bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long Term Follow-up of Intralesional Laser Photocoagulation for Head and Neck Lymphatic Malformations Using Neodymium-Yttrium-Aluminium-Garnet Laser
Authors: Chang Cheng-Jen , Hsiao Yen-Chang 
Published: December 2019

Background
Lymphatic malformations remain a challenge for patients and plastic surgeons. Promising results have been reported using intralesional laser photocoagulation (ILP) for treating vascular anomalies.

Background Data
The objective of our study is to review the long-term results of a large series of lymphatic malformations in patients treated with ILP.

Materials and Methods
A retrospective review of 190 head and neck lymphatic malformations in patients were treated by ILP with an neodymium-yttrium-aluminum-garnet (Nd:YAG) laser (1064 nm) over a period of 20 years (January 1997–January 2016). Patients' ages ranged from 10 months to 12 years and 6 months (mean, 1 year and 11 months). The patient group consisted of 98 female and 92 male patients.

Results
Patients were treated with an Nd:YAG laser (Sharplan Inc, Allendale, New Jersey) delivered through a 600-μm optical fiber. Laser power was set at 7 to 15 W and delivered with a pulse duration of 7 to 15 seconds. All patients demonstrated improvement as judged by clinical assessment of the reduction in lesion size (range, 65%–100%; mean reduction, 85%). One hundred fifty-two (80%) patients had a more than 65% reduction of the volume in lymphatic malformations at 3 months after 1 treatment, and 171 (90%) patients had a more than 85% reduction of the volume after 2 treatments. Excellent results were seen in 19 (10%) patients after 3 treatments. Postoperative complications were related to photocoagulation that was delivered too extensively or superficially, with resultant ulceration, infection, induration, and scarring.

Conclusions
Throughout the course of our long-term study, ILP using an Nd:YAG laser is an effective treatment modality for lymphatic malformations. Complications can be avoided if the potential for harm is kept in mind.
Aspergillus fumigatus Spores Are Not Able to Penetrate Silicone Breast Implant Shells
Authors: Horch Raymund E. , Krappmann Sven , Dümig Michaela , Schmitz Marweh , Kengelbach-Weigand Annika , Schubert Dirk W. , Kremser Thomas , Bogdan Christian , Ludolph Ingo 
Published: December 2019

IntroductionBacterial contamination is hypothesized to be one reason for the development of capsular contracture after alloplastic breast reconstruction using silicone breast implants. The role of fungal colonization or infection in this context as well as the question if microorganisms can penetrate the shell of silicone breast implants remains an unresolved question to date. Therefore, the aim of this study was to assess whether fungal spores are able to penetrate the shell of silicone implants.Materials and MethodsIn an experimental in vitro setup with different arrangements of growth compartments, silicone chambers were placed in culture dishes filled withAspergillusminimal medium or liquid culture medium. Inoculation was performed with conidia ofAspergillus fumigatusand incubated for seven days. On a daily basis, plates were inspected for conidial germination and hyphal growth.ResultsIn none of the different experimental settings nutrients or hyphae ofAspergillus fumigatuswere able to penetrate the silicone material.ConclusionsFungal spores and hyphae do not permeate through an intact silicone shell used in breast implants; thus, the silicone material serves as an impenetrable barrier.
Opioid Use Disorder is Associated With Complications and Increased Length of Stay After Major Abdominal Surgery
Authors: Song Yun , Tang Rebecca , Roses Robert E. , Fraker Douglas L. , DeMatteo Ronald P. , Kelz Rachel R. , Karakousis Giorgos C. 
Published: December 2019

Objective:
The objective of this study was to determine the impact of opioid use disorder (OUD) on perioperative outcomes after major upper abdominal surgeries.

Summary of Background Data:
OUD, defined as dependence/abuse, is a national health epidemic. Its impact on outcomes after major abdominal surgery has not been well characterized.

Methods:
Patients who underwent elective esophagectomy, total/partial gastrectomy, major hepatectomy, and pancreatectomy were identified using the National Inpatient Sample (2003–2015). Propensity score matching by baseline characteristics was performed for patients with and without OUD. Outcomes measured were in-hospital complications, mortality, length of stay (LOS), and discharge disposition.

