bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lighting the Way for Necrosis Excision Through Indocyanine Green Fluorescence–Guided Surgery
Authors: Zajac Jocelyn C , Liu Aiping , Uselmann Adam J , Lin Christie , Hassan Sameeha E , Faucher Lee D , Gibson Angela LF 
Published: September 2022

BACKGROUND:
No objective technique exists to distinguish necrotic from viable tissue, risking over-excision in burns and loss of wound healing potential. Second window indocyanine green (SWIG) is a novel fluorescence-imaging modality being studied to identify residual solid tumors during oncological surgery. SWIG has also been shown to have avidity for necrosis in animal models, but translation of these findings to humans is lacking. The objective of this study was to evaluate SWIG in the identification of burn wound necrosis and compare it with previously published indocyanine green angiography (ICGA) techniques.

STUDY DESIGN:
This study used mouse, human skin xenograft and human patient burn models. Brightfield and SWIG near-infrared imaging were performed on macroscopic tissue samples, which were then cryopreserved, sectioned, and analyzed for microscopic fluorescence. SWIG fluorescence findings were correlated to visual assessment of the burn wound as well as histological markers of necrosis using hematoxylin and eosin and lactate dehydrogenase stains.

RESULTS:
We found that SWIG identified burn necrosis in a manner dependent on the dose and timing of indocyanine green (ICG) administration and had an inverse fluorescence signal compared with ICGA. Furthermore, SWIG fluorescence identified the interface of viable and nonviable tissue.

CONCLUSION:
Our study confirmed that ICGA is an inconsistent and nonstandardized modality to evaluate burn injuries. In contrast, SWIG imaging is a potential imaging modality to objectively prognosticate burn wound healing potential and guide intraoperative burn excision. Further studies are needed to define ratios of fluorescence intensity values to guide surgical decision-making in burn excision and to better define how ICG is retained in necrotic tissue to enhance utility of SWIG in other disease processes.
Long-Term, Prospective, Multicenter Study of Poly-4-Hydroxybutyrate Mesh (Phasix Mesh) for Hernia Repair in Cohort at Risk for Complication: 60-Month Follow-Up
Authors: Roth John Scott , Anthone Gary J , Selzer Don J , Poulose Benjamin K , Pierce Richard A , Bittner James G , Hope William W , Dunn Raymond M , Martindale Robert G , Goldblatt Matthew I , Earle David B , Romanelli John R , Mancini Gregory J , Greenberg Jacob A , Linn John G , Parra-Davila Eduardo , Sandler Bryan J , Deeken Corey R , Badhwar Amit , Salluzzo Jennifer L , Voeller Guy R 
Published: September 2022

BACKGROUND:
Long-term resorbable mesh represents a promising technology for ventral and incisional hernia repair (VIHR). This study evaluates poly-4-hydroxybutyrate mesh (P4HB; Phasix Mesh) among comorbid patients with CDC class I wounds.

STUDY DESIGN:
This prospective, multi-institutional study evaluated P4HB VIHR in comorbid patients with CDC class I wounds. Primary outcomes included hernia recurrence and surgical site infection. Secondary outcomes included pain, device-related adverse events, quality of life, reoperation, procedure time, and length of stay. Evaluations were scheduled at 1, 3, 6, 12, 18, 24, 30, 36, and 60 months. A time-to-event analysis (Kaplan-Meier) was performed for primary outcomes; secondary outcomes were reported as descriptive statistics.

RESULTS:
A total of 121 patients (46 male, 75 female) 54.7 ± 12.0 years old with a BMI of 32.2 ± 4.5 kg/m2 underwent VIHR with P4HB Mesh (mean ± SD). Fifty-four patients (44.6%) completed the 60-month follow-up. Primary outcomes (Kaplan-Meier estimates at 60 months) included recurrence (22.0 ± 4.5%; 95% CI 11.7% to 29.4%) and surgical site infection (10.1 ± 2.8%; 95% CI 3.3 to 14.0). Secondary outcomes included seroma requiring intervention (n = 9), procedure time (167.9 ± 82.5 minutes), length of stay (5.3 ± 5.3 days), reoperation (18 of 121, 14.9%), visual analogue scale–pain (change from baseline –3.16 ± 3.35 cm at 60 months; n = 52), and Carolinas Comfort Total Score (change from baseline –24.3 ± 21.4 at 60 months; n = 52).

