bluuebunny/crossref_metadata_2025_split huggingface dataset:
Muscle versus Fasciocutaneous Free Flaps in Lower Extremity Traumatic Reconstruction: A Multicenter Outcomes Analysis
Authors: Cho Eugenia H. , Shammas Ronnie L. , Carney Martin J. , Weissler Jason M. , Bauder Andrew R. , Glener Adam D. , Kovach Stephen J. , Hollenbeck Scott T. , Levin L. Scott 
Published: September 2017

Background:
Clinical indications are expanding for the use of fasciocutaneous free flaps in lower extremity traumatic reconstruction. The authors assessed the impact of muscle versus fasciocutaneous free flap coverage on reconstructive and functional outcomes.

Methods:
A multicenter retrospective review was conducted on all lower extremity traumatic free flaps performed at Duke University (1997 to 2013) and the University of Pennsylvania (2002 to 2013). Muscle and fasciocutaneous flaps were compared in two subgroups (acute trauma and chronic traumatic sequelae), according to limb salvage, ambulation time, and flap outcomes.

Results:
A total of 518 lower extremity free flaps were performed for acute traumatic injuries (n = 238) or chronic traumatic sequelae (n = 280). Muscle (n = 307) and fasciocutaneous (n = 211) flaps achieved similar cumulative limb salvage rates in acute trauma (90 percent versus 94 percent; p = 0.56) and chronic trauma subgroups (90 percent versus 88 percent; p = 0.51). Additionally, flap choice did not impact functional recovery (p = 0.83 for acute trauma; p = 0.49 for chronic trauma). Flap groups did not differ in the rates of flap thrombosis, flap salvage, flap loss, or tibial nonunion requiring bone grafting. Fasciocutaneous flaps were more commonly reelevated for subsequent orthopedic procedures (p < 0.01) and required fewer secondary skin-grafting procedures (p = 0.01). Reconstructive and functional outcomes remained heavily influenced by injury severity.

Conclusions:
Muscle and fasciocutaneous free flaps achieved comparable rates of limb salvage and functional recovery. Flap selection should be guided by defect characteristics and reconstructive needs.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, III.
Why the p Value Alone Is Not Enough: The Need for Confidence Intervals in Plastic Surgery Research
Authors: Samargandi Osama A. , Al-Taha Mona , Moran Kit , Al Youha Sarah , Bezuhly Michael 
Published: September 2017

Background:
The p value is one of the most used descriptors in statistical analysis; however, when reported in isolation, it does not convey the effect size of a treatment. The reporting of confidence intervals is an essential adjunct to determine the clinical value of treatment, as it permits an assessment of the effect size. The authors assessed the reporting of confidence intervals in clinical trials within the plastic surgery literature.

Methods:
The seven highest impact plastic surgery journals were screened using MEDLINE for clinical trials in the years 2006, 2009, 2012, and 2015. Studies were randomized based on a predetermined sample size, and various characteristics (e.g., Jadad quality score, reporting of statistical significance, journal impact factor, and participation of an individual with formal research training) were documented.

Results:
Two independent reviewers analyzed 135 articles. There was substantial interrater agreement (kappa = 0.78). Although 86.7 percent of studies reported a p value, only 25.2 percent reported confidence intervals. Of all journals assessed, Plastic and Reconstructive Surgery most frequently reported confidence intervals. The quality of the studies had a median Jadad score of 2 of 5. Bivariate analysis revealed that higher Jadad score and involvement of an individual with formal research training were associated with reporting of confidence intervals. Multivariate analysis revealed similar findings, whereas journal impact factor, year of publication, and statistical significance were not correlated with confidence interval reporting.

Conclusions:
Confidence intervals are underreported in the plastic surgery literature. To improve reporting quality of clinical trials, results should always include the confidence intervals to avoid misinterpretation of the effect size of a statistically significant result.
Reconstruction of the Heel, Middle Foot Sole, and Plantar Forefoot with the Medial Plantar Artery Perforator Flap: Clinical Experience with 28 Cases
Authors: Scaglioni Mario F. , Rittirsch Daniel , Giovanoli Pietro 
Published: September 2017

Background:
Defects in the weight-bearing region of the foot sole can represent a substantial restriction in quality of life and pose a challenge for reconstructive plastic surgery. The purpose of this article is to report the authors’ experience with the use of the medial plantar artery perforator flap for reconstruction of defects of the foot sole in three different regions: heel, middle foot sole, and plantar forefoot.

Methods:
From January of 2003 to May of 2016, 28 patients (13 male and 15 female patients) with an average age of 54 years (range, 12 to 84 years) underwent reconstruction with 28 medial plantar artery perforator flaps. Twenty-six flaps were harvested as pedicle perforator flaps and two as free perforator flaps. All flaps were raised from the ipsilateral instep area. The defect locations included the heel (20 cases), middle foot sole (four cases), and forefoot (four cases). The causes of reconstruction were tumors in 18 patients, decubitus in eight patients, and trauma in two patients.

Results:
The flap sizes varied from 2.5 × 2.5 cm to 5.5 × 9.5 cm. All of the flaps survived completely after surgery, apart from one. The donor sites were all covered with a split-thickness skin graft. Follow-up observations were conducted for 4 to 12 months, and all patients had good functional recovery with satisfactory cosmetic results.

Conclusion:
The medial plantar artery perforator flap can be considered an optimal method of foot sole reconstruction not only for covering the weight-bearing area of the heel but also for the middle and forefoot plantar region.

CLINICAL QUESTION/LEVEL OF EVIDENCE:
Therapeutic, IV.
Endotheliopathy of Trauma is an on-Scene Phenomenon, and is Associated with Multiple Organ Dysfunction Syndrome: A Prospective Observational Study
Authors: Naumann David N. , Hazeldine Jon , Davies David J. , Bishop Jon , Midwinter Mark J. , Belli Antonio , Harrison Paul , Lord Janet M. 
Published: September 2017

ABSTRACT

Background:
Trauma patients are vulnerable to coagulopathy and inflammatory dysfunction associated with endotheliopathy of trauma (EoT). In vitro evidence has suggested that tranexamic acid (TXA) may ameliorate endotheliopathy. We aimed to investigate how soon after injury EoT occurs, its association with multiple organ dysfunction syndrome (MODS), and whether TXA ameliorates it.

Methods:
A prospective observational study included 91 trauma patients enrolled within 60 min of injury and 19 healthy controls. Blood was sampled on enrolment and again 4 to 12 h later. ELISAs measured serum concentrations of syndecan-1 and thrombomodulin as biomarkers of EoT. MODS was compared between groups according to biomarker dynamics: persistently abnormal; abnormal to normal; and persistently normal. Timing of EoT was estimated by plotting biomarker data against time, and then fitting generalized additive models. Biomarker dynamics were compared between those who did or did not receive prehospital TXA.

Results:
Median age was 38 (interquartile range [IQR] 24–55) years; 78 of 91 were male. Median injury severity score (ISS) was 22 (IQR 12–36). EoT was estimated to occur at 5 to 8 min after injury. There were no significant differences in ISS between those with or without prehospital EoT. Forty-two patients developed MODS; 31 of 42 with persistently abnormal; 8 of 42 with abnormal to normal; and 3 of 42 with persistently normal biomarkers; P < 0.05. There were no significant differences between TXA and non-TXA groups.

Conclusions:
EoT was present at the scene of injury. MODS was more likely when biomarkers of EoT were persistently raised. There were no significant differences between TXA and non-TXA groups. Prehospital interventions aimed at endothelial restoration may represent a clinically meaningful target for prehospital resuscitation.
Robotic-Assisted Live Donor Ileal Segmentectomy for Intestinal Transplantation
Authors: Wu Guosheng , Li Qianjing , Zhao Qingchuan , Wang Weizhong , Shi Hai , Wang Mian , Zheng Jianyong , Li Mengbing , Fan Daiming 
Published: September 2017

Background
Every effort should be made to optimize surgical techniques and to minimize potential morbidity rates associated with live donor operations. Advances in a minimally invasive approach by robotic surgery to donor nephrectomy have raised the possibility of applying this technique to live donor bowel resections for intestinal transplantation.

Methods
We report the first 5 consecutive cases of a robotic-assisted live donor ileal segmentectomy. We describe the technical aspects of the procedure, discuss the rationale for considering this option, and evaluate potential advantages of this approach.

Results
We found that this new approach is associated with less postoperative discomfort, a shorter hospital length of stay, and a faster recovery of bowel function compared to our previous open surgery.

Conclusions
Our initial experience suggests that robotic surgery is a safe and feasible procedure for live donor ileal resection for intestinal transplantation and is a useful alternative to conventional open surgery.
Prolonged Delayed Renal Graft Function Secondary to Venous Hypertension
Authors: Mishra Suraj , Gupta Gaurav , Moinuddin I. , Strife Brian , Prasad Uma , Massey D. , King Anne , Kumar Dhiren , Bhati Chandra S. 
Published: September 2017

Abstract
The case of a 39-year-old highly sensitized woman who underwent second renal transplantation after being on warfarin because of a history of frequent thromboses of her left femoral arteriovenous graft (AVG) is reported here. The patient received a flow cytometric positive crossmatch kidney transplant from a deceased donor. Her posttransplant course was complicated by prolonged delayed graft function (DGF) lasting for 9 months. Antibody-mediated rejection occurred in the immediate postoperative period. This resolved after treatment, and resolution was confirmed by repeat biopsy. Despite this, she had persistent DGF and remained dialysis dependent. A computed tomography scan due to the development of perinephric hematoma after posttransplant biopsy demonstrated venous collateralization around the allograft. At 7 months posttransplant, a venogram during declotting of AVG revealed chronic thrombus in the inferior vena cava (IVC) above the level of native renal veins with a venous gradient of 26 mmHg. After declotting of the graft, iliac venoplasty, and subsequent IVC stent, her renal function continues to improve with a most recent creatinine of 1.4 mg/dL at 36 months posttransplant. Venous hypertension secondary to IVC thrombosis in presence of patent femoral AVG should be considered as a rare cause of prolonged DGF.
Ancient genomes from North Africa evidence prehistoric migrations to the Maghreb from both the Levant and Europe
Authors: Fregel Rosa , Méndez Fernando L. , Bokbot Youssef , Martín-Socas Dimas , Camalich-Massieu María D. , Santana Jonathan , Morales Jacob , Ávila-Arcos María C. , Underhill Peter A. , Shapiro Beth , Wojcik Genevieve , Rasmussen Morten , Soares Andre E. R. , Kapp Joshua , Sockell Alexandra , Rodríguez-Santos Francisco J. , Mikdad Abdeslam , Trujillo-Mederos Aioze , Bustamante Carlos D. 
Published: September 2017

ABSTRACTThe extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities, or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present the first analysis of individuals’ genome sequences from early and late Neolithic sites in Morocco, as well as Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans are distinct from any other reported ancient individuals and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. Among ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Although an expansion in Early Neolithic times is also plausible, the high divergence observed in Early Neolithic Moroccans suggests a long-term isolation and an early arrival in North Africa for this population. This scenario is consistent with early Neolithic traditions in North Africa deriving from Epipaleolithic communities who adopted certain innovations from neighbouring populations. Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow. Finally, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities of the Iberian Neolithic cultures with that of North African Neolithic sites further reinforce the model of an Iberian migration into the Maghreb.SIGNIFICANCE STATEMENTThe acquisition of agricultural techniques during the so-called Neolithic revolution has been one of the major steps forward in human history. Using next-generation sequencing and ancient DNA techniques, we directly test if Neolithization in North Africa occurred through the transmission of ideas or by demic diffusion. We show that Early Neolithic Moroccans are composed of an endemic Maghrebi element still retained in present-day North African populations and distantly related to Epipaleolithic communities from the Levant. However, late Neolithic individuals from North Africa are admixed, with a North African and a European component. Our results support the idea that the Neolithization of North Africa might have involved both the development of Epipaleolithic communities and the migration of people from Europe.
Streamlined histone-based fluorescence lifetime imaging microscopy reveals ATM regulation of chromatin compaction
Authors: Sherrard Alice , Bishop Paul , Panagi Melanie , Villagomez Maria Beatriz , Alibhai Dominic , Kaidi Abderrahmane 
Published: September 2017

AbstractChanges in chromatin compaction are crucial during genomic responses. Thus, methods that enable such measurements are instrumental for investigating genome function. Here, we address this challenge by developing, validating, and streamlining histone-based fluorescence lifetime imaging microscopy (FLIM) that robustly detects chromatin compaction states in fixed and live cells; in 2D and 3D. We present quality-controlled and detailed method that is simpler and faster than previous approches, and uses FLIMfit open-source software. We demonstrate the versatility of our method through its combination with immunofluorescence and its implementation in immortalised cells and primary neurons. Owing to these developments, we applied this method to elucidate the function of the DNA damage response kinase, ATM, in regulating chromatin organisation after genotoxic-stress. We unravelled a role for ATM in regulating chromatin compaction independently of DNA damage. Collectively, we present an adaptable chromatin FLIM method for examining chromatin structure in cells, and establish its broader utility.
A novel strategy to express different antigens from one modified vaccinia Ankara vaccine vector
Authors: Lauer K. B. , McKenzie E. A. , Hall Y. , Gowda C.P.C. , Klapper P. , Borrow R. , Vallely P.J. , Carroll M. W. , Blanchard T. J. 
Published: September 2017