Results:
Of 376,467 patients, 1096 (0.3%) had OUD. Patients with OUD were younger (mean 53 vs 61 years, P < 0.001) and more often male (55.1% vs 53.2%, P < 0.001), black (15.0% vs 7.6%, P < 0.001), Medicaid beneficiaries (22.0% vs 6.4%, P < 0.001), and in the lowest income quartile (32.6% vs 21.3%, P < 0.001). They also had a higher rate of alcohol (17.2% vs 2.8%, P < 0.001) and nonopioid drug (2.2% vs 0.2%, P = 0.023) dependence/abuse. After matching (N = 1077 OUD, N = 2164 no OUD), OUD was associated with a higher complication rate (52.9% vs 37.3%, P < 0.001), including increased pain [odds ratio (OR) 3.5, P < 0.001], delirium (OR 3.0, P = 0.004), and pulmonary complications (OR 2.0, P = 0.006). Additionally, OUD was associated with increased LOS (mean 12.4 vs 10.6 days, P = 0.015) and nonroutine discharge (OR 1.6, P < 0.001). In-hospital mortality did not differ (OR 2.4, P = 0.10).

Conclusion:
Patients with OUD more frequently experienced complications and increased LOS. Close postoperative monitoring may mitigate adverse outcomes.
Incidence and Symptomatology of Vascular Crossed Aphasia in Bengali
Authors: Lahiri Durjoy , Dubey Souvik , Sawale Vishal M. , Das Gautam , Ray Biman K. , Chatterjee Suparna , Ardila Alfredo 
Published: December 2019

Background:Crossed aphasia (CA) refers to aphasia following a right-hemispheric lesion in right-handed individuals. It has been suggested that the prevalence of CA differs with language, although its worldwide incidence, as reported by most studies, is less than 3%.Objective:To find the incidence of CA in the Bengali language.Methods:From 2016 to 2018, in a hospital located in a Bengali-speaking area of eastern India, 515 cases of first-ever stroke were documented, out of which 208 patients presented with aphasia (40.38%) according to their scores on the Bengali version of the Western Aphasia Battery.Results:Among the patients with aphasia, 14 (6.73%; 8 men and 6 women) presented with CA. Of these, 10 were diagnosed with Broca aphasia and four with transcortical motor aphasia. No patient presented with Wernicke aphasia.Conclusions:The relatively high incidence of CA in our study suggests that bi-hemispheric language representation may be more prevalent in Bengali speakers than in speakers of other languages. The absence of crossed Wernicke aphasia in our study participants may represent a left-hemispheric advantage for receptive language abilities in Bengali speakers. Further studies are required to clarify whether idiosyncrasies in the Bengali language may be responsible for the differential brain representation of language seen in our study participants.
Continuous EEG Findings in Autoimmune Encephalitis
Authors: Moise Anna-Marieta , Karakis Ioannis , Herlopian Aline , Dhakar Monica , Hirsch Lawrence J. , Cotsonis George , LaRoche Suzette , Cabrera Kang Christian M. , Westover Brandon , Rodriguez Andres 
Published: December 2019

Purpose:
Autoimmune encephalitis (AE) is a cause of new-onset seizures, including new-onset refractory status epilepticus, yet there have been few studies assessing the EEG signature of AE.

Methods:
Multicenter retrospective review of patients diagnosed with AE who underwent continuous EEG monitoring.

Results:
We identified 64 patients (male, 39%; white, 49%; median age, 44 years); of whom, 43 (67%) were antibody-proven AE patients. Of the patients with confirmed antibody AE, the following were identified: N-methyl-D-aspartate receptor (n = 17, 27%), voltage-gated potassium channel (n = 16, 25%), glutamic acid decarboxylase (n = 6, 9%), and other (n = 4, 6%). The remaining patients were classified as probable antibody-negative AE (n = 11, 17%), definite limbic encephalitis (antibody-negative) (n = 2, 3%), and Hashimoto encephalopathy (n = 8, 13%). Fifty-three percent exhibited electrographic seizures. New-onset refractory status epilepticus was identified in 19% of patients. Sixty-three percent had periodic or rhythmic patterns; of which, 38% had plus modifiers. Generalized rhythmic delta activity was identified in 33% of patients. Generalized rhythmic delta activity and generalized rhythmic delta activity plus fast activity were more common in anti-N-methyl-D-aspartate AE (P = 0.0001 and 0.0003, respectively). No other periodic or rhythmic patterns exhibited AE subtype association. Forty-two percent had good outcome on discharge. Periodic or rhythmic patterns, seizures, and new-onset refractory status epilepticus conferred an increased risk of poor outcome (OR, 6.4; P = 0.0012; OR, 3; P = 0.0372; OR, 12.3; P = 0.02, respectively).

