bluuebunny/crossref_metadata_2025 huggingface dataset:
Letter: Ocean bathymetry reconstruction from surface data using hydraulics theory
Authors: Kar Subhajit , Guha Anirban
Published: December 2018

Here we propose a technique that successfully reconstructs ocean bathymetry from the free surface velocity and elevation data. This technique is based on the principles of open-channel hydraulics, according to which a sub-critical flow over a seamount creates a free surface dip. The proposed method recognizes that such a free surface dip contains the signature of the bottom topography, hence inverts the free surface to reconstruct the topography accurately. We applied our inversion technique on re-analysis data and reconstructed the Mediterranean Sea and the Red Sea bathymetries of 1/12° resolution with approximately 90% accuracy.
Eliminating the effect of acoustic noise on cantilever spring constant calibration
Authors: Mascaro Aaron , Miyahara Yoichi , Dagdeviren Omur E. , Grütter Peter
Published: December 2018

A common use of atomic force microscopy is quantifying local forces through tip-sample interactions between the probe tip and a sample surface. The accuracy of these measurements depends on the accuracy to which the cantilever spring constant is known. Recent work has demonstrated that the measured spring constant of a cantilever can vary up to a factor of five, even for the exact same cantilever measured by different users on different microscopes. Here, we demonstrate that a standard method for calibrating the spring constant (using oscillations due to thermal energy) is susceptible to ambient acoustic noise, which can alter the result significantly. We demonstrate a step-by-step method to measure the spring constant by actively driving the cantilever to measure the resonance frequency and the quality factor, giving results that are unaffected by acoustic noise. Our method can be performed rapidly on any atomic force microscope without any expensive additional hardware.
Alternative antibiotics from crop plants: effects of black pepper (
Piper nigrum
L.) in broiler nutrition.
Authors: Puvača N. , Ljubojević D. , Ðuragić O. , Popović S. , Könyves T. , Miščević B. , Prodanović R. , Bošković J.
Published: December 2018

Black pepper is considered the most attractive spice throughout the world, owing to its pungent alkaloid piperine, which biologically presents a very important spice in human and animal nutrition. Various experiments have shown that black pepper and its secondary metabolites could be used as an antiapoptotic, antibacterial, antidepressant, antifungal, antidiarrhoeal, anti-inflammatory, antioxidative and hepatoprotective. Black pepper can be used to treat stomach disturbances, bronchitis and cancer caused by the impact of germs. It can cause an increase in digestive juice flow in the stomach. Many experiments have shown an increase in body weight and better food conversion with the use of black pepper in broiler diets. This paper gives a review of the black pepper characteristics and its various effects and mode of action in broiler nutrition.
The connexin26 human mutation N14K disrupts cytosolic intersubunit interactions and promotes channel opening
Authors: Valdez Capuccino Juan M. , Chatterjee Payal , García Isaac E. , Botello-Smith Wesley M. , Zhang Han , Harris Andrew L. , Luo Yun , Contreras Jorge E.
Published: December 2018

A group of human mutations within the N-terminal (NT) domain of connexin 26 (Cx26) hemichannels produce aberrant channel activity, which gives rise to deafness and skin disorders, including keratitis-ichthyosis-deafness (KID) syndrome. Structural and functional studies indicate that the NT of connexin hemichannels is folded into the pore, where it plays important roles in permeability and gating. In this study, we explore the molecular basis by which N14K, an NT KID mutant, promotes gain of function. In macroscopic and single-channel recordings, we find that the N14K mutant favors the open conformation of hemichannels, shifts calcium and voltage sensitivity, and slows deactivation kinetics. Multiple copies of MD simulations of WT and N14K hemichannels, followed by the Kolmogorov–Smirnov significance test (KS test) of the distributions of interaction energies, reveal that the N14K mutation significantly disrupts pairwise interactions that occur in WT hemichannels between residue K15 of one subunit and residue E101 of the adjacent subunit (E101 being located at the transition between transmembrane segment 2 [TM2] and the cytoplasmic loop [CL]). Double mutant cycle analysis supports coupling between the NT and the TM2/CL transition in WT hemichannels, which is disrupted in N14K mutant hemichannels. KS tests of the α carbon correlation coefficients calculated over MD trajectories suggest that the effects of the N14K mutation are not confined to the K15–E101 pairs but extend to essentially all pairwise residue correlations between the NT and TM2/CL interface. Together, our data indicate that the N14K mutation increases hemichannel open probability by disrupting interactions between the NT and the TM2/CL region of the adjacent connexin subunit. This suggests that NT–TM2/CL interactions facilitate Cx26 hemichannel closure.
Between Berlin and Cambridge: classical conceptions of the general economic equilibrium in the late 1920s
Authors: Marchionatti Roberto
Published: December 2018

This paper deals with some contributions to the debate on General Economic Equilibrium between the two world wars. Originating in Cambridge and Berlin, they differed from the Viennese contributions of the Walrasian perspective traditionally considered by the literature. They can be defined to represent the classical approach to general equilibrium. The authors considered are the Italian-born economist Piero Sraffa, the German mathematician Robert Remak and the Russian-born economist Wassily Leontief. The paper focuses in particular on the intellectual origins of their contributions in the Russian-German theoretical debate of the period 1890–1910 involving classical economists, Marx and Walras: these connections emerge clearly in the contributions of the German-Russian Mathematical School between the end of the nineteenth and the beginning of the twentieth centuries.
Social Resources as Compensatory Cognitive Reserve? Interactions of Social Resources With Education in Predicting Late-Life Cognition
Authors: Windsor Tim D , Ghisletta Paolo , Gerstorf Denis
Published: December 2018

Objective

Access to social relationships has been linked with better cognitive performance. We examined whether social resources interact with education to predict cognitive outcomes, which could indicate that social resources fulfill a compensatory role in promoting cognitive reserve.

Method

We applied multilevel growth models to 6-wave, 13-year longitudinal data from the Berlin Aging Study (aged 70–103 years at first occasion; M = 84.9 years, 50% women) and have taken into account key individual difference factors, including sociodemographic variables, medically diagnosed comorbidities, and depressive symptoms. To account for possible reverse causality, analyses were conducted on a subset of the BASE participants without dementia (n = 368), and in follow-up analyses with the full sample (n = 516) using wave-specific longitudinal assessments of probable dementia status as a covariate.

Results

Larger networks were associated with better performance on tests of perceptual speed and verbal fluency, but did not interact with education, providing little support for a compensatory reserve hypothesis. An interaction of education with emotional loneliness emerged in the prediction of perceptual speed, suggesting that the educational divide in speed was minimal among people who reported lower levels of loneliness.

Discussion

We discuss our results in the context of differential implications of social resources for cognition and consider possible mechanisms underlying our findings.
Development of the Cochlear Implant Quality of Life Item Bank
Authors: McRackan Theodore R. , Hand Brittany N. , Velozo Craig A. , Dubno Judy R.
Published: December 2018

Objectives:

Functional outcomes following cochlear implantation have traditionally been focused on word and sentence recognition, which, although important, do not capture the varied communication and other experiences of adult cochlear implant (CI) users. Although the inadequacies of speech recognition to quantify CI user benefits are widely acknowledged, rarely have adult CI user outcomes been comprehensively assessed beyond these conventional measures. An important limitation in addressing this knowledge gap is that patient-reported outcome measures have not been developed and validated in adult CI patients using rigorous scientific methods. The purpose of the present study is to build on our previous work and create an item bank that can be used to develop new patient-reported outcome measures that assess CI quality of life (QOL) in the adult CI population.

Design:

An online questionnaire was made available to 500 adult CI users who represented the adult CI population and were recruited through a consortium of 20 CI centers in the United States. The questionnaire included the 101 question CIQOL item pool and additional questions related to demographics, hearing and CI history, and speech recognition scores. In accordance with the Patient-Reported Outcomes Measurement Information System, responses were psychometrically analyzed using confirmatory factor analysis and item response theory.