CONCLUSIONS:
Five-year outcomes after VIHR with P4HB mesh were associated with infrequent complications and durable hernia repair outcomes. This study provides a framework for anticipated long-term hernia repair outcomes when using P4HB mesh.
High throughput Bioluminescent assay to characterize and monitor the activity of SARS-CoV-2 Methyltransferases
Authors: Hsiao Kevin , Zegzouti Hicham , Goueli Said 
Published: September 2022

AbstractThe fast rate of viral mutations of SARS CoV-2 result in decrease in the efficacy of the vaccines that have been developed before the emergence of these mutations. Thus, it is believed that using additional measures to combat the virus is not only advisable but also beneficial. Two antiviral drugs were authorized for emergency use by the FDA, namely Pfizer’s two-drug regimen sold under the brand name Paxlovid, and Merck’s drug Lagevrio. Pfizer’s two-drug combination consists of nirmatrelvir, a protease inhibitor that blocks coronavirus ability to multiply and another antiviral, ritonavir, that lowers the rate of drug clearance to boost the longevity and activity of the protease inhibitor. Merck’s drug Lagevrio (molnupiravir) is a nucleoside analogue with a mechanism of action that aims to introduce errors into the genetic code of the virus. We believe the armament against the virus can be augmented by the addition of another class of enzyme inhibitors that are required for viral survival and its ability to replicate. Enzymes like nsp14 and nsp10/16 methyltransferases represent another class of drug targets since they are required for viral RNA translation and evading the host immune system. In this communication, we have successfully verified that the Methyltransferase Glo, which is universal and homogeneous methyltransferase assay can be used to screen for inhibitors of the two pivotal enzymes nsp14 and nsp16 of SARS CoV-2. Furthermore, we have carried out extensive studies on those enzymes using different RNA substrates and tested their activity using various inhibitors and verified the utility of this assay for use in drug screening programs. We anticipate our work will be pursued further to screen for large libraries to discover new and selective inhibitors for the viral enzymes particularly that these enzymes are structurally different from their mammalian counterparts.
Functional impairment of the Lateral Geniculate Nucleus in Multiple Sclerosis
Authors: Sardaripour Neda , Asadi Mehrdad , Moghaddam Hamid Abrishami , Khadem Ali , Rajimehr Reza 
Published: September 2022

AbstractVisual impairment is one of the early symptoms of Multiple sclerosis (MS) disease. The objective of this study is evaluating function of Lateral geniculate nucleus, which bridges visual information from retina to other higher order visual processing areas. We collected BOLD fMRI data from 19 MS and 19 control subjects by employing selective visual stimulation tasks to provoke the whole LGN, Magnocellular, Parvocellular, and Koniocellular pathways as part of LGN multilayer structure. Through statistical analysis, we observed a significant reduction (p<0.05) of the average BOLD signal from the whole LGN structure in MS group. Further investigations showed a significant reduction of BOLD signal (p<0.05) in response to Magno and Parvo stimuli compared to healthy controls that suggested a selective functional impairment emerging in primary visual pathways in MS. In summary, we showed functional abnormalities in LGN structure and its M and P subdivisions based on functional MRI.
Pea-adapted biotype of the aphid Acyrthosiphon pisum induces susceptibility of pea to non-adapted biotype enabling improved feeding and performance
Authors: Shih Po-Yuan , Ollivier Rémi , Cherqui Anas , Ameline Arnaud , Morlière Stéphanie , Outreman Yannick , Simon Jean-Christophe , Sugio Akiko 
Published: September 2022