Conclusion:
Our study confirms a signature EEG pattern in anti-N-methyl-D-aspartate AE, termed extreme delta brush, identified as generalized rhythmic delta activity plus fast activity in our study. We found no other pattern association with other AE subtypes. We also found a high incidence of seizures among patients with AE. Finally, periodic or rhythmic patterns, seizures, and new-onset refractory status epilepticus conferred an increased risk of poor outcome regardless of AE subtype.
Metastasis is altered through multiple processes regulated by the E2F1 transcription factor
Authors: Swiatnicki Matthew , Andrechek Eran R. 
Published: December 2019

AbstractThe E2F family of transcription factors is important for many cellular processes, from their canonical role in cell cycle regulation to other roles in angiogenesis and metastasis. Alteration of the Rb/E2F pathway occurs in various forms of cancer, including breast cancer. E2F1 ablation has been shown to decrease metastasis in MMTV-Neu and MMTV-PyMT transgenic mouse models of breast cancer. Here we take a bioinformatic approach to determine the E2F1 regulated genomic alterations involved in the metastatic cascade, in both Neu and PyMT models. Through gene expression analysis, we reveal few transcriptome changes in non-metastatic E2F1−/− tumors relative to transgenic tumor controls. However investigation of these models through whole genome sequencing found numerous differences between the models, including differences in the proposed tumor etiology between E2F1−/− and E2F1+/+ tumors induced by Neu or PyMT. Investigating mutated genes through gene set analysis also found a significant number of genes mutated in the cell adhesion pathway in E2F1−/− tumors, indicating this may be a route for disruption of metastasis in E2F1−/− tumors. Overall, these findings illustrate the complicated nature of uncovering drivers of the metastatic process.
GO: A functional reporter system to identify and enrich base editing activity
Authors: Katti Alyna , Foronda Miguel , Zimmerman Jill , Diaz Bianca , Zafra Maria Paz , Goswami Sukanya , Dow Lukas E 
Published: December 2019

ABSTRACTBase editing (BE) is a powerful tool for engineering single nucleotide variants (SNVs) and has been used to create targeted mutations in cell lines, organoids, and animal models. Recent development of new BE enzymes has provided an extensive toolkit for genome modification; however, identifying and isolating edited cells for analysis has proven challenging. Here we report a “Gene On” (GO) reporter system that indicates precise cytosine or adenine base editing in situ with high sensitivity and specificity. We test GO using an activatable GFP and use it to measure the kinetics, efficiency, and PAM specificity of a range of new BE variants. Further, GO is flexible and can be easily adapted to induce expression of numerous genetically encoded markers, antibiotic resistance genes, or enzymes such as Cre recombinase. With these tools, GO can be exploited to functionally link BE events at endogenous genomic loci to cellular enzymatic activities in human and mouse cell lines and organoids. Thus, GO provides a powerful approach to increase the practicality and feasibility of implementing CRISPR BE in biomedical research.
Shallow Genome Sequencing for Phylogenomics of Mycorrhizal Fungi from Endangered Orchids
Authors: Unruh Sarah A. , Pires J. Chris , Zettler Lawrence , Erba Luigi , Grigoriev Igor , Barry Kerrie , Daum Christopher , Lipzen Anna , Stajich Jason E. 
Published: December 2019

ABSTRACTMost plant species form symbioses with mycorrhizal fungi and this relationship is especially important for orchids. Fungi in the generaTulasnella, Ceratobasidium,andSerendipitaare critically important for orchid germination, growth and development. The goals of this study are to understand the phylogenetic relationships of mycorrhizal fungi and to improve the taxonomic resources for these groups. We identified 32 fungal isolates with the internal transcribed spacer region and used shallow genome sequencing to functionally annotate these isolates. We constructed phylogenetic trees from 408 orthologous nuclear genes for 50 taxa representing 14 genera, 11 families, and five orders in Agaricomycotina. While confirming relationships among the orders Cantharellales, Sebacinales, and Auriculariales, our results suggest novel relationships between families in the Cantharellales. Consistent with previous studies, we found the generaCeratobasidiumandThanatephorusof Cerabotasidiaceae to not be monophyletic. Within the monophyletic genusTulasnella, we found strong phylogenetic signals that suggest a potentially new species and a revision of current species boundaries (e.g.Tulasnella calospora); however it is premature to make taxonomic revisions without further sampling and morphological descriptions. There is low resolution ofSerendipitaisolates collected. More sampling is needed from areas around the world before making evolutionary-informed changes in taxonomy. Our study adds value to an important living collection of fungi isolated from endangered orchid species, but also informs future investigations of the evolution of orchid mycorrhizal fungi.
Comparative population genetic structure of two ixodid tick species (Ixodes ovatusandHaemaphysalis flava) in Niigata Prefecture, Japan
Authors: Regilme Maria Angenica F. , Sato Megumi , Tamura Tsutomu , Arai Reiko , Sato Marcello Otake , Ikeda Sumire , Gamboa Maribet , Monaghan Michael T. , Watanabe Kozo 
Published: December 2019

AbstractIxodid tick species such asIxodes ovatusandHaemaphysalis flavaare essential vectors of tick-borne diseases in Japan. In this study, we investigated the population genetic structures and gene flow ofI. ovatusandH. flavaas affected by the tick host mobility. We hypothesized thatI. ovatusandH. flavamay have differences in their genetic structure due to the low mobility of small rodent hosts ofI. ovatusat the immature stage in contrast to the mediated dispersal of avian hosts for immatureH. flava.We collected 307 adultI. ovatusand 220 adultH. flavafrom 29 and 17 locations across Niigata Prefecture, Japan. We investigated the genetic structure at two mitochondrial loci (cox1, 16S rRNA gene). ForI. ovatus, pairwiseFSTand analysis of molecular variance (AMOVA) analyses ofcox1sequences indicated significant genetic variation among populations. Bothcox1and 16S rRNA markers showed non-significant genetic variation among locations forH. flava. The Bayesian tree and haplotype network ofcox1marker forI. ovatussamples in Niigata Prefecture found 3 genetic groups wherein most haplotypes in group 2 were distributed in low altitudinal areas. When we addedcox1sequences ofI. ovatusfrom China to the phylogenetic analysis, three genetic groups (China 1, China 2, and Niigata and Hokkaido, Japan) were formed in the tree suggesting the potential for cryptic species in the genetic group in Japan. Our results support our hypothesis and suggest that the host preference of ticks at the immature stage may influence the genetic structure and gene flow of the ticks. This information is vital in understanding the tick-host interactions in the field to better understand the tick-borne disease transmission and in designing an effective tick control program.
LncRNA and predictive model to improve the diagnosis of clinically diagnosed pulmonary tuberculosis
Authors: Hu Xuejiao , Chen Hao , Liao Shun , Bai Hao , Gupta Shubham , Zhou Yi , Zhou Juan , Jiao Lin , Wu Lijuan , Wang Minjin , Chen Xuerong , Zhou Yanhong , Lu Xiaojun , Hu Tony Y , Zhang Zhaolei , Ying Binwu 
Published: December 2019

ABSTRACTBackgroundClinically diagnosed pulmonary tuberculosis (PTB) patients lack Mycobacterium tuberculosis (MTB) microbiologic evidence, and misdiagnosis or delayed diagnosis often occurs as a consequence. We investigated the potential of lncRNAs and corresponding predictive models to diagnose these patients.MethodsWe enrolled 1372 subjects, including clinically diagnosed PTB patients, non-TB disease controls and healthy controls, in three cohorts (Screening, Selection and Validation). Candidate lncRNAs differentially expressed in blood samples of the PTB and healthy control groups were identified by microarray and qRT-PCR in the Screening Cohort. Logistic regression models were developed using lncRNAs and/or electronic health records (EHRs) from clinically diagnosed PTB patients and non-TB disease controls in the Selection Cohort. These models were evaluated by AUC and decision curve analysis, and the optimal model was presented as a Web-based nomogram, which was evaluated in the Validation Cohort. The biological function of lncRNAs was interrogated using ELISA, lactate dehydrogenase release analysis and flow cytometry.ResultsThree differentially expressed lncRNAs (ENST00000497872, n333737, n335265) were identified. The optimal model (i.e., nomogram) incorporated these three lncRNAs and six EHR variables (age, hemoglobin, weight loss, low-grade fever, CT calcification and TB-IGRA). The nomogram showed an AUC of 0.89, sensitivity of 0.86 and specificity of 0.82 in the Validation Cohort, which demonstrated better discrimination and clinical net benefit than the EHR model. ENST00000497872 may regulate inflammatory cytokine production, cell death and apoptosis during MTB infection.ConclusionsLncRNAs and the user-friendly nomogram could facilitate the early identification of PTB cases among suspected patients with negative MTB microbiologic evidence.
The amplification of genetic factors for early vocabulary during children’s language and literacy development
Authors: Verhoef Ellen , Shapland Chin Yang , Fisher Simon E. , Dale Philip S. , Pourcain Beate St 
Published: December 2019

AbstractThe heritability of language and literacy skills increases during development. The underlying mechanisms are little understood, and may involve (i) the amplification of early genetic influences and/or (ii) the emergence of novel genetic factors (innovation). Here, we use multivariate structural equation models to quantify these processes, as captured by genome-wide genetic markers. Studying expressive and receptive vocabulary at 38 months and subsequent language, literacy and cognitive skills (7-13 years) in unrelated children (ALSPAC: N≤6,092), we found little support for genetic innovation during mid-childhood and adolescence. Instead, genetic factors for early vocabulary, especially those unique to receptive skills, were amplified. Explaining as little as 3.9%(SE=1.8%) variation in early language, the same genetic influences accounted for 25.7%(SE=6.4%) to 45.1%(SE=7.6%) variation in verbal intelligence and literacy skills, but also performance intelligence, capturing the majority of SNP-heritability (≤99%). This suggests that complex verbal and non-verbal cognitive skills originate developmentaly in early receptive language.
Direct ETTIN-auxin interaction controls chromatin state in gynoecium development
Authors: Kuhn André , Harborough Sigurd Ramans , McLaughlin Heather M. , Kepinski Stefan , Østergaard Lars 
Published: December 2019

AbstractHormonal signalling in animals often involves direct transcription factor-hormone interactions that modulate gene expression1, 2. In contrast, plant hormone signalling is most commonly based on de-repression via the degradation of transcriptional repressors3. Recently, we uncovered a non-canonical signalling mechanism for the plant hormone auxin in organ development with strong similarity to animal hormonal pathways. In this mechanism, auxin directly affects the activity of the auxin response factor ETTIN (ETT) towards regulation of target genes without the requirement for protein degradation4, 5. Here we show that auxin binds ETT to modulate gene expression and that this ETT-auxin interaction leads to the dissociation of ETT from co-repressor proteins of the TOPLESS/TOPLESS-RELATED family followed by histone acetylation and the induction of target gene expression. Whilst canonical ARFs are classified as activators or repressors6, ETT is able to switch chromatin locally between repressive and de-repressive states in an instantly-reversible auxin-dependent manner.
Transformer neural network for protein-specific de novo drug generation as a machine translation problem
Authors: Grechishnikova Daria 
Published: December 2019

AbstractDrug discovery for a protein target is a very laborious, long and costly process. Machine learning approaches and, in particular, deep generative networks can substantially reduce development time and costs. However, the majority of methods imply prior knowledge of protein binders, their physicochemical characteristics or the three-dimensional structure of the protein. The method proposed in this work generates novel molecules with predicted ability to bind a target protein by relying on its amino acid sequence only. We consider target-specific de novo drug design as a translational problem between the amino acid “language” and SMILES (Simplified Molecular Input Line Entry System) representation of the molecule. To tackle this problem, we apply Transformer neural network architecture, a state-of-the-art approach in sequence transduction tasks. Transformer is based on a self-attention technique, which allows the capture of long-range dependencies between items in sequence. The model generates realistic diverse compounds with structural novelty. The computed physicochemical properties and common metrics used in drug discovery fall within the plausible drug-like range of values.
Ex vivo and in vivo imaging of mouse parietal association cortex activity in episodes of cued fear memory formation and retrieval
Authors: Ivashkina Olga I. , Gruzdeva Anna M. , Roshchina Marina A. , Toropova Ksenia A. , Anokhin Konstantin V. 
Published: December 2019

AbstractThe parietal cortex in rodents has an integrative function and participates in sensory and spatial processing, movement planning and decision-making. However, much less is known about its functions in associative memory processing. Here using Fos immunohistochemical mapping of neuronal activity and two-photon imaging in Fos-eGFP mice we show an involvement of anterior part of the parietal cortex (PtA) in the formation and retrieval of recent fear memory in mice. Using ex vivo c-fos imaging we demonstrate the specific activation of the PtA during recent memory retrieval. In vivo two-photon c-fos imaging confirms these results as well as establishes the activation of the PtA neurons during fear memory formation. Additionally, we describe a design of Fos-Cre-GCaMP transgenic mice to investigate long-term changes of calcium dynamics in neurons captured with Fos-TRAP technique during fear conditioning training.