bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reproducibility of NIRS Oxidative Capacity Measurements in the Vastus Lateralis and Medial Hamstring Muscles
Authors: Gosalia Jigar , Hanna Rewais B. , Vairo Giampietro L. , Irving Brian A. , McCully Kevin M. , Proctor David N. 
Published: April 2020

Oxidative capacity within selected muscles can be measured non‐invasively using Near Infrared Spectroscopy (NIRS) by employing a series of transient arterial occlusion cuffs after a metabolic stimulus. Traditionally, this protocol involves voluntary contraction of a single limb followed by up to 22 transient ischemic occlusions per measurement. Our lab has adapted an established protocol
1 to develop a novel protocol that allows for an increased number of measurements using fewer (i.e. 6) ischemic occlusions combined with surface electrical stimulation (E‐stim) in both limbs simultaneously. However, reproducibility has not yet been established with this protocol.PURPOSETo determine the within‐day and between‐day reproducibility of this protocol in both the vastus lateralis and medial hamstring muscles.METHODSThe protocol involved 2 NIRS probes placed over the vastus lateralis (VL) muscles or the medial hamstring (MH) muscles in healthy adults to sense changes in muscle oxygenation. E‐stim pads were placed adjacent to the NIRS probe and were used to increase metabolic rate (>3 fold) using a biphasic setting at 20 Hz, with an intensity (mV) that is within the participant’s tolerance. The mitochondrial oxidative capacity protocol involved 4 consecutive sets of 30 seconds of E‐stim followed by 6 x 5 sec cuff inflation/5 sec cuff deflation cycles using upper thigh rapid inflation cuffs. Analysis consisted of calculating oxygenation recovery rate constants (k) for each muscle (i.e., 4 repeated measurements per muscle, per limb) using a customized software program. Coefficient of variation (CV) and intraclass correlation coefficients [ICC(2,k)] were used to assess reproducibility.RESULTSVariability of within‐day repeated tests (CV) averaged 3.8% (0.9%–6.7%) in the VL (n=12) with an average rate constant (min−1) of 1.96 +/− 0.07 and 4.9% (1.0%–14.1%) in the MH (n=10) with an average rate constant (min−1) of 2.05 +/− 0.11. Variability of between‐day repeated tests averaged 11.7% (8.7% – 14.8%) in the VL (n=4) and 10.4% (7.5% – 12.0%) in the MH (n=4). [ICC(2,k)] was calculated as 0.98, 95% CI [0.95, 0.99] for the VL and 0.93, 95% CI [0.81, 0.98] for the MH muscles.CONCLUSIONThese results suggest the proposed protocol demonstrates good to excellent reproducibility in both muscles, with a higher rate associated with the VL. These outcomes provide investigators with an efficient alternative for measuring muscle oxidative capacity non‐invasively in the vastus lateralis and medial hamstring muscles.Support or Funding InformationCenter for Orthopedic Research and Translational Science, Penn State College of MedicineExperimental setup of bilateral NIRS oxidative capacity protocolFigure 1
Abductor Pollicis Longus distal muscle belly variation in a male human cadaver
Authors: Bowman Carley , Rosario Martin 
Published: April 2020

BackgroundTypically, five muscles of the posterior forearm intersect the wrist joint and contribute tendons to the first two digits.PurposeDepict the anatomical variation in the muscles and tendons of the extrinsic musculature of the thumb in one human cadaver.MethodsOne specimen was dissected and reported in this work. During dissection, an extra muscle belly was found embedded within the tendon of abductor pollicis longus. This variation was discovered near the distolateral attachment site at the base of the first metacarpal joint.ResultsThe additional muscle belly is located between abductor pollicis brevis and extensor carpi radialis muscles. Typically, the proximal muscle belly originates at the posterior proximal half of the ulna and middle one‐third of the radius inserting at the typical site of attachment, lateral aspect of the base of the first metatarsal, via the tendon. However, the tendon continues distally to a second muscle belly embedded within the distolateral one‐third of the abductor pollicis longus tendon where the attachment site can be found at the traditional lateral aspect of the base of the first metacarpal bone.ConclusionThe extrinsic extensors of the thenar region in this cadaver had an additional distal muscle belly embedded within the distal (extra) portion of the tendon differing from the standard structures. Knowledge of this additional structure may help medical professionals understand possible functional differences among individuals with this morphological variation.Picture of thumb with extra tendon anatomy variation.Figure 1
PROTECTIVE EFFECT OF LOW LEVEL LASER THERAPY ON DORSAL SKIN FLAPS SURVIVAL: RELEVANCE TO CYTOKINES SECRETION.
Authors: Chang Alexandre Jin Bok Audi , Silva Luciana Miato Gonçalves , Silva Deiwet Ribeiro , Zamuner Stella Regina 
Published: April 2020

