First report of three bunya-like viruses, apple luteovirus 1, and apple hammerhead viroid in apples from Hakkari, Türkiye.

Türkiye is a major apple fruit producer in the crossroads of Europe and the Middle East. Several reports have described the presence of multiple viruses affecting apple production in Türkiye, including apple stem grooving virus (ASGV), apple stem pitting virus (ASPV), apple chlorotic leafspot virus (ACLSV), and apple mosaic virus (ApMV) (Kurçman 1977; Fidan 1994; Çaglayan et al. 2003). However, there are no reports of the presence of the recently discovered bunya-like viruses citrus concave gum-associated virus (CCGaV), and apple rubbery wood viruses 1 and 2 (ARWV1 and 2), as well as apple luteovirus 1 (ALV-1), and apple hammerhead viroid (AHVd) in Türkiye, all of which have been previously reported in other apple-producing countries (Wright et al. 2018; Liu et al. 2018; Zhang et al. 2014). Leaves from one Gala, two Granny Smith, and one Golden Delicious apple trees showing mild symptoms of curling, chlorosis, and yellowing were collected from four different orchards in the province of Hakkari, southeast Türkiye during June 2022 and sent to USDA APHIS Plant Germplasm Quarantine Program (under permit) for virus and viroid HTS-based diagnostics. Total RNA was isolated using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer's guidelines to prepare RNAseq libraries using the TruSeq Stranded Total RNA Library Plant Kit (Illumina, Inc) as described in Malapi-Wight et al. (2021). Libraries were sequenced on the NextSeq500 sequencer (PE 2x75), and approximately 45 million reads were obtained per each sample on average. Bioinformatic analysis was performed as described in Costa et al. (2022) using Phytopipe, where unclassified pathogen-derived reads were de novo assembled and contigs were compared to the NCBI viral nucleotide and protein databases by BlastN and BlastX respectively using a 10-4 e-value cutoff. Nearly complete genome contigs were obtained for ACLSV (OR640150) and ASPV (OR640151) in all four samples and for ASGV (OR640152) in 3 of the 4 samples. The average BlastN identity to sequences in GenBank was 92.3% for ACLSV, ranging from 89-94 %. BlastN identity for ASPV was 86%, ranging from 81-92 % while the ASGV average BlastN identity was 98.2%. Nearly complete genomes with average genome coverage of 92.4% and 95.6% for RNA1 and RNA2 of CCGaV (OR640153 and OR640154), were found in two of the four samples with BlastN identity of 94.7% and 94.8% to GenBank sequences. Additionally, nearly complete genome of the large (L), medium (M), and small (S) segments for ARWV1 were found in two samples with average genome coverage of 99.9%, 99.4%, and 100% respectively and BlastN identity of 98.8%, 95.2%, and 98.4% (OR640155, OR640156, OR640157). ARWV2 contigs were also found in 1 sample where M and S segments had a coverage of 99.8% and BlastN identity of 95.4% (OR640158 and OR640159). The nearly complete genome of ALV-1 was also found in two of four samples with genome coverage of 94.1% and an average BlastN identity of 93.4% (OR640160). AHVd was found in one of the Granny Smith trees with 19,260 mapped reads to the reference GenBank MH049335.1 and identity of 98.3% (OR640149). The HTS findings of CCGaV, ARWV1, ARWV2, and ALV-1, from Türkiye were later confirmed by Sanger sequencing using custom-designed primers targeting the coat protein, the RNA-dependent RNA polymerase, or ~390bp for the AHVd genome (Supplementary Table 1). To further learn about the incidence of these agents, we tested 12 other apple samples from six different neighboring orchards and found them at 18.8% rate for CCGaV, 12.5% for both ARWV1 and ARWV2, 25% for ALV-1, and 37.5% for AHVd respectively. To our knowledge, this is the first report of the apple viruses CCGaV, ARWV1, ARWV2, and ALV-1, and the AHVd viroid in Türkiye. Further studies of the impact of these agents on orchard's health are necessary, including their prevalence in high apple production regions of Türkiye.

Accelerated and Concerted Aza-Michael Addition and SuFEx Reaction in Microdroplets in Unitary and High-Throughput Formats.

The sulfur fluoride exchange (SuFEx) reaction is significant in drug discovery, materials science, and chemical biology. Conventionally, it involves installation of SO2 F followed by fluoride exchange by a catalyst. We report catalyst-free Aza-Michael addition to install SO2 F and then SuFEx reaction with amines, both occurring in concert, in microdroplets under ambient conditions. The microdroplet reaction is accelerated by a factor of ∼104 relative to the corresponding bulk reaction. We suggest that the superacidic microdroplet surface assists SuFEx reaction by protonating fluorine to create a good leaving group. The reaction scope was established by performing individual reactions in microdroplets of 18 amines in four solvents and confirmed using high-throughput desorption electrospray ionization experiments. The study demonstrates the value of microdroplet-assisted accelerated reactions in combination with high-throughput experimentation for characterization of reaction scope.

Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

In the version of this article initially published, the authors erroneously reported the search mode that was used for ProSightPC 3.0 in the Online Methods and in Supplementary Table 3.