AbstractMost insect herbivores are adapted to feed on a few host plants only, but the mechanisms underlying plant specialization are poorly understood. One of the dominant hypotheses is that insects inject an oral secretion into the plant that manipulates the plant’s defences resulting in induced susceptibility. We tested this hypothesis on the pea aphid (Acyrthosiphon pisum), which forms multiple biotypes, each specialized on specific legume hosts. In particular, we tested whether a pea-adapted biotype can induce host susceptibility on pea, which should positively affect the fitness of a non-pea-adapted biotype. We found that survival and fecundity of an alfalfa-adapted biotype on pea were enhanced by co-infestation but not pre-infestation with a pea-adapted biotype. The electrical penetration graph (EPG) method was then used to dissect the components of alfalfa biotype feeding behaviour on pea with and without co-infestation by the pea biotype. While probing time did not differ between these two conditions, differences were observed in most other EPG parameters. When co-infested with the pea-adapted biotype, the alfalfa-adapted biotype was more likely to establish a phloem feeding and exhibited a longer ingestion time on pea. Our results clearly indicated that the pea-adapted biotype induced pea susceptibility by increasing the accessibility of non-pea-adapted aphids to the host phloem sap, and as a result, the alfalfa biotype increased its survival rate and fecundity. These results contribute to understanding how aphids manipulate their specific host plants.
Effect of Nitrogen Fertilizer Rate on Yield and Quality Parameters of Malt Barley Varieties for Beer Production in South Gonder, Ethiopia
Authors: Abebe Admas Alemu , Hagos Fikre 
Published: September 2022

ABSTRACTThe objective of this study was to examine the effect of different nitrogen rates on the yield and malt barley quality parameters of two malting barley varieties (Holker and miskal-21). The experiment was carried out during 2013 cropping season at three locations, namely Ebnat, Estie and Farta. The following nitrogen rates were applied: 0, 60, 120and 180 kg ha-1 and a factorial experiment arranged in RCBD was applied to conduct the research. The result of this study indicated that nitrogen significantly increased the grain yield (648.2 to 1657.4and 666.7 to 1851.8 kg ha-1for Holker and Miskal-21 respectively). Malt quality was decreased by increasing nitrogen rates (1.28 to 2.34%). Apart from nitrogen rates, the varieties also affected the yield and nature of the protein content levels. As indicated in this result Holker variety gave optimum grain yield and lowest protein content, therefore, this variety is advisable to be used by malt brewers to satisfy their requirements. The optimal malt quality and yield was achieved by applying between 60-120 kg N ha-1 beyond this rate, grain yield might be significantly increased but malt qualities at the same time significantly decreased therefore it is recommended to obtain optimum yield as well as high malt qualities
Understanding changes in genetic literacy over time and in genetic research participants
Authors: Little India D. , Koehly Laura M. , Gunter Chris 
Published: September 2022

AbstractAs genomic and personalized medicine becomes mainstream, assessing and understanding the public’s genetic literacy is paramount. Because genetic research drives innovation in this area and involves much of the public, it is equally important to assess its impact on genetic literacy. We designed a survey to assess genetic literacy in three ways (familiarity, knowledge, and skills) and distributed it to two distinct samples: 2050 members of the general population, and 2023 individuals currently enrolled in a large-scale genetic research study. We compared these data to a similar survey implemented in 2013. The results indicate that familiarity with basic genetic terms in 2021 (M = 5.36, p<.001) and knowledge of genetic concepts in 2021 (M = 9.06, p = 0.002) is significantly higher compared to 2013 (M = 5.08; M = 8.72). Those currently enrolled in a genetic study were also significantly more familiar with genetic terms (M = 5.79, p<.001), more knowledgeable of genetic concepts (M = 10.27, p<.001), and scored higher in skills (M = 3.57, p<.001) than the general population (M = 4.98; M = 9.06; M = 2.65).The results suggest that genetic literacy is improving over time, though there is room for improvement. The data also suggest that participating in genetic research is one avenue for improving genetic literacy. We conclude that educational interventions are needed to ensure familiarity with and comprehension of basic genetic concepts. We also suggest further exploration of the impact of genetic research participation on genetic literacy to determine mechanisms for potential interventions.
Mangroves deviate from other angiosperms in their genome size, leaf cell size, and cell packing density relationships
Authors: Jiang Guo-Feng , Li Su-Yuan , Dinnage Russell , Cao Kun-Fang , Simonin Kevin A. , Roddy Adam B. 
Published: September 2022

