bluuebunny/crossref_metadata_2025 huggingface dataset:
External Levator Advancement versus Müller Muscle–Conjunctival Resection for Aponeurotic Blepharoptosis: A Randomized Clinical Trial
Authors: Saonanon Preamjit , Sithanon Supapan
Published: January 2018

Background:

The purpose of this study was to compare the efficacy of external levator advancement and Müller muscle–conjunctival resection in aponeurotic blepharoptosis repair.

Methods:

Mild to moderate blepharoptosis patients with good levator function and a positive phenylephrine test were randomized to upper blepharoplasty with either external levator advancement or Müller muscle–conjunctival resection. The primary outcome was marginal reflex distance 1 at 1 month after surgery. Secondary outcomes were cosmetic outcome, complications, and operating room time.

Results:

Forty patients were enrolled, six men and 34 women, with an average age of 62.4 years. The mean preoperative marginal reflex distance 1 in the levator group (39 eyes/20 subjects) and the Müller group (38 eyes/20 subjects) was 1.2 ± 0.8 mm and 1.5 ± 0.7 mm, respectively. The mean postoperative marginal reflex distance 1 in the levator and Müller groups was 3.0 ± 1.0 mm and 3.2 ± 1.0 mm, respectively. The difference in the mean change was 0.008, and was not statistically different (95 percent CI, −0.59 to 0.61; p = 0.978). The mean cosmetic outcome was 2.69 ± 0.81 for the levator group and 3.07 ± 0.68 for the Müller group, with a mean difference of 0.373 (95 percent CI, 0.06 to 0.69; p = 0.020). The average operating room time was 75 ± 19.2 minutes for the levator group and 71 ± 23.6 minutes for the Müller group (p = 0.439). There were four eyes that underwent reoperation, three in the levator group (7.7 percent) and one in the Müller group (2.6 percent).

Conclusions:

External elevator advancement and Müller muscle–conjunctival resection are both effective in correction of mild to moderate blepharoptosis. However, Müller muscle–conjunctival resection yields a statistically significant better cosmetic outcome and causes less eyelid asymmetry.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, II.
Plastic Surgeon–Led Ultrasound
Authors: Oni Georgette , Chow Whitney , Ramakrishnan Venkat , Griffiths Matthew
Published: January 2018

Background:

Portable high-frequency ultrasound is a useful adjunct to a plastic surgeon's practice. With a short learning curve, this patient-friendly imaging modality has a variety of uses that aid patient management/treatment plans. The authors describe clinical cases and review the literature regarding ultrasound performed by the surgeon.

Methods:

The Sonosite S-Nerve machine with the L25X transducer was used (depth, 4.3 cm). Clinical cases that ordinarily would have been referred to the radiology department were taken from the day-to-day practice of the senior author (M.G.). The clinical scenarios ranged from acute presentations to planned elective settings.

Results:

Ultrasound was a useful adjunct in a variety of applications, ranging from acute hand trauma visualizing neurovascular bundles and tendons, to elements of reconstructive breast surgery such as fat grafting over an implant and scar release. The ultrasound machine was also used for determination of the depth and size of collections such as seromas to facilitate drainage, for identification of lymph nodes before transfer, and for acute presentations of conditions ranging from undiagnosed swelling to foreign body localization.

Conclusions:

The portable ultrasound machine has become an invaluable tool in the senior author’s practice. In a short time and with a short learning curve, the authors’ unit identified numerous applications for its use. From a patient perspective, it is noninvasive/nonpainful and has no deleterious radiation effects, and treatment plans can be enacted without delay. It is highly recommended that surgeons become familiar with this imaging modality and assimilate it into their daily practice.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, V.
Virtual Monoenergetic Images From a Novel Dual-Layer Spectral Detector Computed Tomography Scanner in Portal Venous Phase: Adjusted Window Settings Depending on Assessment Focus Are Essential for Image Interpretation
Authors: Hickethier Tilman , Iuga Andra-Iza , Lennartz Simon , Hauger Myriam , Byrtus Jonathan , Luetkens Julian A. , Haneder Stefan , Maintz David , Doerner Jonas
Published: January 2018

Objective

We aimed to determine optimal window settings for conventional polyenergetic (PolyE) and virtual monoenergetic images (MonoE) derived from abdominal portal venous phase computed tomography (CT) examinations on a novel dual-layer spectral-detector CT (SDCT).

Methods

From 50 patients, SDCT data sets MonoE at 40 kiloelectron volt as well as PolyE were reconstructed and best individual window width and level values manually were assessed separately for evaluation of abdominal arteries as well as for liver lesions. Via regression analysis, optimized individual values were mathematically calculated. Subjective image quality parameters, vessel, and liver lesion diameters were measured to determine influences of different W/L settings.

Results

Attenuation and contrast-to-noise values were significantly higher in MonoE compared with PolyE. Compared with standard settings, almost all adjusted W/L settings varied significantly and yielded higher subjective scoring. No differences were found between manually adjusted and mathematically calculated W/L settings.

Conclusions

PolyE and MonoE from abdominal portal venous phase SDCT examinations require appropriate W/L settings depending on reconstruction technique and assessment focus.
Establishing a Virtual Community of Practice in Simulation
Authors: Thoma Brent , Brazil Victoria , Spurr Jesse , Palaganas Janice , Eppich Walter , Grant Vincent , Cheng Adam
Published: January 2018

Summary Statement

Professional development opportunities are not readily accessible for most simulation educators, who may only connect with simulation experts at periodic and costly conferences. Virtual communities of practice consist of individuals with a shared passion who communicate via virtual media to advance their own learning and that of others. A nascent virtual community of practice is developing online for healthcare simulation on social media platforms. Simulation educators should consider engaging on these platforms for their own benefit and to help develop healthcare simulation educators around the world. Herein, we describe this developing virtual community of practice and offer guidance to assist educators to engage, learn, and contribute to the growth of the community.
How has the Affordable Care Act changed outcomes in emergency general surgery?
Authors: Hamel Michelle G. , Godat Laura N. , Coimbra Raul , Doucet Jay J.
Published: January 2018

INTRODUCTION

Lack of insurance coverage increases complications and mortality from surgical procedures. The 2014 Affordable Care Act (ACA) Open Enrollment (OE) insured more Americans, but it is unknown if this improved outcomes from emergency general surgery (EGS) procedures. This study seeks to determine how ACA OE coverage changes outcomes in EGS.

METHODS

This is a retrospective review using the Nationwide Inpatient Sample database from 2012 to 2014. Patients aged 18 to 64 years undergoing EGS procedures were identified by International Classification of Diseases, Ninth Revision, codes. Medicare patients were excluded. Patient demographics, hospital characteristics, and Charlson comorbidity index were obtained. Outcomes were measured by mortality, complications, and calculated costs. Univariate and difference-in-differences multivariate analyses were performed to determine the effect of the ACA OE on EGS outcomes.

RESULTS

A total of 304,110 EGS cases were identified. After Medicare patients were excluded, there were 275,425 cases. In 2014, Medicaid admissions increased 18.2% from 18,495 to 22,615 (p < 0.001) and self-pay admissions decreased 33% from 14,938 to 10,630 (p < 0.001). Mortality significantly increased for self-pay patients in 2014 from 0.81% to 1.22% (p < 0.001). Difference-in-differences analysis indicated that, after risk adjustment, the ACA OE was associated with a small reduction in mortality for insured patients (−0.12%, p = 0.034), increased complications (1.4%, p = 0.009), and increased wage-index adjusted mean costs (4.6%, p < 0.001). There was a significant increase in Medicare (+26.5%) and private (+12.2%, p < 0.001) insurance admissions in teaching hospitals, while nonteaching hospitals had fewer EGS admissions with a greater reduction in uninsured EGS admissions.

CONCLUSIONS

The ACA OE created a significant reduction in uninsured EGS admissions but did not reduce EGS mortality. Mortality decreased in insured patients but increased in uninsured patients, indicating that the ACA OE primarily insured lower-risk patients. The ACA OE did increase cost and complications in insured admissions. Teaching hospitals saw the majority of the increase in Medicaid and private insurance EGS admissions. A national registry would improve future study of insurance policy on EGS outcomes.

LEVEL OF EVIDENCE

Economic analysis, level IV.
Fresh whole blood resuscitation does not exacerbate skeletal muscle edema and long-term functional deficit after ischemic injury and hemorrhagic shock
Authors: Aurora Amit , Roe Janet L. , Umoh Nsini A. , Dubick Michael , Wenke Joseph C. , Walters Thomas J.
Published: January 2018

BACKGROUND

Hemorrhagic shock caused by extremity vascular injuries is common in combat injuries. Fluid resuscitation is the standard treatment for severe hemorrhage (HEM). Tourniquets (TKs) used for HEM control cause ischemia-reperfusion (I/R) injury that induces edema formation in the injured muscle. Resuscitation fluids affect edema formation; however, its effect on long-term functional response remains unknown. The objectives of this study are to (1) compare acute muscle damage; (2) determine long-term functional recovery of ischemic muscle; and (3) compare local and systemic inflammatory response including the expression of junctional proteins following early resuscitation with Hextend and fresh whole blood using a rodent model of combined HEM and TK-induced limb I/R.

METHODS

Anesthetized Sprague-Dawley rats underwent 42.5% arterial HEM, followed by 3 hours of TK application. Animals were either not resuscitated or resuscitated with Hextend or fresh whole blood. Two time points were evaluated, 2 and 28 days. Plasma cytokine concentrations were determined at baseline and end resuscitation. At 2 days, edema formation, expression of junctional proteins, and tissue level cytokines concentrations were evaluated. At 28 days, in vivo muscle contractile properties were determined. At both time points, routine histology was performed and graded using a semiquantitative grading system.

RESULTS

All animals developed hemorrhagic hypovolemia; the mortality rate was 100% in nonresuscitated rats. Hextend resuscitation exacerbated muscle edema (~11%) and muscle strength deficit (~20%). Fresh whole blood resuscitation presented edema and muscle strength akin to TK only. Fresh whole blood resuscitation upregulated expression of junctional proteins including proangiogenic factors and dampened the inflammatory response.

