bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting Microsurgical Complications with ViOptix Tissue Oximetry in a Pediatric Myocutaneous Free Flap: Case Presentation and Literature Review
Authors: Kozusko Steven , Gbulie Uzoma 
Published: February 2018

Background Microvascular compromise from arterial or venous occlusion is a common cause of free flap failure. The salvage rate following a microvascular compromise is dependent on detecting the problem early and intervening quickly.
Methods The ViOptix tissue oximeter measures tissue oxygen saturation using the near-infrared spectroscopy technology. The ViOptix device has an alarm capability to warn of potential compromise to tissue perfusion. The tissue oximetry readings are visible on the bedside monitor and are relayed to a webpage link, which is accessible on a personal computer or mobile device, allowing real-time monitoring. This article presents a case where real-time monitoring allowed almost immediate detection of inadvertent pedicle compromise allowing flap salvage by repositioning without surgical intervention.
Results In the case presented, the patient's nurse inadvertently positioned a pillow under the location of the vascular pedicle likely causing microvascular compression. The ViOptix reading dropped and for this reason the nurse contacted the Plastic Surgery team. The drop was confirmed remotely and the flap was urgently evaluated in person. Once the pillow was removed, the ViOptix readings normalized and Doppler signals strengthened in the flap.
Discussion While tissue oximetry monitoring does not by itself ensure flap survival, it provides critical information than conventional flap monitoring would allow giving the microsurgeon the opportunity to make a quicker decision. ViOptix tissue oximeters are able to detect vascular compromise even before conventional clinical symptoms are present. Alas in several cases by the time clinical symptoms develop the flap may be beyond salvage.
Development of a golf‐specific load monitoring tool: Content validity and feasibility
Authors: Williams Scott B. , Gastin Paul B. , Saw Anna E. , Robertson Sam 
Published: February 2018

AbstractAthletes often record details of their training and competitions, supported by information such as environmental conditions, travel, as well as how they felt. However, it is not known how prevalent these practices are in golfers, or how valuable this process is perceived. The purpose of this study was to develop a golf‐specific load monitoring tool (GLMT), and establish the content validity and feasibility of this tool amongst high‐level golfers. In the first phase of development, 21 experts were surveyed to determine the suitability of items for inclusion in the GLMT. Of the 36 items, 21 received >78% agreement, a requirement to establish content validity and for inclusion in the GLMT. Total duration was the preferred metric for golf‐specific activities, whilst rating of perceived exertion (RPE) was preferred for measuring physical training. In the second phase, feasibility of the tool was assessed by surveying 13 high‐level male golfers following 28‐days of daily GLMT use. All items included in the GLMT were deemed feasible to record, with all players participating in the feasibility study providing high to very high ratings. Golfers responded that they would consider using a load monitoring tool of this nature long term, provided it can be completed in less than five minutes per day.
In‐season changes in ventricular morphology and systolic function in adolescent female athletes
Authors: Watson Andrew M. , Coutinho Carol , Haraldsdottir Kristin , Brickson Stacey , Dunn Warren , Eldridge Marlowe 
Published: February 2018

AbstractPurpose: To evaluate the influence of physical maturity on the changes in ventricular morphology and function with sport training in female youth athletes.Methods: Thirty‐two female athletes (age 13–18 years) underwent height and weight measurement and 2‐D echocardiographic evaluation immediately prior to, and following, a 20‐week soccer season. Pre‐ and post‐season left ventricular end‐diastolic diameter (LVEDD), end‐diastolic volume (LVEDV), ejection fraction (LVEF), stroke volume (LVSV), mass (LVM), and posterior wall thickness (LVPWT), right ventricular end‐diastolic diameter (RVEDD), end‐diastolic area (RVEDA), and fractional area change (RVFAC), and interventricular septal thickness (IVST) were compared. In‐season change in each variable was compared across pre‐season hours of vigorous physical activity (0–1, 2–3, >3 hours).Results: Significant increases were identified in LVEDV (51.3 ± 10.4 v 56.4 ± 9.6 ml/m2, p = 0.001) and RVEDA (10.5 ± 1.9 v 11.3 ± 2.5 cm2/m2, p = 0.040), but not LVEDD, LVM, LVPWT, LVSV, RVEDD, RVEDA, RVFAC, or IVST (p > 0.05 for all). In‐season changes in echocardiographic variables did not differ across hours of pre‐season vigorous physical activity (p > 0.05 for all).Conclusion: Among female adolescent soccer players, in‐season training elicits changes in resting ventricular volume, but not wall thickness or systolic function. These adaptations do not appear to be influenced by pre‐season physical activity level.
Quantum return probability of a system of N non-interacting lattice fermions
Authors: Krapivsky P L , Luck J M , Mallick K 
Published: February 2018

Abstract
We consider N non-interacting fermions performing continuous-time quantum walks on a one-dimensional lattice. The system is launched from a most compact configuration where the fermions occupy neighboring sites. We calculate exactly the quantum return probability (sometimes referred to as the Loschmidt echo) of observing the very same compact state at a later time t. Remarkably, this probability depends on the parity of the fermion number—it decays as a power of time for even N, while for odd N it exhibits periodic oscillations modulated by a decaying power law. The exponent also slightly depends on the parity of N, and is roughly twice smaller than what it would be in the continuum limit. We also consider the same problem, and obtain similar results, in the presence of an impenetrable wall at the origin constraining the particles to remain on the positive half-line. We derive closed-form expressions for the amplitudes of the power-law decay of the return probability in all cases. The key point in the derivation is the use of Mehta integrals, which are limiting cases of the Selberg integral.
Long-read sequencing across theC9orf72‘GGGGCC’ repeat expansion: implications for clinical use and genetic discovery efforts in human disease
Authors: Ebbert Mark T. W. , Farrugia Stefan , Sens Jonathon , Jansen-West Karen , Gendron Tania F. , Prudencio Mercedes , McLaughlin lan J. , Bowman Brett , Seetin Matthew , DeJesus-Hernandez Mariely , Jackson Jazmyne , Brown Patricia H , Dickson Dennis W. , van Blitterswijk Marka , Rademakers Rosa , Petrucelli Leonard , Fryer John D. 
Published: February 2018

AbstractBackground:Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like theC9orf72‘GGGGCC’ (G4C2) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too long to sequence using short-read sequencing technologies. It is unclear whether long-read sequencing technologies can traverse these long, challenging repeat expansions. Here, we demonstrate that two long-read sequencing technologies, Pacific Biosciences’ (PacBio) and Oxford Nanopore Technologies’ (ONT), can sequence through disease-causing repeats cloned into plasmids, including the FTD/ALS-causing G4C2repeat expansion. We also report the first long-read sequencing data characterizing theC9orf72G4C2repeat expansion at the nucleotide level in two symptomatic expansion carriers using PacBio whole-genome sequencing and a no-amplification (No-Amp) targeted approach based on CRISPR/Cas9.Results:Both the PacBio and ONT platforms successfully sequenced through the repeat expansions in plasmids. Throughput on the MinlON was a challenge for whole-genome sequencing; we were unable to attain reads covering the humanC9orf72repeat expansion using 15 flow cells. We obtained 8x coverage across theC9orf72locus using the PacBio Sequel, accurately reporting the unexpanded allele at eight repeats, and reading through the entire expansion with 1324 repeats (7941 nucleotides). Using the No-Amp targeted approach, we attained >800x coverage and were able to identify the unexpanded allele, closely estimate expansion size, and assess nucleotide content in a single experiment. We estimate the individual’s repeat region was >99% G4C2content, though we cannot rule out small interruptions.Conclusions:Our findings indicate that long-read sequencing is well suited to characterizing known repeat expansions, and for discovering new disease-causing, disease-modifying, or risk-modifying repeat expansions that have gone undetected with conventional short-read sequencing. The PacBio No-Amp targeted approach may have future potential in clinical and genetic counseling environments. Larger and deeper long-read sequencing studies inC9orf72expansion carriers will be important to determine heterogeneity and whether the repeats are interrupted by non-G4C2content, potentially mitigating or modifying disease course or age of onset, as interruptions are known to do in other repeat-expansion disorders. These results have broad implications across all diseases where the genetic etiology remains unclear.
Transcranial focused ultrasound neuromodulation of the human primary motor cortex
Authors: Legon Wynn , Bansal Priya , Tyshynsky Roman , Ai Leo , Mueller Jerel K. 
Published: February 2018