AbstractTo enhance global control of encephalitis and hepatitis caused by rabies-(RABV), Japanese encephalitis-(JEV), hepatitis B-virus (HBV), and enterovirus 71 (EV71) novel immunisation strategies are needed. Therefore, a multipathogen modified Vaccinia Ankara vector, expressing antigens from the above pathogens, was constructed. Two recombinants, one carrying the EV71 and JEV pathogen sequence and one the RABV-HBV pathogen sequence were generated. To ensure similar expression of the antigens, a T7-promoter was linked to the expression cassettes of all pathogen sequences. Direct regulation of this promoter was achieved through co-infection with a second T7-polymerase expressing MVA. Protein expression using this co-infection model of expression was demonstrated in vitro. To investigate the co-infection model of antigen delivery in vivo, a murine immunogenicity study was performed using the MVA-RABV-HBV recombinant. Although, serum antibodies against MVA were induced in all mice, no serum antibodies against RABV or HBV could be detected.
A structural approach to disentangle the visualization of bipartite biological networks
Authors: Garcia-Algarra J. , Pastor J. M. , Mouronte M. L. , Galeano J. 
Published: September 2017

AbstractInteractions between two different guilds of entities are pervasive in biology. They may happen at molecular level, like in a diseasome, or amongst individuals linked by biotic relationships, such as mutualism or parasitism. These sets of interactions are complex bipartite networks. Visualization is a powerful tool to explore and analyse them but the most common plots, the bipartite graph and the interaction matrix, become rather confusing when working with real biological networks. We have developed two new types of visualization that exploit the structural properties of these networks to improve readability. A technique calledk-core decompositionidentifies groups of nodes that share connectivity properties. With the results of this analysis it is possible to build a plot based on information reduction (Polar Plot) and another which takes the groups as elementary blocks for spatial distribution (Ziggurat plot). We describe the applications of both plots and the software to create them.
Distributed and dynamic intracellular organization of extracellular information
Authors: Granados Alejandro A. , Pietsch Julian M. J. , Cepeda-Humerez Sarah A. , Tkačik Gašsper , Swain Peter S. 
Published: September 2017

AbstractAlthough cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for ten transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: generalists (Msn2/4, Tod6/Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. Each transcription factor reports differently, and it is only their collective response that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change, and we predict that such multi-dimensional representations are common in cellular decision-making.Significance StatementTo thrive in diverse environments, cells must represent extracellular change intracellularly despite stochastic biochemistry. Here we introduce a quantitative framework for investigating the organization of information within a cell. Combining single-cell measurements of intracellular dynamics with a new, scalable methodology for estimating mutual information between time-series and a discrete input, we demonstrate that extracellular information is encoded in the dynamics of the nuclear localization of transcription factors and that information is lost with alternative static statistics. Any one transcription factor is usually insufficient, but the collective dynamics of multiple transcription factors can represent complex extracellular change. We therefore show that a cell’s internal representation of its environment can be both distributed across diverse proteins and dynamically encoded.
USA300 MRSA lineages persist on multiple body sites following infection
Authors: Read Timothy D. , Petit Robert A. , Yin Zachary , Montgomery Tuyaa , McNulty Moira C. , David Michael Z. 
Published: September 2017

AbstractBACKGROUNDUSA300 methicillin-resistantStaphylococcus aureus(MRSA) is a community- and hospital- acquired pathogen that frequently causes infections but also can survive on the human body asymptomatically as a part of the normal flora. We devised a comparative genomic strategy to track colonizing USA300 at different body sites afterS. aureusinfection.METHODSWe sampled ST8S. aureusfrom subjects at the site of a first known MRSA infection. Within 60 days of this infection and again 12 months later, each subject was tested for asymptomatic colonization in the nose, throat and perirectal region. 93S. aureusstrains underwent whole genome shotgun sequencing.RESULTSGenome sequencing revealed that 23 patients carried USA300 intra-subject lineages (ISLs), defined as having an index infection isolate (III) and closely related strains. Pairwise distance between strains in different ISLs was 48 to 162 single nucleotide polymorphisms (SNPs), whereas within the same ISL it was 0 to 26 SNPs. At the initial sampling time among 23 subjects, we isolatedS. aureusfrom the nose, throat and perirectal sites from 15, 11 and 15 of them, respectively. Twelve months later we isolatedS. aureuswithin the same ISL from 9 subjects, with 6, 3 and 3 strains from the nose, throat and perirectal area, respectively. The median time from initial acquisition of theS. aureusUSA300 strains to culture of the index infection was estimated at 18 weeks. Strains in ISLs from the same subject differed in plasmid and prophage content, and contained deletions that removed themecA-containing SCCmecand ACME regions. Five strains contained frameshift mutations inagrtoxin-regulating genes. Persistence of an ISL was not associated with clinical or demographic subject characteristics.CONCLUSIONClonal lineages of USA300 may continue to colonize people at one or more anatomic sites up to a year after an initial infection and experience loss of the SCCmec, loss and gain of other mobile genetic elements, and mutations in the agr operon.