CONCLUSION

Fresh whole blood resuscitation does not exacerbate either TK-induced edema or muscle strength deficit. Fresh whole blood resuscitation may reduce both acute and long-term morbidity associated with extremity trauma. To our knowledge, this is the first study to demonstrate the nature of the resuscitation fluid administered following HEM impacts short- and long-term indices of I/R in skeletal muscle.
Staff officers as blood suppliers: Effects of repeated donations and autologous reinfusions of untransfused units
Authors: Strandenes Geir , Sivertsen Joar , Eliassen Håkon , Braathen Hanne , Hervig Tor A.
Published: January 2018

BACKGROUND

Limited blood inventory and resupply chains in combat settings can result in preventable deaths from traumatic hemorrhage. One way of mitigating this could be to establish donor pools where blood is collected in advance of high-risk missions and then reinfused back to the donor if not needed to treat casualties.

METHODS

Four hundred fifty milliliters plus 56 mL of blood was collected, rested for 2 hours in room temperature, and stored at 4°C. The blood was reinfused 22 to 24 hours after donation and the donor observed for adverse reactions. Samples were collected before and 20 minutes after each donation for hematology, immunoglobulin G, ferritin, C-reactive protein, total protein, lactate dehydrogenase, bilirubin, haptoglobin, and activated partial thromboplastin time.

RESULTS

Nine participants went through a total of 36 donation and reinfusion procedures. Four donors participated in five rounds, two in four rounds, two in three rounds, and one in two rounds. A significant drop was seen in hemoglobin (14.6 ± 0.9 to 13.9 ± 0.9) and ferritin (179 ± 70 to 149 ± 78) from before the first donation to after the last reinfusion (p < 0.05). Other parameters were unaffected.

CONCLUSION

This small pilot study suggests that repeated donations and reinfusions may be both feasible and safe. Blood collected in this way should be labeled with the donor’s full name and social security number (or similar) and the identity visually verified by the donor immediately before both donation and reinfusion. To further reduce risk, this form of donation should be restricted to scenarios where there is no other option for making blood available.

LEVEL OF EVIDENCE

Therapeutic/Care management study, level V.
The history and promising future of phage therapy in the military service
Authors: Gelman Daniel , Eisenkraft Arik , Chanishvili Nina , Nachman Dean , Coppenhagem Glazer Shunit , Hazan Ronen
Published: January 2018

The continuous evolvement of bacterial resistance to most, if not all, available antibiotics is a worldwide problem. These strains, frequently isolated from military-associated environments, have created an urgent need to develop supplementary anti-infective modalities. One of the leading directions is phage therapy, which includes the administration of bacteriophages, viruses that specifically target bacteria, as biotherapies. Although neglected in the West until recent years, bacteriophages have been widely studied and clinically administered in the former Soviet Union and Eastern Europe for over a century, where they were found to be incredibly efficient at battling numerous infectious diseases.

In this review, we discuss the high potential of phage therapy as a solution for resistant bacterial infectious diseases relating to military medicine. By describing the historical development and knowledge acquired on phage therapy, we define the advantages of bacteriophages for combating resistant bacteria in multiple settings, such as trauma injuries and foodborne illnesses, as a preventive tool and therapy against biological warfare agents, and more. We also present the most recent successful clinical applications of bacteriophages in military settings worldwide.

We believe that augmenting military medicine by integrating phage therapy is an important and required step in preparedness for the rapidly approaching post–antibiotic era.
Analysis of isolated transverse process fractures sustained during blast-related events
Authors: Newell Nicolas , Pearce A. Phillip , Spurrier Edward , Gibb Iain , Webster Claire E. , Clasper Jonathan C. , Masouros Spyros D.
Published: January 2018

BACKGROUND

Personnel have sustained a range of devastating blast injuries during recent conflicts. Previous studies have focused on severe injuries, including to the spine; however, no study has specifically focused on the most common spinal injury—transverse process (TP) fractures. Although their treatment usually requires limited intervention, analysis of TP fractures may help determine injury mechanisms.

METHODS

Data were collected from victims with spinal fractures who were injured in improvised explosive device attacks, from the UK’s Joint Theatre Trauma Registry. The level and side of each TP fracture were recorded, as well as associated injuries, whether they were mounted or dismounted, and outcome (survivor or fatality).

RESULTS

Most (80%) of the TP fractures were lumbar. More bilateral (both left and right fractures at the same level), and L5 TP fractures, were seen in fatalities than survivors. In the mounted group, lumbar TP fractures were statistically significantly associated with fatality, head injury, noncompressible torso hemorrhage, pelvic injury, and other spinal injuries. In the dismounted group, thoracic TP fractures were associated with head, chest wall, and other spinal injuries; and lumbar TP fractures were associated with pelvic and other spinal injuries.

CONCLUSIONS

Different injury mechanisms of the TP in the mounted and dismounted groups are likely. Inertial forces acting within the torso due to rapid loading being transferred through the seat, or high intra-abdominal pressures causing the tensile forces acting through the lumbar fascia to avulse the TPs are likely mechanisms in the mounted group. Blunt trauma, violent lateral flexion-extension forces, or rapid flail of the lower extremities causing tension of the psoas muscle, avulsing the TP, are likely causes in the dismounted group. Isolated lumbar TP fractures can be used as markers for more severe injuries, and fatality, in mounted blast casualties.

LEVEL OF EVIDENCE

Prognostic and epidemiological, level III.
Permissive hypotension versus conventional resuscitation strategies in adult trauma patients with hemorrhagic shock: A systematic review and meta-analysis of randomized controlled trials
Authors: Tran Alexandre , Yates Jeffrey , Lau Aaron , Lampron Jacinthe , Matar Maher
Published: January 2018

BACKGROUND

Aggressive fluid resuscitation in trauma promotes deleterious effects such as clot disruption, dilutional coagulopathy and hypothermia. Animal studies suggest that permissive hypotension maintains appropriate organ perfusion, reduces bleeding and improves mortality. This review assesses the efficacy and safety of permissive hypotension in adult trauma patients with hemorrhagic shock.

METHODS

We searched the MEDLINE and EMBASE databases from inception to May 2017 for randomized controlled trials comparing permissive hypotension vs. conventional resuscitation following traumatic injury. We included preoperative and intraoperative resuscitation strategies. The primary outcome was 30-day or in-hospital mortality. Secondary outcomes included blood product utilization, estimated blood loss and in-hospital complications. Pooling was performed with a random-effects model.

RESULTS

We screened 722 abstracts, from which five randomized trials evaluating 1,158 patients were included. Blood pressure targets in the intervention arms varied from systolic BP 50 mm Hg to 70 mm Hg or mean arterial pressure of 50 mm Hg or higher as compared to systolic BP 65 mm Hg to 100 mm Hg or mean arterial pressure of 65 or higher in the control arms. Two studies evaluated only patients with penetrating injury while the remaining three additionally included blunt injuries. Four trials suggested a survival benefit for 30-day or in-hospital mortality with hypotensive resuscitation, although three studies were insufficiently powered to find statistical significance. Studies were of poor to moderate quality due to poor protocol reporting and lack of blinding. The pooled odds ratio was 0.70 (95% confidence interval, 0.53–0.92), suggesting a survival benefit for permissive hypotension. Those patients received fewer blood products and had lesser estimated blood loss.

CONCLUSION

Permissive hypotension may offer a survival benefit over conventional resuscitation for patients with hemorrhagic injury. It may additionally reduce blood loss and blood product utilization. However, the majority of studies were underpowered, thus reflecting a need for high quality, adequately powered trials.

PROSPERO REGISTRATION

Systematic Review, level II.

CRD42017070526.
Socioeconomic Inequalities in the Kidney Transplantation Process: A Registry-Based Study in Sweden
Authors: Zhang Ye , Gerdtham Ulf-G. , Rydell Helena , Jarl Johan
Published: January 2018

Background

Few studies have examined the association between individual-level socioeconomic status and access to kidney transplantation. This study aims to investigate the association between predialysis income and education, and access to (i) the kidney waitlist (first listing), and (ii) kidney transplantation conditional on waitlist placement. Adjustment will be made for a number of medical and nonmedical factors.

Methods

The Swedish Renal Register was linked to national registers for adult patients in Sweden who started dialysis during 1995 to 2013. We employed Cox proportional hazards models.

Results

Nineteen per cent of patients were placed on the waitlist. Once on the waitlist, 80% received kidney transplantation. After adjusting for covariates, patients in the highest income quintile were found to have higher access to both the waitlist (hazard ratio [HR], 1.73; 95% confidence interval [CI], 1.53-1.96) and kidney transplantation (HR, 1.33; 95% CI, 1.16-1.53) compared with patients in the lowest income quintile. Patients with higher education also had better access to the waitlist and kidney transplantation (HR, 2.16; 95% CI, 1.94-2.40; and HR, 1.16; 95% CI, 1.03-1.30, respectively) compared with patients with mandatory education.

Conclusions

Socioeconomic status-related inequalities exist with regard to both access to the waitlist, and kidney transplantation conditional on listing. However, the former inequality is substantially larger and is therefore expected to contribute more to societal inequalities. Further studies are needed to explore the potential mechanisms and strategies to reduce these inequalities.
Function of BriC Peptide in the Pneumococcal Competence and Virulence Portfolio
Authors: Aggarwal Surya D. , Eutsey Rory , West-Roberts Jacob , Domenech Arnau , Xu Wenjie , Abdullah Iman Tajer , Mitchell Aaron P. , Veening Jan-Willem , Yesilkaya Hasan , Hiller N. Luisa
Published: January 2018