ABSTRACTBackground and AimsWhile genome size limits the minimum sizes and maximum numbers of cells that can be packed into a given leaf volume, mature cell sizes can be substantially larger than their meristematic precursors and vary in response to abiotic conditions. Mangroves are iconic examples of how abiotic conditions can influence the evolution of plant phenotypes.MethodsHere, we examined the coordination between genome size, leaf cell sizes, and cell packing densities, and leaf size in 13 mangrove species across four sites. Four of these species occurred at more than one site, allowing us to test the effect of climate on leaf anatomy.ResultsWe found that genome sizes of mangroves were very small compared to other angiosperms, and, like other angiosperms, mangrove cells were always larger than the minimum size defined by genome size. Increasing mean annual temperature of a growth site led to higher packing densities of veins (Dv) and stomata (Ds) and smaller epidermal cells but had no effect on stomatal size. Contrary to other angiosperms, mangroves exhibited (1) a negative relationship between guard cell size and genome size; (2) epidermal cells that were smaller than stomata, and (3) coordination between Dv and Ds that was not mediated by epidermal cell size. Furthermore, mangrove epidermal cell sizes and packing densities covaried with leaf size.ConclusionsWhile mangroves exhibited coordination between veins and stomata and attained a maximum theoretical stomatal conductance similar to other angiosperms, the tissue-level tradeoffs underlying these similar relationships across species and environments was markedly different, perhaps indicative of the unique structural and physiological adaptations of mangroves to their stressful environments.
Function of cell adhesion molecules in differentiation of ray sensory neurons in C. elegans
Authors: Sakai Naoko , Sun Peter , Kim Byunghyuk , Emmons Scott W. 
Published: September 2022

AbstractFor proper functioning of the nervous system, it is crucial that neurons find their appropriate partners and build the correct neural connection patterns. Although cell adhesion molecules (CAMs) have been studied for many years as essential players in neural connections, we have yet to unravel the code by which CAMs encode synaptic specificity. We analyzed the effects of mutations in CAM genes on the morphology and synapses of a set of sensory neurons in the C. elegans male tail. B-type ray sensory neurons express ten genes encoding CAMs. We examined the effect on axon trajectory and localization of presynaptic components in viable mutants of nine of these. We found axon trajectory defects in mutants of UNC-40/DCC, SAX-3/ROBO, and FMI-1/Flamingo/Celsr1. In none of the mutants was presence of presynaptic components in axons lost, and in several the level appeared to increase, suggesting possible accumulation. B-type sensory neurons fasciculate with a second type of ray sensory neuron, the A-type, in axon commissures. We found cell non-autonomous effects consistent with each promoting the trajectory of the other. Overall, single and multiple mutants of CAM genes had limited effects on ray neuron trajectories and accumulation of synaptic components.
Identifying the engagement of a brain network during a targeted tDCS-fMRI experiment using a machine learning approach
Authors: Shinde A. B. , Mohapatra S. , Schlaug G. 
Published: September 2022

AbstractTranscranial direct current stimulation (tDCS) can noninvasively modulate behavior, cognition, and physiologic brain functions depending on polarity and dose of stimulation as well as montage of electrodes. Concurrent tDCS-fMRI presents a novel way to explore the parameter space of non-invasive brain stimulation and to inform the experimenter as well as the participant if a targeted brain region or a network of spatially separate brain regions has been engaged and modulated. We compared a multi-electrode (ME) with a single electrode (SE) montage and both active conditions with a no-stimulation (NS) control condition to assess the engagement of a brain network and the ability of different electrode montages to modulate network activity. The multi-electrode montage targeted nodal regions of the right Arcuate Fasciculus Network (AFN) with anodal electrodes placed over the skull position of the posterior superior temporal/middle temporal gyrus (STG/MTG), supramarginal gyrus (SMG), posterior inferior frontal gyrus (IFG) and a return cathodal electrode over the left supraorbital region. In comparison, the single electrode montage used only one anodal electrode over a nodal brain region of the AFN, but varied the location between STG/MTG, SMG, and posterior IFG for different participants. Whole-brain rs-fMRI was obtained every three seconds. The tDCS-stimulator was turned on at 3 minutes after the scanning started. A 4D rs-fMRI data set was converted to dynamic functional connectivity (DFC) matrices using a set of ROI pairs belonging to the AFN as well as other unrelated brain networks. In this study, we evaluated the performance of five algorithms to classify the DFC matrices from the three conditions (ME, SE, NS) into three different categories. The highest accuracy of 0.92 was obtained for the classification of the ME condition using the K Nearest Neighbor (KNN) algorithm. In other words, applying the classification algorithm allowed us to identify the engagement of the AFN and the ME condition was the best montage to achieve such an engagement. The top 5 ROI pairs that made a major contribution to the classification of participant’s rs-fMRI data were identified using model performance parameters; ROI pairs were mainly located within the right AFN. This proof-of-concept study using a classification algorithm approach can be expanded to create a real-time feedback system at a participant level to detect the engagement and modulation of a brain network that spans multiple brain lobes.
Meggie – easy-to-use graphical user interface for M/EEG analysis based on MNE-python
Authors: Heinilä Erkka , Parviainen Tiina 
Published: September 2022