The loss of skin flaps (SF) due to tissue necrosis can be catastrophic, even with mortality, especially when there is exposure of large vessels or noble structures. This outcome occurs between 2 to 20% of the procedures performed. There is no currently adjuvant treatment that improves the survival of cutaneous flaps, without side effects or significant risks. Recent studies have sought to prove the efficiency of photobiomodulation (PBM) by means of Low Level Laser Therapy (LLLT) and present promising results for increased SF survival.OBJECTIVETo evaluate the effect of LLLT in dorsal skin flaps of mice in terms of tissue necrosis extent as well as biochemical analysis of pro and anti‐inflammatory cytokines.METHODSForty‐eighth Balb/C (20–25 g) male mice were randomly distributed into two groups with twenty‐four animals each; (1) control group that was not submitted to laser irradiation and (2) experimental group that was submitted to laser irradiation on the flap pedicle with a 660 nm wavelength, exposure radiant of 2.25 J/cm2 for a total time of 20 s/point. The treatment started immediately after performing the cranial base random skin flap (3× 1 cm dimension). The animals were euthanized after the evaluation of the percentage of necrosis area, blood and skin tissue was collected for analysis of cytokines and histology on 4th, 7th and 10th postoperative days. Results demonstrated that LLLT irradiation reduced the area of necrosis, significantly decreased IL‐1, IL‐6 and TNF‐α and increased IL‐10 cytokines compared to the non‐irradiated control group. In conclusion, LLLT may improve the healing of skin flaps by decreasing pro‐inflammatory cytokines and increasing the anti‐inflammatory IL‐10.Serum Interleukines after low level laser therapy (gray) versus control group (black). Significant decrease in pro‐inflamatories interleukines 1, 6 and tumor necrosis factor alfa and significant increase in anti‐inflamatory interleukin 10 after 4, 7 and 10 days post‐op.Figure 1
Cerebellar Transcranial Magnetic Stimulation Disrupts Vestibular Reflexes in Standing Balance
Authors: Donald Joshua R. , Peters Ryan M. , Kiss Zelma H. T. , Day Trevor A. , Strzalkowski Nicholas D.J. 
Published: April 2020

Despite its seemingly effortless execution, standing balance is a complex task maintained by the integration of sensory feedback from visual, somatosensory (muscle, skin, joint receptors), and vestibular (inner ear) systems. The vestibular system provides feedback about head acceleration and can be manipulated experimentally by passing an electrical current percutaneously through the mastoid processes. The cerebellum plays an important role in standing balance by integrating sensory feedback to refine activity in postural muscles. A recent study has shown that experimentally depressing cerebellar activity with repetitive transcranial magnetic stimulation can influence postural sway and muscle reflex responses following electrical vestibular stimulation. The aim of this study was to investigate the impact of acute cerebellar stimulation on vestibular muscle reflex responses in different head positions during standing balance. We applied a novel combination of stochastic electrical vestibular stimulation (SVS, ±2.5 mA, 0–20 Hz) and single‐pulse cerebellum transcranial magnetic stimulation (TMS, 60% maximum stimulator output) on fifteen healthy adults (6 males, 9 females; 21–32 years old) in two head positions: head forward and head right. Muscle reflexes were recorded bilaterally with surface electromyography (EMG) from lower leg (soleus and medial gastrocnemius) and neck (sternocleidomastoid) muscles. Time‐based cumulant density and frequency‐based coherence analyses were used to evaluate the relationship between the SVS and evoked EMG responses one second before (Pre) and one second after (Post) cerebellar TMS. 50 TMS pulses were delivered per head position. Preliminary analysis performed on left medial gastrocnemius (LMG) head right data indicated a significant reduction in the short latency (SL, P = 0.0377) and medium latency (ML, P < 0.0001) reflexes following cerebellar TMS (Fig.
1). In addition, a significant drop in the coherence between the SVS and LMG Pre to Post was found using a difference of coherence test. These findings support the cerebellum to be an important center for the integration of vestibular feedback for the control of standing balance.Support or Funding InformationMount Royal University Faculty of Science and TechnologyFigure 1
Sugar Responsive Ubiquitylation mediated Endosomal Trafficking of N‐acetylglucosamine Transporter (Ngt1) in Candida albicans.
Authors: Rao Kongara Hanumantha , Ghosh Swagata 
Published: April 2020