Streptococcus pneumoniae (pneumococcus) is an opportunistic pathogen that causes otitis media, sinusitis, pneumonia, meningitis and sepsis. The progression to this pathogenic lifestyle is preceded by asymptomatic colonization of the nasopharynx. This colonization is associated with biofilm formation; the competence pathway influences the structure and stability of biofilms. However, the molecules that link the competence pathway to biofilm formation are unknown. Here, we describe a new competence-induced gene, called briC, and demonstrate that its product promotes biofilm development and stimulates colonization in a murine model. We show that expression of briC is induced by the master regulator of competence, ComE. Whereas briC does not substantially influence early biofilm development on abiotic surfaces, it significantly impacts later stages of biofilm development. Specifically, briC expression leads to increases in biofilm biomass and thickness at 72h. Consistent with the role of biofilms in colonization, briC promotes nasopharyngeal colonization in the murine model. The function of BriC appears to be conserved across pneumococci, as comparative genomics reveal that briC is widespread across isolates. Surprisingly, many isolates, including strains from clinically important PMEN1 and PMEN14 lineages, which are widely associated with colonization, encode a long briC promoter. This long form captures an instance of genomic plasticity and functions as a competence-independent expression enhancer that may serve as a precocious point of entry into this otherwise competence-regulated pathway. Moreover, overexpression of briC by the long promoter fully rescues the comE-deletion induced biofilm defect in vitro, and partially in vivo. These findings indicate that BriC may bypass the influence of competence in biofilm development and that such a pathway may be active in a subset of pneumococcal lineages. In conclusion, BriC is a part of the complex molecular network that connects signaling of the competence pathway to biofilm development and colonization.
Endotoxin Tolerance Induced by Different TLR Ligands
Authors: Butcher Suzanne K. , O’Carroll Christine , Wells Christine A. , Carmody Ruaidhrí J.
Published: January 2018

Endotoxin tolerance is a long-recognised property of macrophages that leads to an altered response to repeated or chronic exposure to Toll-like receptor (TLR) ligands. The physiological role of tolerance is to limit the potential damage to host tissue that may otherwise result from prolonged production of pro-inflammatory cytokines. Endotoxin tolerance is induced by all TLRs tested to date, however, tolerance induced by the TLR4 ligand lipopolysaccharide (LPS) is by far the best studied. LPS tolerance involves a global transcriptional shift from a pro-inflammatory response toward one characterised by the expression of anti-inflammatory and pro-resolution factors. Although largely reversible, LPS-tolerance leads to a hybrid macrophage activation state that is pro-inflammatory in nature but possesses distinct regulatory anti-inflammatory features. Remarkably, a comparative transcriptomic analysis of tolerance induced by different TLR ligands has not previously been reported. Here we describe the transcriptomic profiles of mouse macrophages tolerised with ligands for TLR2, TLR3, TLR4 and TLR 9. While we identified TLR-specific transcriptional profiles in macrophages tolerised with each ligand, tolerance induced by TLR4 was the most comprehensive state, such that each gene tolerised by any of the TLRs tested was also found to be tolerised by TLR4. Pro-inflammatory cytokines are not universally supressed in all tolerant cells but distinct patterns of cytokine expression distinguished TLR-specific tolerance. Analysis of gene regulatory regions revealed specific DNA sequence motifs associated with distinct states of TLR tolerance, implicating previously identified as well as novel transcriptional regulators of tolerance in macrophages. These data provide a basis for the future exploitation of TLR-specific tolerant states to achieve therapeutic re-programming of the innate immune response.
Structural variability of EspG chaperones from mycobacterial ESX-1, ESX-3 and ESX-5 type VII secretion systems
Authors: Tuukkanen Anne T. , Freire Diana , Chan Sum , Arbing Mark A. , Reed Robert W. , Evans Timothy J. , Zenkeviciutė Grasilda , Kim Jennifer , Kahng Sara , Sawaya Michael R. , Chaton Catherine T. , Wilmanns Matthias , Eisenberg David , Parret Annabel H. A. , Korotkov Konstantin V.
Published: January 2018

Type VII secretion systems (ESX) are responsible for transport of multiple proteins in mycobacteria. How different ESX systems achieve specific secretion of cognate substrates remains elusive. In the ESX systems, the cytoplasmic chaperone EspG forms complexes with heterodimeric PE-PPE substrates that are secreted from the cells or remain associated with the cell surface. Here we report the crystal structure of the EspG1 chaperone from the ESX-1 system determined using a fusion strategy with T4 lysozyme. EspG1 adopts a quasi 2-fold symmetric structure that consists of a central β-sheet and two α-helical bundles. Additionally, we describe the structures of EspG3 chaperones from four different crystal forms. Alternate conformations of the putative PE-PPE binding site are revealed by comparison of the available EspG3 structures. Analysis of EspG1, EspG3 and EspG5 chaperones using small-angle X-ray scattering (SAXS) reveals that EspG1 and EspG3 chaperones form dimers in solution, which we observed in several of our crystal forms. Finally, we propose a model of the ESX-3 specific EspG3-PE5-PPE4 complex based on the SAXS analysis.

Highlights

The crystal structure of EspG1 reveals the common architecture of the type VII secretion system chaperones

Structures of EspG3 chaperones display a number of conformations that could reflect alternative substrate binding modes

EspG3 chaperones dimerize in solution

A model of EspG3 in complex with its substrate PE-PPE dimer is proposed based on SAXS data
Whole genome sequencing for predicting clarithromycin resistance in Mycobacterium abscessus
Authors: Lipworth Samuel , Hough Natasha , Leach Laura , Morgan Marcus , Jeffery Katie , Andersson Monique , Robinson Esther , Smith E. Grace , Crook Derrick , Peto Tim , Walker Timothy
Published: January 2018

Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases with concern regarding patient to patient transmission. The recent introduction of routine whole genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterise the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there was paired genotype/phenotype data. A search for novel resistance determining mutations was conducted using an heuristic algorithm.

The sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% CI 89 – 98%) and the specificity was 66% (95% CI 54 – 76%). Subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance conferring SNPs were identified. WGS demonstrates probable resistance determining SNPs in regions the NTM-DR line probe cannot detect. These mutations are potentially clinically important as they all occurred in samples predicted to be inducibly resistant, and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.
Canopy cover and structural complexity affect the phylogenetic composition of a pond-dwelling Neotropical anuran metacommunity
Authors: Provete Diogo B.
Published: January 2018

Phylogenetic information has been increasingly included into (meta)community assembly studies. However, recent studies have challenged the framework commonly used to infer processes from phylogenetic structure. Amphibians are good model organisms to study processes promoting structure in metacommunities, since they are subjected to different environmental and spatial processes throughout their biphasic life cycle. Pond canopy cover is one of these environmental factors that strongly influence the distribution of species and traits of several freshwater taxa, including larval amphibians (e.g., behavior, color, fin height, and length of intestine). Here, I tested the influence of pond canopy cover, floating vegetation, and pond morphology on the phylogenetic structure of an anuran metacommunity in the Atlantic Forest of Southeastern Brazil. I sampled tadpoles in 13 ponds and marshes from June 2008 and July 2009 in the Serra da Bocaina National Park, São Paulo. After building a metacommunity phylogeny, I used an eigenvector-based technique to describe the metacommunity phylogenetic composition (Principal Coordinates of Phylogenetic Structure, PCPS). I then run a db-RDA to evalute whether a subset of these eigenvectors can be explained by environmental variables. I found that pond canopy cover and floating vegetation were the main variables influencing lineage sorting in this metacommunity. Canopy cover separated hylid lineages from other families that were associated with open areas. Floating vegetation separated two hylid tribes (Cophomantini and Dendropsophini). Our results mainly suggest that the effect of canopy cover and floating vegetation on the structure of anuran metacommunity may affect not only species, but also entire lineages.
Characterizing concentration-dependent neural dynamics of 4-aminopyridine-induced epileptiform activity
Authors: Myers Timothy L , González Oscar C , Stein Jacob B , Bazhenov Maxim
Published: January 2018

Epilepsy remains one of the most common neurological disorders. In patients, it is characterized by unprovoked, spontaneous, and recurring seizures or ictal events. Typically, inter-ictal events or large bouts of population level activity can be measured between seizures and are generally asymptomatic. Decades of research has focused on understanding the mechanisms leading to the development of seizure-like activity using various proconvulsive pharmacological agents, including 4-aimnopyridine (4AP). However, the lack of consistency in the concentrations used for studying 4AP-induced epileptiform activity in animal models may give rise to differences in the results and interpretation thereof. Indeed, the range of 4AP concentration in both in vivo and in vitro studies varies from 3μM to 40mM. Here, we explored the effects of various 4AP concentrations on the development and characteristics of hippocampal epileptiform activity in acute mouse brain slices of either sex. Using multielectrode array recordings, we show that 4AP induces hippocampal epileptiform activity for broad range of concentrations. The frequency component and the spatio-temporal patterns of the epileptiform activity revealed a dose-dependent response. Finally, in the presence of 4AP, reduction of KCC2 co-transporter activity by KCC2 antagonist VU0240551 prevented the manifestation of the frequency component differences between different concentrations of 4AP. Overall, the study predicts that different concentrations of 4AP can result in the different mechanisms behind hippocampal epileptiform activity, of which some are dependent on the KCC2 co-transporter function.
Guiding Vaccine Efficacy Trial Design During Public Health Emergencies: An interactive web-based decision support tool
Authors: Bellan Steven E. , Eggo Rosalind M , Gsell Pierre-Stéphane , Kucharski Adam J , Dean Natalie E , Donohue Richard , Zook Matt , Odhiambo Frank , Longini Ira , Brisson Marc , Mahon Barbara E , Henao-Restrepo Ana Maria
Published: January 2018

The design and execution of rigorous, fast, and ethical vaccine efficacy trials can be challenging during epidemics of emerging pathogens, such as the 2014-2016 Ebola virus and 2015-2016 Zika virus epidemics. Response to an urgent public health crisis requires accelerated research even as emerging epidemics themselves change rapidly and are inherently less well understood than well-established diseases. As part of the World Health Organization Research and Development Blueprint, we designed a web-based interactive decision support system (InterVax-Tool) to help diverse stakeholders navigate the epidemiological, logistical, and ethical decisions involved in designing a vaccine efficacy trial during a public health emergency. In contrast to existing literature on trial design, InterVax-Tool offers high-level visual and interactive assistance through a set of four decision trees, guiding users through selection of 1) the Primary Endpoint, (2) the Target Population, (3) Randomization, and (4) the Comparator. Guidance is provided on how each of fourteen key considerations–grouped as Epidemiological, Vaccine-related, Infrastructural, or Sociocultural–should be used to inform each decision in the trial design process. The tool is not intended to provide a black box decision framework for identifying an optimal trial design, but rather to facilitate transparent, collaborative and comprehensive discussion of the relevant decisions, while recording the decision process. The tool can also assist capacity building by providing a cross-disciplinary picture of trial design using concepts from epidemiology, study design, vaccinology, biostatistics, mathematical modeling and clinical research ethics. Here, we describe the goals and features of InterVax-Tool as well as its application to the design of a Zika vaccine efficacy trial.