AbstractBackgroundIn the last decades, electrophysiological imaging methodology has seen many advances and the computational power in the neuroscience laboratories has steadily increased. Still, the new methodologies are unavailable for many. There is a need for more versatile analysis approaches for neuroscience specialists without a programming background.New methodUsing a software which provides standard pipelines, provides good default values for parameters, has a good multi-subject support, and stores the used analysis steps with the parameters in one place for reporting, is efficient and fast. In addition to enabling analysis for people without background in programming, it enables analysis for people with background in programming but a limited background in neuroscience. When constructed with care, the GUI may guide the researcher to apply analysis steps in correct order with reasonable default parameters.Comparison to existing methodsTwo existing software, EEGLAB and Brainstorm, both provide an easy-to-use graphical user interface for end-to-end analysis for multiple subjects. The key difference to work presented here is the choice of language. The scientific community is moving en masse towards the python programming language, thus making it an ideal platform for extendable software. Another problem with Matlab is that it is not free - both from the perspective of open source and concrete monetary resources. Within the current trend towards increasing open science, covering data, analysis and reporting, the need for open source software is imperative.ResultsMeggie is an open source software for running MEG and EEG analysis with easy-to-use graphical user interface. It is written in Python 3, runs on Linux, macOS and Windows, and uses the MNE-python library under the hood to do heavy lifting. It is designed to allow end-to-end analysis of MEG and EEG datasets from multiple subjects with common sensor-level analysis steps such as preprocessing, epoching and averaging, spectral analysis and time-frequency analysis. Most of the analysis steps can be run for all the subjects in one go, and combining the results across subjects is made possible with grand averages. We have emphasized the extendibility of Meggie by implementing most of the Meggie itself as plugins, thus ensuring that new plugins have access to all necessary core features.ConclusionMeggie answers the demand for easy-to-use and extendable python-based graphical user interface that provides an end-to-end analysis environment for M/EEG data analysis. It is freely available at https://github.com/cibr-jyu/meggie under the BSD license. Installation instructions, documentation and tutorials are found on that website.Highlights- MNE-python-based graphical user interface for M/EEG analysis- Easy to use even without programming background- Has good support for multiple subjects- Written in python, and can be easily extended with plugins- Free and open source with BSD license
Photoselective sequencing: microscopically-guided genomic measurements with subcellular resolution
Authors: Mangiameli Sarah , Chen Haiqi , Earl Andrew S. , Dobkin Julie , Lesman Daniel , Buenrostro Jason , Chen Fei 
Published: September 2022

AbstractIn biological systems, spatial organization is interconnected with genome function and regulation. However, methods that couple high-throughput genomic and epigenomic profiling with spatial information are lacking. Here, we developed Photoselective Sequencing, a spatially-informed DNA sequencing method to assay collections of cells or subcellular regions that share a unifying morphological trait. In Photoselective Sequencing, we prepare a blocked fragment library within a fixed biological specimen. Guided by fluorescence imaging, we remove the block in specific regions of interest using targeted illumination with near-UV light, ultimately allowing high-throughput sequencing of the selected fragments. To validate Photoselective Sequencing, we profile chromatin openness in fluorescently-labeled cell types within the mouse brain and demonstrate strong agreement with published single-cell ATAC-seq data. Using Photoselective Sequencing, we characterize the accessibility profiles of oligodendrocyte-lineage cells within the cortex and corpus-callosum regions of the brain. We develop a new computational strategy for decomposing bulk accessibility profiles by individual cell types, and report a relative enrichment of oligodendrocyte-progenitor-like cells in the cortex. Finally, we leverage Photoselective Sequencing for unbiased profiling of DNA at the nuclear periphery, a key chromatin organizing region. We compare and contrast the Photoselective Sequencing profile with lamin ChIP-seq data, and identify features beyond lamin interaction that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that Photoselective Sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties.