bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using a Second Free Fibula Osteocutaneous Flap after Repeated Mandibulectomy Is Associated with a Low Complication Rate and Acceptable Functional Outcomes
Authors: Mericli Alexander F. , Schaverien Mark V. , Hanasono Matthew M. , Yu Peirong , Largo Rene D. , Villa Mark T. , Reece Greg , Butler Charles E. , Garvey Patrick B. 
Published: July 2017

Background:
A significant percentage of patients who undergo segmental mandibulectomy for head and neck cancer will develop a new or recurrent cancer or osteoradionecrosis, necessitating a second mandibulectomy and reconstruction. In this scenario, many surgeons are reluctant to perform a reconstruction with an osseous flap because of the presumed increased morbidity and complexity. The purpose of this study was to evaluate the safety and efficacy of performing a second free fibula flap reconstruction after repeated segmental mandibulectomy.

Methods:
The authors retrospectively reviewed their prospectively maintained departmental database for mandible reconstructions performed between 1991 and 2016, identifying patients who had two sequential free fibula flap reconstructions. Patient, disease, and treatment characteristics were recorded and analyzed.

Results:
Twenty patients underwent a second free fibula flap reconstruction after a second mandibulectomy. The median follow-up was 72.5 months (range, 16 to 243 months). Preoperative virtual planning was used more often for the second fibula flap compared with the first (50 percent versus 10 percent; p = 0.004). The mean operative times were statistically similar for the first versus second fibula flap (673 minutes versus 586 minutes, respectively; p = 0.13). The postoperative complication rates (50 percent versus 30 percent, respectively; p = 0.19) and functional outcomes were similar between the first and second fibula flap reconstructions.

Conclusion:
Despite the increased technical complexity, the use of a second free fibula flap after repeated segmental mandibulectomy appears to be safe and to confer no higher risk than that for the first fibula flap.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
BFACE: A Framework for Evaluating Breast Aesthetics
Authors: Martinovic Maryann E. , Blanchet Nadia P. 
Published: July 2017

Summary:
Although much has been written about breast aesthetics, the literature lacks a simple yet systematic and comprehensive approach for preoperative breast assessment. With use of the mnemonic “BFACE,” the breast surgeon will analyze the bony skeleton and the breast footprint, areola, conus, and envelope. The authors present a thorough review of the important parameters that define the ideal breast, and several techniques for perceiving asymmetries more clearly. Strategic surgical planning is enabled by accurate perception.
Direct Anthropometry of Repaired Bilateral Complete Cleft Lip: A Long-Term Assessment
Authors: Kim David C. , Mulliken John B. 
Published: July 2017

Background:
Repair of bilateral complete cleft lip requires more than following a design in a textbook. The operative strategy should incorporate knowledge of anticipated nasolabial changes with growth.

Methods:
Direct nasolabial anthropometry was recorded in 174 children with bilateral complete cleft lip before and immediately after primary repair. Serial measurements were taken in 66 Caucasian patients between the ages of 6 months and 15 years and compared to Farkas’ normal values. Data for upper philtral width were unavailable; therefore, this dimension was measured in 454 nonsyndromic Caucasian male and female subjects aged 1 year to adulthood. Rates and types of revision were also documented.

Results:
Inter–medial canthal width stayed above the mean and within normal limits throughout puberty. Interalar width was initially narrowed and hovered in the high normal range throughout adolescence. Columellar height and nasal projection were constructed slightly long and paralleled normal growth. Available cutaneous philtral length was used in the primary repair; however, this dimension remained short. The philtrum was made narrow and matched normal values throughout adolescence. Normal inferior/superior philtral width ratio was 1.60 for female subjects and 1.59 for male subjects. A full median tubercle was built at primary repair but, sometimes in late childhood, necessitated secondary augmentation with a dermal graft in 31 of 174 patients (18 percent), usually performed in late childhood or adolescence.

Conclusions:
Serial anthropometry documented postoperative changes in nasolabial dimensions compared to normal growth curves. Repair of bilateral complete cleft lip requires primary correction of nasal and labial features based on their differential growth, with special attention to nasal width, philtral height and proportions, and size of the median tubercle.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Outcomes of Muscle Brachialis Transfer to Restore Finger Flexion in Brachial Plexus Palsy
Authors: DeGeorge Brent R. , Becker Hillary A. , Faryna John H. , Spinner Robert J. , Bishop Allen T. , Shin Alexander Y. 
Published: July 2017

Background:
In adults with lower trunk brachial plexus injury, proximal nerve surgery for restoration of prehension demonstrates poor outcomes secondary to long distances required for nerve regeneration and time-dependent degradation of motor endplates. Options for reconstruction are limited to distal tendon or nerve transfers and free-functioning muscle transfers. In this article, the authors describe the long-term outcomes of brachialis muscle–to–flexor digitorum profundus transfer to restore prehension in patients with traumatic lower trunk brachial plexus injuries.

Methods:
Eighteen adult patients with lower trunk brachial plexus palsy underwent brachialis muscle–to–flexor digitorum profundus transfer with the goal of restoring rudimentary prehensile function at a single institution. The patients were followed throughout their recovery with functional outcomes and patient satisfaction ratings.

Results:
Brachialis muscle transfer resulted in restoring modified British Medical Research Council grade 3 or better function in 11 of 18 patients and grade 4 function in eight of 18 patients. Eleven of the 18 patients demonstrated a postoperative functional grasp for assistance with activities of daily living. Overall patient satisfaction following brachialis muscle transfer was 56 percent. Patient preoperative wrist extension (p < 0.018) and finger extension (p < 0.029) strength correlated with improved outcomes, whereas concomitant upper extremity fracture (p < 0.023) was associated with poorer outcomes.

Conclusions:
Brachialis muscle transfer is an option for reconstruction of prehensile function in patients with lower trunk brachial plexus palsy with preserved wrist extension. Brachialis muscle transfer is particularly useful in patients who are poor candidates for microsurgical free-functioning muscle transfer for grasp; however, its functional outcomes are not universally successful.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Identifying Simultaneous Rearrangements in Cancer Genomes
Authors: Oesper Layla , Dantas Simone , Raphael Benjamin J. 
Published: July 2017

AbstractThe traditional view of cancer evolution states that a cancer genome accumulates asequentialordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such aschromothripsis, where a large number of mutations instead occursimultaneously. A number of potential signatures of chromothripsis have been proposed. In this work we provide a rigorous formulation and analysis of the “ability to walk the derivative chromosome” signature originally proposed by Korbel and Campbell (2013). In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, theH/T alternating fraction, which allows us to overcome some of the limitations of the original signature. We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion. An implementation of the H/T alternating fraction is available athttps://bitbucket.org/oesperlab/ht-altfrac.
Dynamical origins of heat capacity changes in enzyme catalysed reactions
Authors: van der Kamp Marc W , Prentice Erica J. , Kraakmann Kirsty L. , Connolly Michael , Mulholland Adrian J. , Arcus Vickery L. 
Published: July 2017

AbstractHeat capacity changes are emerging as essential for explaining the temperature dependence of enzyme-catalysed reaction rates. This has important implications for enzyme kinetics, thermoadaptation and evolution, but the physical basis of these heat capacity changes is unknown. Here we show by a combination of experiment and simulation, for two quite distinct enzymes (dimeric ketosteroid isomerase and monomeric alpha-glucosidase), that the activation heat capacity change for the catalysed reaction can be predicted through atomistic molecular dynamics simulations. The simulations reveal subtle and surprising underlying dynamical changes: tightening of loops around the active site is observed as expected, but crucially, changes in energetic fluctuations are evident across the whole enzyme including important contributions from oligomeric neighbours and domains distal to the active site. This has general implications for understanding enzyme catalysis and demonstrating a direct connection between functionally important microscopic dynamics and macroscopically measurable quantities.
Evaluation of Topramezone on Zebrafish Retinoid Signaling
Authors: Liu Haixing , Xu Pengxing , Fan Yu , Zhang Weizhi 
Published: July 2017

ABSTRACTTopramezone is a highly selective herbicide developed for broadleaf and grass weeds control in corn. In this study, the effects of topramezone on zebrafish, especially in retinoid signaling were investigated. Zebrafish embryos were treated with topramezone from 4 hours post-fertilization (hpf) to 144 hpf. Exposed to topramezone significantly reduced the retinal and retinoic levels compared to controls. The transcriptional expression levels of retinol dehydrogenase (rdh1), retinoic acid receptor subunit (raraa), retinal dehydrogenase (raldh2), retinol binding protein (rbp1a), and cellular retinoic acid binding protein (crabp1aandcrabp2a) were significantly decreased. Our results suggested that topramezone significantly impaired zebrafish retinoid signaling during a short time exposure. However, treatment with topramezone significantly increased the mRNA expression levels ofzfblue,zfrho,zfgr1, zfuv, andzfred. Our data demonstrated that topramezone treatment could interrupt retinoid signaling and further affect zebrafish eye development.
Vacuolar invertase activity shapes photosynthetic stress response ofArabidopsis thalianaand stabilizes central energy supply
Authors: Weiszmann Jakob , Fürtauer Lisa , Weckwerth Wolfram , Nägele Thomas 
Published: July 2017

AbstractStabilization of the central carbohydrate and energy metabolism plays a key role in plant stress response. As the primary photosynthetic products, carbohydrates are substrate for numerous metabolic and stress-protective reactions. Further, they have been shown to be involved in diverse signalling processes finally affecting and regulating plant stress response on a whole plant level. Sucrose metabolism is known to be central to many stress-related processes and enzymes catalysing its biosynthesis, transport and degradation have been shown to significantly impact stress resistance and acclimation output. However, due to the cyclic structure of sucrose metabolism involving sucrose cleavage in multiple compartments as well as energy-demanding re-synthesis via hexose phosphorylation, it is challenging to derive an unambiguous picture of its contribution to stress reactions. In the present study, a combined stress experiment comprising cold and high-light identified metabolism of sucrose and fumaric acid to significantly separate the stress response of a cold susceptible and a tolerant natural accession ofArabidopsis thaliana. Kinetic modelling and simulation of subcellular rates of invertase-driven sucrose cleavage revealed a contrasting picture between the susceptible and the tolerant accession pointing to an important role of vacuolar invertase during initial stress response. Using a T-DNA insertion mutant with a dramatically reduced invertase activity provided evidence for a central role of the enzyme in stabilizing photosynthesis and the central energy metabolism during freezing and high-light stress. Reducing vacuolar invertase activity to about 3% of the wild type resulted in a strong increase of ADP and ATP levels indicating a severe effect on cytosolic and plastidial energy balance. Together with a significant decrease of maximum quantum yield of photosystem II (Fv/Fm) these results suggest that vacuolar invertase activity stabilizes cytosolic energy metabolism by supplying hexose equivalents being phosphorylated in the cytosol. Finally, the accompanying ATP consumption is essential for cytosolic phosphate balance which directly affects photosynthetic performance by the supply of ADP being crucial for photosynthetic ATP production.
Architecture of TAF11/TAF13/TBP complex suggests novel regulatory state in General Transcription Factor TFIID function
Authors: Gupta Kapil , Watson Aleksandra A. , Baptista Tiago , Scheer Elisabeth , Chambers Anna L. , Koehler Christine , Zou Juan , Obong-Ebong Ima , Kandiah Eaazhisai , Temblador Arturo , Round Adam , Forest Eric , Man Petr , Bieniossek Christoph , Laue Ernest D. , Lemke Edward A. , Rappsilber Juri , Robinson Carol V. , Devys Didier , Tora Laszlo , Berger Imre 
Published: July 2017

AbstractGeneral transcription factor TFIID is a key component of RNA polymerase II transcription initiation. Human TFIID is a megadalton-sized complex comprising TATA-binding protein (TBP) and 13 TBP-associated factors (TAFs). TBP binds to core promoter DNA, recognizing the TATA-box. We identified a ternary complex formed by TBP and the histone fold (HF) domain-containing TFIID subunits TAF11 and TAF13. We demonstrate that TAF11/TAF13 competes for TBP binding with TATA-box DNA, and also with the N-terminal domain of TAF1 previously implicated in TATA-box mimicry. In an integrative approach combining crystal coordinates, biochemical analyses and data from cross-linking mass-spectrometry (CLMS), we determine the architecture of the TAF11/TAF13/TBP complex, revealing TAF11/TAF13 interaction with the DNA binding surface of TBP. We identify a highly conserved C-terminal TBP-binding domain (CTID) in TAF13 which is essential for supporting cell growth. Our results thus have implications for cellular TFIID assembly and suggest a novel regulatory state for TFIID function.
Information topology of gene expression profile in dopaminergic neurons
Authors: Tapia Pacheco Mónica , Baudot Pierre , Dufour Martial A. , Formisano-Tréziny Christine , Temporal Simone , Lasserre Manon , Gabert Jean , Kobayashi Kazuto , Goaillard Jean-Marc 
Published: July 2017

SUMMARY PARAGRAPHExtracting high-degree interactions and dependences between variables (pairs, triplets, …k-tuples) is a challenge posed by all omics approaches1, 2. Here we used multivariate mutual information (Ik) analysis3on single-cell retro-transcription quantitative PCR (sc-RTqPCR) data obtained from midbrain neurons to estimate the k-dimensional topology of their gene expression profiles. 41 mRNAs were quantified and statistical dependences in gene expression levels could be fully described for 21 genes: Ikanalysis revealed a complex combinatorial structure including modules of pairs, triplets (up to 6-tuples) sharing strong positive, negative or zero Ik, corresponding to co-varying, clustering and independent sets of genes, respectively. Therefore, Ikanalysis simultaneously identified heterogeneity (negative Ik) of the cell population under study and regulatory principles conserved across the population (homogeneity, positive Ik). Moreover, maximum information paths enabled to determine the size and stability of such transcriptional modules. Ikanalysis represents a new topological and statistical method of data analysis.
CINNA: An R/CRAN package to decipher Central Informative Nodes in Network Analysis
Authors: Ashtiani Minoo , Mirzaie Mehdi , Jafari Mohieddin 
Published: July 2017

AbstractIn network science, usually there is a critical step known as centrality analysis. This is an important step, since by using centrality measures, a large number of vertices with low priority are set aside and only a few ones remain to be used for further inferential outcomes. In the other words, these measures help us to sieve our large network and distinguish coarse vertices. By that, important decisions could be made based on the circumstances of these vertices on the overall behavior of networks. These vertices are potentially assumed as central or essential nodes. However, the centrality analysis has always been accompanied by a series of ambiguities, since there are a large number of well-known centrality measures, with different algorithms pointing to these essential nodes and there is no well-defined preference. Which measure explore more information in a given network about node essentiality according to the topological features? While here, we tried to provide a pipeline to have a comparison among all proper centrality measures regarding the network structure and choose the most informative one according to dimensional reduction methods. Central Informative Nodes in Network Analysis (CINNA) package is prepared to gather all required function for centrality analysis in the weighted/unweighted and directed/undirected networks.Availability and implementationCINNAis available in CRAN, including a tutorial. URL:https://cran.r-proiect.org/web/packages/CINNA/index.htmlContact:miafari@pasteur.ac.ir
PFKFB4 control of Akt signaling is essential for premigratory and migratory neural crest formation
Authors: Figueiredo Ana Leonor , Maczkowiak Frédérique , Borday Caroline , Pla Patrick , Sittewelle Meghane , Pegoraro Caterina , Monsoro-Burq Anne H. 
Published: July 2017

Summary statementPFKFB4 controls neural crest final specification and migration by regulation of AKT signaling or glycolysis.AbstractNeural crest (NC) specification comprises an early phase, initiating immature NC progenitors formation at neural plate stage, and a later phase at neural fold stage, resulting into functional premigratory NC, able to delaminate and migrate. We found that the NC-GRN triggers up-regulation ofpfkfb4(6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase4) during this late specification phase. As shown in previous studies, PFKFB4 controls AKT signaling in gastrulas and glycolysis rate in adult cells. Here, we focus on PFKFB4 function in NC during and after neurulation, using time-controlled or hypomorph depletionsin vivo. We find that PFKFB4 is essential both for specification of functional premigratory NC and for its migration. PFKFB4-depleted embryos fail activatingn-cadherinand late NC specifiers, exhibit severe migration defects, resulting in craniofacial defects. AKT signaling mediates PFKFB4 function in NC late specification, while both AKT signaling and glycolysis regulate migration. These findings highlight novel and critical roles of PFKFB4 activity in later stages of NC development, wired into the NC-GRN.
Cell Lineage and Communication Network Inference via Optimization for Single-cell Transcriptomics
Authors: Wang Shuxiong , Karikomi Matthew , MacLean Adam L. , Nie Qing 
Published: July 2017

AbstractThe use of single-cell transcriptomics has become a major approach to delineate cell subpopulations and the transitions between them. While various computational tools using different mathematical methods have been developed to infer clusters, marker genes, and cell lineage, none yet integrate these within a mathematical framework to perform multiple tasks coherently. Such coherence is critical for the inference of cell-cell communication, a major remaining challenge. Here we present similarity matrix-based optimization for single-cell data analysis (SoptSC), in which unsupervised clustering, pseudotemporal ordering, lineage inference, and marker gene identification are inferred via a structured cell-to-cell similarity matrix. SoptSC then predicts cell-cell communication networks, enabling reconstruction of complex cell lineages that include feedback or feedforward interactions. Application of SoptSC to early embryonic development, epidermal regeneration, and hematopoiesis demonstrates robust identification of subpopulations, lineage relationships, and pseudotime, and prediction of pathway-specific cell communication patterns regulating processes of development and differentiation.
Functional significance of spectrotemporal response functions obtained using magnetoencephalography
Authors: Constantino Francisco Cervantes , Villafañe-Delgado Marisel , Camenga Elizabeth , Dombrowski Katya , Walsh Benjamin , Simon Jonathan Z. 
Published: July 2017

AbstractThe spectrotemporal response function (STRF) model of neural encoding quantitatively associates dynamic auditory neural (output) responses to a spectrogram-like representation of a dynamic (input) stimulus. STRFs were experimentally obtained via whole-head human cortical responses to dynamic auditory stimuli using magnetoencephalography (MEG). The stimuli employed consisted of unpredictable pure tones presented at a range of rates. The predictive power of the estimated STRFs was found to be comparable to those obtained from the cortical single and multiunit activity literature. The STRFs were also qualitatively consistent with those obtained from electrophysiological studies in animal models; in particular their local-field-potential-generated spectral distributions and multiunit-activity-generated temporal distributions. Comparison of these MEG STRFs with others obtained using natural speech and music stimuli reveal a general structure consistent with common baseline auditory processing, including evidence for a transition in low-level neural representations of natural speech by 100 ms, when an appropriately chosen stimulus representation was used. It is also demonstrated that MEG-based STRFs contain information similar to that obtained using classic auditory evoked potential based approaches, but with extended applications to long-duration, non-repeated stimuli.Author summaryThe spectrotemporal response function (STRF) model of linking dynamic acoustic stimuli to dynamic neural responses is applied to whole-head non-invasive magnetoencephalography (MEG) recordings of the human auditory cortex. MEG STRFs were consistent predictors of neural activity, quantitatively and qualitatively, by comparison to those obtained from animal models using local field potential or multiunit activity as neural responses. Comparison of STRFs using stimuli as diverse as tone clouds, natural speech, and music revealed a common structure consistent with shared baseline auditory processing, when an appropriately chosen stimulus representation was used.