Informed-Proteomics: open-source software package for top-down proteomics.

Top-down proteomics, the analysis of intact proteins in their endogenous form, preserves valuable information about post-translation modifications, isoforms and proteolytic processing. The quality of top-down liquid chromatography-tandem MS (LC-MS/MS) data sets is rapidly increasing on account of advances in instrumentation and sample-processing protocols. However, top-down mass spectra are substantially more complex than conventional bottom-up data. New algorithms and software tools for confident proteoform identification and quantification are needed. Here we present Informed-Proteomics, an open-source software suite for top-down proteomics analysis that consists of an LC-MS feature-finding algorithm, a database search algorithm, and an interactive results viewer. We compare our tool with several other popular tools using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.

Different roles for inhibition in the rhythm-generating respiratory network.

Unraveling the interplay of excitation and inhibition within rhythm-generating networks remains a fundamental issue in neuroscience. We use a biophysical model to investigate the different roles of local and long-range inhibition in the respiratory network, a key component of which is the pre-Bötzinger complex inspiratory microcircuit. Increasing inhibition within the microcircuit results in a limited number of out-of-phase neurons before rhythmicity and synchrony degenerate. Thus unstructured local inhibition is destabilizing and cannot support the generation of more than one rhythm. A two-phase rhythm requires restructuring the network into two microcircuits coupled by long-range inhibition in the manner of a half-center. In this context, inhibition leads to greater stability of the two out-of-phase rhythms. We support our computational results with in vitro recordings from mouse pre-Bötzinger complex. Partial excitation block leads to increased rhythmic variability, but this recovers after blockade of inhibition. Our results support the idea that local inhibition in the pre-Bötzinger complex is present to allow for descending control of synchrony or robustness to adverse conditions like hypoxia. We conclude that the balance of inhibition and excitation determines the stability of rhythmogenesis, but with opposite roles within and between areas. These different inhibitory roles may apply to a variety of rhythmic behaviors that emerge in widespread pattern-generating circuits of the nervous system.NEW & NOTEWORTHY The roles of inhibition within the pre-Bötzinger complex (preBötC) are a matter of debate. Using a combination of modeling and experiment, we demonstrate that inhibition affects synchrony, period variability, and overall frequency of the preBötC and coupled rhythmogenic networks. This work expands our understanding of ubiquitous motor and cognitive oscillatory networks.

Comparison of Surgical Treatments for Zenker Diverticulum: A Systematic Review and Network Meta-analysis.

Importance: Zenker diverticulum (ZD) can cause significant dysphagia, and symptoms can return or persist after surgery. This systematic review and network meta-analysis is the first to our knowledge to compare 3 common surgical techniques for ZD. Objective: To compare the 3 most common surgical techniques-endoscopic laser-assisted diverticulotomy, endoscopic stapler-assisted diverticulotomy, and transcervical diverticulectomy with cricopharyngeal myotomy-in adult patients with ZD. Data Sources: The published literature was searched using strategies designed by a medical librarian (search performed September 21, 2018). Strategies were established using a combination of controlled vocabulary terms and keywords and were executed in Ovid MEDLINE (1946 to September 21, 2018), Embase (1947 to September 21, 2018), Scopus (1823 to September 21, 2018), Cochrane Library, and ClinicalTrials.gov. Results were limited to English using database-supplied filters, which generated studies from 1997 to 2017. Study Selection: Inclusion criteria were cohort studies or randomized clinical trials. Studies that included patients needing revision surgery or undergoing an alternative technique were excluded. Data Extraction and Synthesis: The Preferred Reporting Items for Systematic Reviews and Meta-analyses-Network Meta-analyses (PRISMA-NMA) checklist was used to report the study findings. Two authors independently reviewed the studies. Main Outcome and Measure: The primary outcome measure was the incidence of persistent or recurrent symptoms following surgery. The primary study outcome was planned before data collection began. Results: The search generated 529 studies. After applying inclusion and exclusion criteria, 9 cohort studies remained, consisting of 903 patients treated with either laser-assisted diverticulotomy (n = 283), transcervical diverticulectomy (n = 150), or stapler-assisted diverticulotomy (n = 470). A network meta-analysis was performed. Between endoscopic laser-assisted diverticulotomy and open diverticulectomy, the open approach showed a statistically lower likelihood of persistent/recurrent symptoms following treatment (odds ratio [OR], 0.20; 95% CI, 0.04-0.91). Comparing laser-assisted diverticulotomy with the stapler-assisted technique, there was not a significant difference between the 2 techniques (OR, 0.83; 95% CI, 0.43-1.60). The consistency model for the network meta-analysis was supported (χ21 = 0.12; P = .73). Conclusions and Relevance: This systematic review and meta-analysis compared 3 common techniques for treating ZD. The open approach showed a decreased likelihood of persistent or recurrent symptoms following surgery compared with the 2 other techniques.

A Comprehensive Analysis of Complications of Free Flaps for Oromandibular Reconstruction.