One Sentence Summary

An interactive web-based decision support tool was developed to assist in the design of vaccine efficacy trials during emerging outbreaks.
Unsupervised clustering of temporal patterns in high-dimensional neuronal ensembles using a novel dissimilarity measure
Authors: Grossberger Lukas , Battaglia Francesco P. , Vinck Martin
Published: January 2018

Temporally ordered multi-neuron patterns likely encode information in the brain. We introduce an unsupervised method, SPOTDisClust (Spike Pattern Optimal Transport Dissimilarity Clustering), for their detection from high-dimensional neural ensembles. SPOTDisClust measures similarity between two ensemble spike patterns by determining the minimum transport cost of transforming their corresponding normalized cross-correlation matrices into each other (SPOTDis). Then, it performs density-based clustering based on the resulting inter-pattern dissimilarity matrix. SPOTDisClust does not require binning and can detect complex patterns (beyond sequential activation) even when high levels of out-of-pattern “noise” spiking are present. Our method handles efficiently the additional information from increasingly large neuronal ensembles and can detect a number of patterns that far exceeds the number of recorded neurons. In an application to neural ensemble data from macaque monkey V1 cortex, SPOTDisClust can identify different moving stimulus directions on the sole basis of temporal spiking patterns.

Author summary

The brain encodes information by ensembles of neurons, and recent technological developments allow researchers to simultaneously record from over thousands of neurons. Neurons exhibit spontaneous activity patterns, which are constrained by experience and development, limiting the portion of state space that is effectively visited. Patterns of spontaneous activity may contribute to shaping the synaptic connectivity matrix and contribute to memory consolidation, and synaptic plasticity formation depends crucially on the temporal spiking order among neurons. Hence, the unsupervised detection of spike sequences is a sine qua non for understanding how spontaneous activity contributes to memory formation. Yet, sequence detection presents major methodological challenges like the sparsity and stochasticity of neuronal output, and its high dimensionality. We propose a dissimilarity measure between neuronal patterns based on optimal transport theory, determining their similarity from the pairwise cross-correlation matrix, which can be taken as a proxy of the “trace” that is left on the synaptic matrix. We then perform unsupervised clustering and visualization of patterns using density clustering on the dissimilarity matrix and low-dimensional embedding techniques. This method does not require binning of spike times, is robust to noise, jitter and rate fluctuations, and can detect more patterns than the number of neurons.
The Folding Pathway of an Ig Domain is Conserved On and Off the Ribosome
Authors: Tian Pengfei , Steward Annette , Kudva Renuka , Su Ting , Shilling Patrick J. , Nickson Adrian A. , Hollins Jeffrey J. , Beckmann Roland , Heijne Gunnar von , Clarke Jane , Best Robert B.
Published: January 2018

Proteins that fold cotranslationally may do so in a restricted configurational space, due to the volume occupied by the ribosome. How does this environment, coupled with the close proximity of the ribosome, affect the folding pathway of a protein? Previous studies have shown that the cotranslational folding process for many proteins, including small, single domains, is directly affected by the ribosome. Here, we investigate the cotranslational folding of an all-b immunoglobulin domain, titin I27. Using an arrest peptide-based assay and structural studies by cryo-EM, we show that I27 folds in the mouth of the ribosome exit tunnel. Simulations that use a kinetic model for the force-dependence of escape from arrest, accurately predict the fraction of folded protein as a function of length. We used these simulations to probe the folding pathway on and off the ribosome. Our simulations - which also reproduce experiments on mutant forms of I27 - show that I27 folds, while still sequestered in the mouth of the ribosome exit tunnel, by essentially the same pathway as free I27, with only subtle shifts of critical contacts from the C to the N terminus.

Significance Statement

Most proteins need to fold into a specific three-dimensional structure in order to function. The mechanism by which isolated proteins fold has been thoroughly studied by experiment and theory. However, in the cell proteins do not fold in isolation, but are synthesized as linear chains by the ribosome during translation. It is therefore natural to ask at which point during synthesis proteins fold, and whether this differs from the folding of isolated protein molecules. By studying folding of a well characterized protein domain, titin I27, stalled at different points during translation, we show that it already folds in the mouth of the ribosome exit tunnel, and that the mechanism is almost identical to that of the isolated protein.
Natural variation in stomata size contributes to the local adaptation of water-use efficiency in Arabidopsis thaliana
Authors: Dittberner H. , Korte A. , Mettler-Altmann T. , Weber A.P.M. , Monroe G. , de Meaux J.
Published: January 2018

Stomata control gas exchanges between the plant and the atmosphere. How natural variation in stomata size and density contributes to resolve trade-offs between carbon uptake and water-loss in response to local climatic variation is not yet understood. We developed an automated confocal microscopy approach to characterize natural genetic variation in stomatal patterning in 330 fully-sequenced Arabidopsis thaliana accessions collected throughout the European range of the species. We compared this to variation in water-use efficiency, measured as carbon isotope discrimination (δ13C). We detect substantial genetic variation for stomata size and density segregating within Arabidopsis thaliana. A positive correlation between stomata size and δ13C further suggests that this variation has consequences on water-use efficiency. Genome-wide association analyses indicate a complex genetic architecture underlying not only variation in stomata patterning but also to its co-variation with carbon uptake parameters. Yet, we report two novel QTL affecting δ13C independently of stomata patterning. This suggests that, in A. thaliana, both morphological and physiological variants contribute to genetic variance in water-use efficiency. Patterns of regional differentiation and co-variation with climatic parameters indicate that natural selection has contributed to shape some of this variation, especially in Southern Sweden, where water availability is more limited in spring relative to summer. These conditions are expected to favor the evolution of drought avoidance mechanisms over drought escape strategies.
Chromosome evolution at the origin of the ancestral vertebrate genome
Authors: Sacerdot Christine , Louis Alexandra , Bon Céline , Roest Crollius Hugues
Published: January 2018

About 450 million years ago, a marine chordate was subject to two successive whole genome duplications (WGDs) before becoming the common ancestor of vertebrates and diversifying into the more than 60,000 species found today. Here, we reconstruct in details the evolution of chromosomes of this early vertebrate along successive steps of the two WGD. We first compared 61 extant animal genomes to build a highly contiguous order of genes in a 326 million years old ancestral Amniota genome. In this genome, we established a well-supported list of duplicated genes originating from the WGDs to link chromosomes in tetrads, a telltale signature of these events. This enabled us to reconstruct a scenario where a pre-vertebrate genome composed of 17 chromosomes duplicated into 34 chromosomes, and was subject to 7 chromosome fusions before duplicating again into 54 chromosomes. After the separation of Agnatha (jawless fish) and Gnathostomata, four more fusions took place to form the ancestral Euteleostomi genome of 50 chromosomes. These results firmly establish the occurrence of the two WGD, resolving in particular the ambiguity raised by the analysis of the lamprey genetic map. In addition, we provide insight into the origin of homologous micro-chromosomes found in the chicken and the gar genomes. This work provides a foundation for studying the evolution of vertebrate chromosomes from the standpoint of a common ancestor, and particularly the pattern of duplicate gene retention and loss that resulted in the gene composition of extant genomes.
Analysis of heat-induced protein aggregation in human mitochondria
Authors: Wilkening Anne , Rüb Cornelia , Sylvester Marc , Voos Wolfgang
Published: January 2018

As proteins in mammalian cells exhibit optimal stability at natural temperatures, small temperature variations may cause unfolding and subsequent non-specific aggregation. As this process leads to a loss of function of the affected polypeptides as well as to further cytotoxic stress, aggregate formation has been recognized as a major pathogenic factor in human diseases. In this study we determined the impact of physiological heat stress on mammalian mitochondria on a proteomic level. The overall solubility of endogenous mitochondrial proteins was only marginally affected by a treatment at elevated temperatures. However, we identified a small subset of polypeptides that exhibited an exceptionally high sensitivity to heat stress. The mitochondrial translation elongation factor Tu (Tufm), a protein essential for organellar protein biosynthesis, was highly aggregation-prone and lost its solubility already under mild heat stress conditions. In parallel, mitochondrial translation as well as the import of cytosolic proteins was defective in heat stressed mitochondria. Both types of nascent polypeptides, derived from translation as well as from import exhibited a strong heat-induced aggregation tendency. We propose a model that a quick and specific inactivation of elongation factors may prevent an accumulation of misfolded nascent polypeptides and thereby attenuate proteotoxicity under stress.
Reliability of Whole-Exome Sequencing for Assessing Intratumor Genetic Heterogeneity
Authors: Shi Weiwei , Ng Charlotte K. Y. , Lim Raymond S. , Jiang Tingting , Kumar Sushant , Li Xiaotong , Wali Vikram B. , Piscuoglio Salvatore , Gerstein Mark B. , Chagpar Anees B. , Weigelt Britta , Pusztai Lajos , Reis-Filho Jorge S. , Hatzis Christos
Published: January 2018

Multi-region sequencing is used to detect intratumor genetic heterogeneity (ITGH) in tumors. To assess whether genuine ITGH can be distinguished from sequencing artifacts, we whole-exome sequenced (WES) three anatomically distinct regions of the same tumor with technical replicates to estimate technical noise. Somatic variants were detected with three different WES pipelines and subsequently validated by high-depth amplicon sequencing. The cancer-only pipeline was unreliable, with about 69% of the identified somatic variants being false positive. Even with matched normal DNA where 82% of the somatic variants were detected reliably, only 36%-78% were found consistently in technical replicate pairs. Overall 34%-80% of the discordant somatic variants, which could be interpreted as ITGH, were found to constitute technical noise. Excluding mutations affecting low mappability regions or occurring in certain mutational contexts was found to reduce artifacts, yet detection of subclonal mutations by WES in the absence of orthogonal validation remains unreliable.