AbstractTranscranial focused ultrasound is a form of non-invasive neuromodulation that uses acoustic energy to affect neuronal excitability. The effect of ultrasound on human motor cortical excitability is currently unknown. We apply ultrasound to the primary motor cortex in humans using a novel transcranial ultrasound and magnetic stimulation (TUMS) paradigm that allows for concurrent and concentric ultrasound stimulation with transcranial magnetic stimulation (TMS). This allows for non-invasive inspection of the effect of ultrasound on motor neuronal excitability using the motor evoked potential (MEP) generated by TMS. We test the effect of ultrasound on single pulse MEP recruitment curves and paired pulse protocols including short interval intracortical inhibition (SICI) and intracortical facilitation (ICF). We also test the longevity of the effect and the effect of ultrasound on the cortical silent period in a small sub-sample of participants. In addition, we test the effect of ultrasound to motor cortex on a stimulus response reaction time task. Results show ultrasound inhibits the amplitude of single-pulse MEPs and attenuates intracortical facilitation but does not affect intracortical inhibition. Early evidence suggests that ultrasound does not affect cortical silent period duration and that the duration of inhibition may be related to the duration of stimulation. Finally, ultrasound reduces reaction time on a simple stimulus response task. This is the first report of the effect of ultrasound on human motor cortical excitability and motor behavior and confirms previous results in the somatosensory cortex that ultrasound results in effective neuronal inhibition that confers a performance advantage.
Structure of APP-C991-99and Implications for Role of Extra-Membrane Domains in Function and Oligomerization
Authors: Pantelopulos George A. , Straub John E. , Thirumalai D. , Sugita Yuji 
Published: February 2018

AbstractThe 99 amino acid C-terminal fragment of Amyloid Precursor Protein APP-C99 (C99) is cleaved by γ-secretase to form Aβ peptide, which plays a critical role in the etiology of Alzheimer’s Disease (AD). The structure of C99 consists of a single transmembrane domain flanked by intra and intercellular domains. While the structure of the transmembrane domain has been well characterized, little is known about the structure of the flanking domains and their role in C99 processing by γ-secretase. To gain insight into the structure of full-length C99, REMD simulations were performed for monomeric C99 in model membranes of varying thickness. We find equilibrium ensembles of C99 from simulation agree with experimentally-inferred residue insertion depths and protein backbone chemical shifts. In thin membranes, the transmembrane domain structure is correlated with extra-membrane structural states. Mean and variance of the transmembrane and G37G38hinge angles are found to increase with thinning membrane. The N-terminus of C99 forms β-strands that may seed aggregation of Aβ on the membrane surface, promoting amyloid formation. The N-terminus, which forms α-helices that interact with the nicastrin domain of γ-secretase. The C-terminus of C99 becomes more α-helical as the membrane thickens, forming structures that may be suitable for binding by cytoplasmic proteins, while C-terminal residues essential to cytotoxic function become α-helical as the membrane thins. The heterogeneous but discrete extra-membrane domain states analyzed here open the path to new investigations of the role of C99 structure and membrane in amyloidogenesis.
Herpes ICP8 protein stimulates homologous recombination in human cells
Authors: Valledor Melvys , Myers Richard S. , Schiller Paul C. 
Published: February 2018