OBJECTIVES/HYPOTHESIS: To determine the frequency and management of short- and long-term complications related to oromandibular free flap reconstruction and identify potentially predictive factors of hardware complications. STUDY DESIGN: Retrospective chart review. METHODS: A retrospective database from chart review was formed consisting of 266 oromandibular free flap reconstructions performed at a single institution over a 15-year period. Data were collected on demographics, surgical treatment, complications, and management of complications. Subgroup univariate and multivariate analyses were performed to compare patients with hardware complications and those without. RESULTS: Eighty-one of 266 patients (30.5%) that underwent oromandibular reconstruction had an early complication (<4 weeks after surgery), and the most common complications were cervical wound dehiscence (11.3%) and fistulas (9.40%). Eighty of 266 patients (30.1%) had a long-term complication (>4 weeks after surgery) and the most common complication was plate exposure (26.7%). Univariate and multivariate analyses showed no association between whether there was hardware extrusion and fibula versus scapula, smoking history, virtual surgical planning (VSP), and dental implantation (P > .05). Only early complications (OR, 3.59, 95% CI, 1.83-7.05, P < .01) and patients undergoing oromandibular reconstruction for osteoradionecrosis (OR, 2.26, 95% CI, 1.10-4.64, P = .03) were strongly and independently associated with subsequent hardware extrusion on univariate analysis. CONCLUSIONS: Both short- and long-term complications are common after oromandibular reconstruction. The most important predictive factor for a late complication is an early complication and prior radiation. There was no difference of plate complications among the various free flap types. Dental implantation and use of VSP were not associated with hardware complications. LEVEL OF EVIDENCE: 4 Laryngoscope, 131:1997-2005, 2021.

The 100 Most Cited Papers About Cancer Epigenetics.

Introduction Although bibliometric analyses have been performed in the past on cancer and genomics, little is known about the most frequently cited articles specifically related to cancer epigenetics. Therefore, the purpose of this study is to use citation count to identify those papers in the scientific literature that have made key contributions in the field of cancer epigenetics and identify key driving forces behind future investigations. Materials and methods The Thomas Reuters Web of Science services was queried for the years 1980-2018 without language restrictions. Articles were sorted in descending order of the number of times they were cited in the Web of Science database by other studies, and all titles and abstracts were screened to identify the research areas of the top 100 articles. The number of citations per year was calculated. Results We identified the 100 most-cited articles on cancer epigenetics, which collectively had been cited 147,083 times at the time of this writing. The top-cited article was cited 7,124 times, with an average of 375 citations per year since publication. In the period 1980-2018, the most prolific years were the years 2006 and 2010, producing nine articles, respectively. Twenty-eight unique journals contributed to the 100 articles, with the Nature journal contributing most of the articles (n=22). The most common country of article origin was the United States of America (n=78), followed by Germany (n=4), Switzerland (n=4), Japan (n=3), Spain (n=2), and United Kingdom (n=2). Conclusions In this study, the 100 most-cited articles in cancer epigenetics were examined, and the contributions from various authors, specialties, and countries were identified. Cancer epigenetics is a rapidly growing scientific field impacting translational research in cancer screening, diagnosis, classification, prognosis, and targeted treatments. Recognition of important historical contributions to this field may guide future investigations.

Reconstruction of animal bite injuries to the head and neck.

PURPOSE OF REVIEW: The aim if this review is to provide an update on the existing literature of animal bite treatment strategies and provide a systematic approach to animal bites from presentation to reconstruction. RECENT FINDINGS: Dog bites cause 80-90% of animal bites with 26.8-56.5% occurring in the head and neck. Infection rates may be as low as 5.7-9.7%. Primary closure alone is sufficient in 69.8% of dog bites within the first 24 h. SUMMARY: Animal bite injuries to the head and neck are common, especially in the younger population. Dogs cause a majority of these bite injuries. Injuries can include simple lacerations or punctures, avulsions with tissue present, or avulsions with loss of tissue. The most common locations are the cheek, nose, and lips. It is important to gather the vaccination status of the animal and patient and to administer tetanus/rabies prophylaxis if indicated. Antibiotics are typically prescribed for 3-5 and 7-14 days for uninfected and infected wounds, respectively. These wounds require evaluation, irrigation, and occasionally debridement or repair in the operating room. The type of repair is determined based on the location and extent of injury and can range from primary closure to microsurgical replantation, skin grafts, flaps, or even facial transplantation.

An account of the Speech-to-Song Illusion using Node Structure Theory.

In the Speech-to-Song Illusion, repetition of a spoken phrase results in it being perceived as if it were sung. Although a number of previous studies have examined which characteristics of the stimulus will produce the illusion, there is, until now, no description of the cognitive mechanism that underlies the illusion. We suggest that the processes found in Node Structure Theory that are used to explain normal language processing as well as other auditory illusions might also account for the Speech-to-Song Illusion. In six experiments we tested whether the satiation of lexical nodes, but continued priming of syllable nodes may lead to the Speech-to-Song Illusion. The results of these experiments provide evidence for the role of priming, activation, and satiation as described in Node Structure Theory as an explanation of the Speech-to-Song Illusion.