N‐acetylglucosamine (GlcNAc) signals a wide array of functions in diverse organisms ranging from bacteria to humans but in Candida albicans the dynamics associated with GlcNAc import, a prerogatory step in GlcNAc signalling is unrevealed. In this study, we have shown the molecular mechanism involved in the dynamics of a novel GlcNAc transporter (Ngt1) at the cell surface. Ngt1 showed sugar responsive endosomal trafficking to modulate its cell surface levels by interacting with key players of ubiquitylation machinery, viz. CaRsp5 ubiquitin ligase, CaArt1 adaptor protein and Snf1 protein kinase by following trafficking route of endosomes‐TransGolgi and finally vacuole. We have employed time‐lapse microscopy, LC‐MS/MS analysis, Fat‐blot technique and Site Directed Mutagenesis (SDM) along Immuno‐precipitation and immunoblot analysis to understand the intricate molecular events involved in the Endosomal trafficking. Ngt1 showed interaction with novel sphingolipids, disialoganglioside (GD3) and sulfatides that confirms its localization within lipid rafts of the plasma membrane. This study also elucidates the role of UBI4 locus and Ras1 signalling component in Ngt1 ubiquitylation and its endocytosis. Being a first of its kind report, elaborating the molecular mechanism of endosomal trafficking in Candida albicans, this study can undoubtedly provide a platform for basic research in trafficking as well as applied research towards the development of therapeutics.Support or Funding InformationScience and Engineering Research Board (SERB), Govt of IndiaGlcNAc transporter (Ngt1) undergoes ubiquitylation and internalization in response to GlcNAc.A‐Western blotting analysis showing expression, ubiquitylation and degradation of Ngt1‐GFPγ. The upshifted bands indicate ubiquitylated (Ubi) form of Ngt1‐GFPγ, supported by western blot analysis with anti‐ubiquitin antibody in panel C. B‐Localization pattern of Ngt1‐GFPγ in response to GlcNAc at 60 and 120 min after induction and it is co‐localized with a vacuole specific maker‐CMAC.Figure 1Life Cycle of Ngt1.Ngt1 is a membrane resident protein having 12 membrane‐spanning domains as predicted by TMHMM server v. 2.0. Ngt1 undergoes sugar‐responsive ubiquitylation followed by Endosomal trafficking to undergo degradation in the vacuole. The transporter shows association with novel components of the lipid rafts.Figure 2
Identification of Predictors of Physical Frailty and Sarcopenia through a New Multi‐ Marker Approach
Authors: Marzetti Emanuele 
Published: April 2020

Background and ObjectivesPhysical frailty & sarcopenia (PF&S) is a prototypical geriatric condition characterized by reduced physical function and low muscle mass. Biomarker discovery for PF&S requires a comprehensive approach to cope with the multifaceted pathophysiology of the condition. The aim of the present study was to provide an initial selection of biomarkers for PF&S using a novel multivariate analytic strategy.MethodsTwo‐hundred older community‐dwellers, 100 with PF&S and 100 non‐sarcopenic, non‐frail (nonPF&S) controls aged 70 and older were enrolled as part of the BIOmarkers associated with Sarcopenia and Physical frailty in EldeRly pErsons (BIOSPHERE) study. A panel of 74 circulating analytes involved in inflammation, muscle growth and remodeling, neuromuscular junction damage, and amino acid metabolism was assayed. Biomarker selection was accomplished through sequential and orthogonalized covariance selection (SO‐CovSel) analysis.ResultsSeveral SO‐CovSel models were constructed. The model with the best prediction ability obtained with the smallest number of variables was built using seven biomolecules. This model allowed correct classification of 80.6 ± 5.3% PF&S participants and 79.9 ± 5.1% nonPF&S controls. The PF&S biomarker profile was characterized by higher serum levels of asparagine, aspartic acid, and citrulline. Higher serum concentrations of platelet‐derived growth factor‐BB, heat shock protein 72, myeloperoxidase, and alpha‐aminobutyric acid defined the serum profile of nonPF&S participants.ConclusionSO‐CovSel analysis allowed identifying a set of potential biomarkers for PF&S. The adoption of such an innovative multivariate approach could help address the complex pathophysiology of PF&S, translate biomarker discovery from bench to bedside, and unveil novel targets for interventions.Support or Funding Information‐ Innovative Medicines Initiative – Joint Undertaking (IMI‐JU 115621)‐ Fondazione Roma (NCDs Call for Proposals 2013)‐ Nonprofit research foundation “Centro Studi Achille e Linda Lorenzon”Candidate biomarkers for physical frailty & sarcopenia (PF&S) identified through sequential and orthogonalized covariance selection (SOCovSel) analysis and their putative roles in PF&S pathophysiology. Abbreviations: Hsp72, heat shock protein 72; MPO, myeloperoxidase; PDGF‐BB, platelet‐derived growth factor BB.Figure 1
Phosphorylation of SR Proteins and the Effect of Hydrogen Peroxide Stress on the Splicing Cycle in S. pombe Fission Yeast
Authors: Davis Moriah Hope , Piening Cole , Marvin Micheal 
Published: April 2020