ABSTRACTRecombineering has transformed functional genomic analysis. Genome modification by recombineering using the phage lambda Red SynExo homologous recombination proteins Beta inEscherichia colihas approached 100% efficiency. While highly efficient inE. coli, recombineering using the Red SynExo in other organisms declines in efficiency roughly correlating with phylogenetic distance fromE. coli. SynExo recombinases are common to double-stranded DNA viruses infecting a variety of organisms, including humans. Human Herpes virus Type 1 (HHV1) encodes a SynExo comprised of ICP8 synaptase and UL12 exonuclease. In a previous study, the Herpes SynExo was reconstitutedin vitroand shown to catalyze a model recombination reaction. Here we describe stimulation of gene targeting to edit a novel fluorescent protein gene in the human genome using ICP8 and compared its efficiency to that of a “humanized” version of Beta protein from phage λ. ICP8 significantly enhanced gene targeting rates in HEK 293 T cells while Beta was not only unable to catalyze recombineering but inhibited gene targeting using endogenous recombination functions, despite both synaptases being well-expressed and localized to the nucleus. This proof of concept encourages developing species-specific SynExo recombinases for genome engineering.SIGNIFICANCEGenome modification by recombineering using SynExo viral recombination proteins has transformed functional genomic analysis in bacteria. Single-stranded DNA (ssDNA) recombineering approaches 100% efficiency inE. coliusing Beta protein from bacteriophage lambda, but recombineering has not been extended to eukaryotic genomes. Efficient recombineering requires SynExos that co-evolved with a viral host, however SynExos are common to viruses infecting a variety of organisms, including humans. The ICP8 protein of Human Herpes virus Type 1 is a SynExo protein similar to Beta. In this pioneering study, Herpes ICP8 stimulated gene targeting in a human genome by homologous recombination while the bacterial virus Beta protein inhibited recombination in human cells. This is the first demonstration of host-specific recombineering in human cells using a human viral SynExo protein.
Nuclear localization of TORC1 and cellular co-localization of TORC1 and c-Fos in the visceral neuraxis after systemic LiCl injection
Authors: Kimbrough Adam , Houpt Thomas A. 
Published: February 2018

AbstractCyclic–AMP response element binding protein (CREB)-mediated gene expression is critical for the processing of visceral information, including learning about visceral stimuli (e.g. conditioned taste aversion). However, CREB requires additional co-factors to induce gene expression, including transducer of regulated CREB-activity (TORC). The nuclear localization of TORC1 has not been examined previously in the visceral neuraxis. c-Fos, a widely-used marker of activity, is induced by visceral stimulation. If CREB-mediated gene transcription is necessary for c-Fos induction in the visceral neuraxis after systemic LiCl injection, then TORC should be active following stimulation, and co-localized with c-Fos in activated neurons. We examined nuclear (activated) TORC1 in the visceral neuraxis at 30, 60, and 180 minutes after LiCl, as compared to c-Fos induction. Consistent with previous studies we found increases in c-Fos 60 min after LiCl in all regions. Nuclear TORC1 was also increased in the area postrema, NTS, and paraventricular nucleus after LiCl. Surprisingly, in the central amygdala, TORC1 was deactivated after LiCl, such that almost all TORC1 was cytoplasmic, whereas control rats had almost all nuclear TORC1. Fluorescent double-labeling of TORC1 and c-Fos after LiCl found that cellular co-localization of c-Fos and TORC1 was very low across the visceral neuraxis. Nuclear TORC1 expression reveals a population of cells in the visceral neuraxis, independent of c-Fos-positive cells, that are regulated by LiCl. TORC1, and in turn CREB-mediated gene transcription, may not be necessary for c-Fos induction in the visceral neuraxis after LiCl.
Sensations from a single M-cone depend on the activity of surrounding S-cones
Authors: Schmidt Brian P. , Sabesan Ramkumar , Tuten William S. , Neitz Jay , Roorda Austin 
Published: February 2018

ABSTRACTColor vision requires the activity of cone photoreceptors to be compared in post-receptoral circuitry. Decades of psychophysical measurements have quantified the nature of these comparative interactions on a coarse scale. How such findings generalize to a cellular scale remains unclear. To answer that question, we quantified the influence of surrounding light on the appearance of spots targeted to individual cones. The eye’s aberrations were corrected with adaptive optics and retinal position was precisely tracked in real-time to compensate for natural movement. Subjects reported the color appearance of each spot. A majority of L-and M-cones consistently gave rise to the sensation of white, while a smaller group repeatedly elicited hue sensations. When blue sensations were reported they were more likely mediated by M- than L-cones. Blue sensations were elicited from M-cones against a short-wavelength light that preferentially elevated the quantal catch in surrounding S-cones, while stimulation of the same cones against a white background elicited green sensations. In one of two subjects, proximity to S-cones increased the probability of blue reports when M-cones were probed. We propose that M-cone increments excited both green and blue opponent pathways, but the relative activity of neighboring cones favored one pathway over the other.
RECTA: Regulon Identification Based on Comparative Genomics and Transcriptomics Analysis
Authors: Chen Xin , Ma Anjun , McDermaid Adam , Zhang Hanyuan , Liu Chao , Cao Huansheng , Ma Qin 
Published: February 2018

ABSTRACTRegulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, RECTA, for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA onLactococcus lactisMG1363 data to elucidate acid-response regulons.Lactococcus lactisis one of the most important Gram-positive lactic acid-producing bacteria, widely used in food industry and has been proved to have advantages in oral delivery of drug and vaccine. The pipeline carries out differential gene expression, gene co-expression analysis,cis-regulatory motif finding, and comparative genomics to predict and validate regulons related to acid stress response. A total of 51 regulonswere identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to be connected with acid stress response with (i) known transcriptional factors in MEME suite database successfully mapped inLactococcus lactisMG1363; and (ii) differentially expressed genes between pH values of 6.5 (control) and 5.1 (treatment). Validated by 36 literature confirmed acid stress response related proteins and genes, 33 genes inLactococcus lactisMG1363 were found having orthologous genes using BLAST, associated to six regulons. An acid response related regulatory network was constructed, involving two trans-membrane proteins, eight regulons (llrA, llrC, hllA, ccpA, NHP6A,rcfB, regulons #8 and #39), nine functional modules, and 33 genes with orthologous genes known to be associated to acid stress. Our RECTA pipeline provides an effective way to construct a reliable gene regulatory network through regulon elucidation. The predicted response pathways could serve as promising candidates for better acid tolerance engineering inLactococcus lactis. RECTA has strong application power and can be effectively applied to other bacterial genomes where the elucidation of the transcriptional regulation network is needed.
Growth potential ofListeria monocytogenesin twelve different types of RTE salads: impact of food matrix, storage temperature and shelf life
Authors: Ziegler Matthias , Kent David , Stephan Roger , Guldimann Claudia 
Published: February 2018

AbstractListeriosis is a food borne disease associated with high hospitalization and fatality rates; in 2014, EU member states reported 2194 cases with 98.9% hospitalization rates and 210 fatalities. Proper risk analysis and the development of effective food safety strategies critically depend on the knowledge of the growth characteristics ofL. monocytogeneson the product in question. Ready-to-eat (RTE) salads present a challenge in this context due to the absence of a heat treatment step before consumption and the interaction of pathogens with the plant microbial microbiota. This study provides challenge-test based data of the growth characteristics ofL. monocytogeneson twelve RTE salads. The food matrix, storage time and storage temperature were factors with a significant impact on the growth ofL. monocytogenes. While most tested salads permitted a significant increase ofL. monocytogenesin at least one of the tested conditions, no growth was observed on celeriac, carrot and corn salad products. There was a considerable increase in growth at 8 °C compared to 5 °C. Our data indicate that the reduction of the storage temperature at retail level to 5 °C and product shelf life could help mitigate the risk ofL. monocytogenesin RTE salads.
Regulation of ATM and ATR by Smarcal1 and BRG1
Authors: Sethy Ramesh , Rakesh Radhakrishnan , Patne Ketki , Arya Vijendra , Sharma Tapan , Haokip Dominic Thangminlen , Kumari Reshma , Muthuswami Rohini 
Published: February 2018

ABSTRACTThe G2/M checkpoint is activated on DNA damage by the ATM and ATR kinases that are regulated by post-translational modifications. In this paper, the transcriptional co-regulation of ATM and ATR by SMARCAL1 and BRG1, both members of the ATP-dependent chromatin remodeling protein family, is described. SMARCAL1 and BRG1 co-localize on the promoters of ATM and ATR; downregulation of SMARCAL1/BRG1 results in transcriptional repression of ATM/ATR and therefore, overriding of the G2/M checkpoint leading to mitotic abnormalities. On doxorubicin-induced DNA damage, SMARCAL1 and BRG1 are upregulated and in turn, upregulate the expression of ATM/ATR.Phosphorylation of ATM/ATR is needed for the transcriptional upregulation of SMARCAL1 and BRG1, and therefore, of ATM and ATR on DNA damage. The regulation of ATM/ATR is rendered non-functional if SMARCAL1 and/or BRG1 are absent or if the two proteins are mutated such that they are unable to hydrolyze ATP, as in for example in Schimke Immuno-Osseous Dysplasia and Coffin-Siris Syndrome. Thus, an intricate transcriptional regulation of DNA damage response genes mediated by SMARCAL1 and BRG1 is present in mammalian cells.