interacts with ADAR1, a cellular enzyme responsible for converting adenosine (A) to inosine (I) in RNA. The RNA binding domains, but not the catalytic domain, of ADAR1 are required for this interaction. The OV20.0-ADAR1 association affects the functions of both proteins; OV20.0 suppressed the A-to-I editing of ADAR1, while ADAR1 elevated OV20.0 expression. The proviral role of ADAR1 is likely due to the inhibition of PKR phosphorylation. As RNA editing by ADAR1 contributes to the stability of the genetic code and the structure of RNA, these observations suggest that in addition to serving as a PKR inhibitor, OV20.0 might modulate ADAR1-dependent gene expression to combat antiviral responses or achieve efficient viral infection.
Common spatiotemporal processing of visual features shapes object representation
Authors: Papale Paolo , Betta Monica , Handjaras Giacomo , Malfatti Giulia , Cecchetti Luca , Rampinini Alessandra , Pietrini Pietro , Ricciardi Emiliano , Turella Luca , Leo Andrea 
Published: November 2018

AbstractBiological vision relies on representations of the physical world at different levels of complexity. Relevant features span from simple low-level properties, as contrast and spatial frequencies, to object-based attributes, as shape and category. However, how these features are integrated into coherent percepts is still debated. Moreover, these dimensions often share common biases: for instance, stimuli from the same category (e.g., tools) may have similar shapes. Here, using magnetoencephalography, we revealed the temporal dynamics of feature processing in human subjects attending to pictures of items pertaining to different semantic categories. By employing Relative Weights Analysis, we mitigated collinearity between model-based descriptions of stimuli and showed that low-level properties (contrast and spatial frequencies), shape (medial-axis) and category are represented within the same spatial locations early in time: 100-150ms after stimulus onset. This fast and overlapping processing may result from independent parallel computations, with categorical representation emerging later than the onset of low-level feature processing, yet before shape coding. Categorical information is represented both before and after shape also suggesting a role for this feature in the refinement of categorical matching.
Discovering human transcription factor interactions with genetic variants, novel DNA motifs, and repetitive elements using enhanced yeast one-hybrid assays
Authors: Shrestha Shaleen , Sewell Jared Allan , Santoso Clarissa Stephanie , Forchielli Elena , Pro Sebastian Carrasco , Martinez Melissa , Fuxman Bass Juan Ignacio 
Published: November 2018

ABSTRACTIdentifying transcription factor (TF) binding to noncoding variants, uncharacterized DNA motifs, and repetitive genomic elements has been technically and computationally challenging. Current experimental methods, such as chromatin immunoprecipitation, generally test one TF at a time, and computational motif algorithms often lead to false positive and negative predictions. To address these limitations, we developed two approaches based on enhanced yeast one-hybrid assays. The first approach interrogates the binding of >1,000 human TFs to repetitive DNA elements, while the second evaluates TF binding to single nucleotide variants, short insertions and deletions (indels), and novel DNA motifs. Using the first approach, we detected the binding of 75 TFs, including several nuclear hormone receptors and ETS factors, to the highly repetitive Alu elements. Using the second approach, we identified cancer-associated changes in TF binding, including gain of interactions involving ETS TFs and loss of interactions involving KLF TFs to different mutations in the TERT promoter, and gain of a MYB interaction with an 18 bp indel in the TAL1 super-enhancer. Additionally, we identified the TFs that bind to three uncharacterized DNA motifs identified in DNase footprinting assays. We anticipate that these approaches will expand our capabilities to study genetic variation and under-characterized genomic regions.
Studying Human Behaviour with Virtual Reality: The Unity Experiment Framework
Authors: Brookes Jack , Warburton Matthew , Alghadier Mshari , Mon-Williams Mark , Mushtaq Faisal 
Published: November 2018

AbstractVirtual Reality systems offer a powerful tool for human behaviour research. The ability to create three-dimensional visual scenes and measure responses to the visual stimuli enables the behavioural researcher to test hypotheses in a manner and scale that were previously unfeasible. For example, a researcher wanting to understand interceptive timing behaviour might wish to violate Newtonian mechanics, so objects move in novel 3D trajectories. The same researcher may wish to collect such data with hundreds of participants outside the laboratory, and the use of a VR headset makes this a realistic proposition. The difficulty facing the researcher is that sophisticated 3D graphics engines (e.g. Unity) have been created for game designers rather than behavioural scientists. In order to overcome this barrier, we have created a set of tools and programming syntaxes that allow logical encoding of the common experimental features required by the behavioural scientist. The Unity Experiment Framework (UXF) allows the researcher to readily implement several forms of data collection, and provides researchers with the ability to easily modify independent variables. UXF does not offer any stimulus presentation features, so the full power of the Unity game engine can be exploited. We use a case study experiment, measuring postural sway in response to an oscillating virtual room, to show how UXF can replicate and advance upon behavioural research paradigms. We show that UXF can simplify and speed up development of VR experiments created in commercial gaming software and facilitate the efficient acquisition of large quantities of behavioural research data.