The spliceosome, a large and dynamic RNA‐protein complex, is responsible for effective pre‐mRNA splicing. Correct spliceosome assembly, function, and regulation have often been shown to involve SR proteins, which are dynamically phosphorylated. Alterations in the splicing process can lead to a variety of human diseases and the fission yeast, Schizosaccharomyces pombe, is one model organism for this research. It was previously determined that the conserved SR protein kinase in fission yeast, Dsk1 (Srpk1 in humans), is required for efficient splicing of introns. Previous identification of Dsk1 substrates and alanine mutation to prevent phosphorylation showed a minor splicing defect in the two fission yeast SR proteins (Srp1 and Srp2) under optimal growth conditions. Our current research takes a chemical‐genetic approach to exploring phosphorylation’s physical effects on specifically Srp1 and Srp2 protein substrates, and whether environmental stress, simulated by hydrogen peroxide exposure, can cause a higher retention rate of introns in a regulated way. Through the use of RT‐qPCR we can determine whether there is a splicing defect under the stress condition, and how phosphorylation of SR proteins affects the level of pre‐mRNA splicing defect.Support or Funding InformationPrevious work in Christine Guthrie’s lab in collaboration with Kevan Shokat and postdoctoral fellow Jesse Lipp, as well as previous work by Alex Piening of Rockhurst class 2018 and Clayton Carroll of Rockhurst class 2019. Thanks to Jeff Pleiss for microarray design as well as Nick Hertz & Alma Burlingame for mass spectrometry analysis. In addition, NIH NRSA postdoctoral fellowship for funding. Current funding and support provided by Rockhurst University.Rpl25a intron splicing in WT SR protein yeast strains and alanine mutated strains under optimal conditions.Figure 1S. pombe cell responses due to increasing concentrations of hydrogen peroxide (Veal, E. 2014).Figure 2
FLAVi‐Web: A Web Annotator for Viral Genomes of Flaviviridae with a Revised Phylogeny of the Family
Authors: Guirales Sayal , Machado Denis Jacob , de Bernardi Schneider Adriano , Janies Daniel 
Published: April 2020

The ongoing and severe public health threat of viruses of the family Flaviviridae, including dengue, hepatitis C, West Nile, yellow fever, and zika, demand a greater understanding of how these viruses evolve, emerge and spread in order to respond. Central to this understanding is an updated phylogeny of the entire family. Accurate gene annotations are pivotal to allow researchers to question how the fundamental genetic elements for these viruses evolve and function knowing they are comparing homologous genomic regions. To tackle these problems, our team has published a pipeline called FLAVi ("Fast Loci Annotation of Viruses"), an annotation pipeline for Flaviviridae that uses a combination of ab initio and homology‐based strategies. The pipeline recovered 100% of the genes in reference genomes and annotated over 97% of the expected genes in the remaining noncurated sequences. It was also further demonstrated that the combined analysis of genomes of all genera of Flaviviridae (Flavivirus, Hepacivirus, Pegivirus, and Pestivirus), as made possible by this annotation strategy, improves the phylogenetic analyses of these viruses for all optimality criteria that were tested (parsimony, maximum likelihood, and posterior probability). Here, we propose a user‐friendly web‐based application version of FLAVi, FLAVi‐Web (available at flavi‐web.com). FLAVi‐Web was created using Flask (Grinberg, 2018), a Python‐based application for the creation of web interfaces. Flask uses HTML and JavaScript to create the aesthetic properties of the web interface. The web application takes as input a FASTA file with the pathogen genomic information and outputs a compressed file with the main annotation results in a GFF3 file format. This novel web implementation enhances our ability to maintain and improve the FLAVi pipeline over time, ultimately promoting its usage among the virology community.Left ‐ Homepage of flavi‐web. com, Right ‐ Flowchart describing the application pipeline.Figure 1
Ecological implications of removing a concrete gas platform in the North Sea
Authors: Coolen Joop W.P. , Bittner Oliver , Driessen Floor M.F. , van Dongen Udo , Siahaya Midas S. , de Groot Wim , Mavraki Ninon , Bolam Stefan G. , van der Weide Babeth 
Published: April 2020

ABSTRACTArtificial structures such as offshore oil and gas platforms can significantly alter local species communities. It has been argued that this effect should be considered during decisions over their removal during decommissioning. In the North Sea, leaving such structures in place is prohibited but derogations are allowed for large concrete installations. To assess removal options for one such installation, the Halfweg GBS (gravity-based structure) a concrete platform foundation off the Dutch coast, we studied the resident fouling macrofauna community. The faunal structure, biomass and trophic composition of the Halfweg was then compared with those from the surrounding seabed sediments, other local artificial structures and a natural rocky reef.In total, 65 macrofaunal species were observed on the concrete (52 species), steel legs (32) and surrounding rock dump (44) of Halfweg. Mean Simpson diversity per sample was highest on the rock dump (0.71) but concrete (0.54) and steel (0.60) of the GBS were lower than seabed (0.69). Ten of the species observed on the concrete were not reported on other substrates while 10 of the species were also observed in the surrounding seabed. The GBS structure was numerically dominated by Arthropoda which comprised 98% of the total abundance. Mean ash free dry weight (AFDW) was significantly higher (p<0.001) on the Halfweg substrates (204 g AFDW per m2) than in the surrounding seabed (65 g AFDW per m2). Over 94% of the biomass on Halfweg consisted of the plumose anemoneMetridium senile. While common on other reefs, this species was absent from the surrounding seabed. Macrofaunal feeding mechanisms of the concrete and rock dump communities on the GBS were similar to those of nearby sediments, although these differed from those on the Halfweg steel legs. Therefore, the presence of Halfweg alters the local community feeding modes. Multivariate analysis revealed that taxonomic structure of the GBS and other artificial structures significantly differed from that of the sedimentary habitats. Low numbers of non-indigenous species on Halfweg indicated that the structure does not act as a stepping stone for species invasions.Our data show that the Halfweg structures significantly increase local biodiversity and biomass. Removal of the concrete and steel legs of the GBS (leaving the rock dump) will significantly reduce local macrofauna biodiversity. The long-term impact on macrofaunal biomass is low. Leaving the complete Halfweg structure in place will result in an enriched local macrofaunal biodiversity and feeding mode diversity.
Multi-task Deep Learning Based CT Imaging Analysis For COVID-19: Classification and Segmentation
Authors: Amyar A. , Modzelewski R. , Ruan S. 
Published: April 2020

ABSTRACTThe fast spreading of the novel coronavirus COVID-19 has aroused worldwide interest and concern, and caused more than one million and a half confirmed cases to date. To combat this spread, medical imaging such as computed tomography (CT) images can be used for diagnostic. An automatic detection tools is necessary for helping screening COVID-19 pneumonia using chest CT imaging. In this work, we propose a multitask deep learning model to jointly identify COVID-19 patient and segment COVID-19 lesion from chest CT images. Our motivation is to leverage useful information contained in multiple related tasks to help improve both segmentation and classification performances. Our architecture is composed by an encoder and two decoders for reconstruction and segmentation, and a multi-layer perceptron for classification. The proposed model is evaluated and compared with other image segmentation and classification techniques using a dataset of 1044 patients including 449 patients with COVID-19, 100 normal ones, 98 with lung cancer and 397 of different kinds of pathology. The obtained results show very encouraging performance of our method with a dice coefficient higher than 0.78 for the segmentation and an area under the ROC curve higher than 93% for the classification.