Results:

Of the 500 questionnaires sent, 371 (74.2%) subjects completed the questionnaire. Subjects represented the full range of age, durations of CI use, speech recognition abilities, and listening modalities of the adult CI population; subjects were implanted with each of the three CI manufacturers’ devices. The initial item pool consisted of the following domain constructs: communication, emotional, entertainment, environment, independence, listening effort, and social. Through psychometric analysis, after removing locally dependent and misfitting items, all of the domains were found to have sound psychometric properties, with the exception of the independence domain. This resulted in a final CIQOL item bank of 81 items in 6 domains with good psychometric properties.

Conclusions:

Our findings reveal that hypothesis-driven quantitative analyses result in a psychometrically sound CIQOL item bank, organized into unique domains comprised of independent items which measure the full ability range of the adult CI population. The final item bank will now be used to develop new instruments that evaluate and differentiate adult CIQOL across the patient ability spectrum.
The FDP-FDS-FDP Dual Tendon Transfer: A Simple, Single-stage Reconstruction Technique for Chronic, Isolated Flexor Digitorum Profundus Tendon Injuries
Authors: Morrell Nathan T.
Published: December 2018

The reconstruction of chronic flexor tendon injuries remains one of the more challenging injuries facing the hand and upper extremity surgeon. In the setting of an intact flexor digitorum superficialis (FDS), there are few indications for isolated flexor digitorum profundus (FDP) reconstruction. Because of the interplay of the FDP system, the reestablishment of normal tension of the FDP tendons and lumbricals is particularly challenging, and postoperative stiffness, quadriga, or lumbrical plus phenomena can actually lead to a deterioration of digital function with surgery. We present a technique for single-stage reconstruction of chronic FDP lacerations, particularly in the setting of “lumbrical plus” fingers. The key features of this technique are: the FDS is detached from the middle phalanx and advanced to the distal FDP stump; and the proximal stump of the FDP is advanced to reestablish proper lumbrical tension and sewn to the FDS tendon proximally. Postoperative therapy is according to standard, well-accepted flexor tendon rehabilitation protocols. This procedure avoids the need for tendon autograft harvest, and avoids the tensioning challenges of other FDP reconstruction techniques; it addresses the potential paradoxical extension with lumbrical tension by eliminating the retraction of the lumbrical and eliminates the potential for quadriga by separating FDP function from the adjacent digit. An illustrative case is presented.

Level of Evidence: Level V.
A Randomized, Split-Face, Evaluator-Blind Clinical Trial Comparing Monopolar Radiofrequency Versus Microfocused Ultrasound With Visualization for Lifting and Tightening of the Face and Upper Neck
Authors: Alhaddad Marwan , Wu Douglas C. , Bolton Joanna , Wilson Monique J. , Jones Isabela T. , Boen Monica , Goldman Mitchel P.
Published: December 2018

BACKGROUND

Over the past decade, 2 major modalities for noninvasive skin tightening have emerged: monopolar capacitive-coupled radiofrequency (MRF) and microfocused ultrasound with visualization (MFU-V). Up to date, no comparative clinical trials have been performed.

OBJECTIVE

To compare the efficacy and safety of MRF versus MFU-V for the lifting and tightening of the face and neck.

MATERIALS AND METHODS

Twenty subjects with mild to moderate skin laxity received MFU-V over one-side of the face and MRF over the other side of the face at the same time. Subjects were followed for 6 months.

RESULTS

Both MRF and MFU-V led to a decrease in the Fasil Face and Neck Laxity Grading Scale (FLR). These differences became significant at Day 30 and remained significantly improved through Days 90 and 180 in both groups. There was no statistically significant difference in the FLR Scale between MRF-treated and MFU-V–treated sides. Subjects' Global Aesthetic Improvement Scale showed improvement at Day 30, 90, and 180.

CONCLUSION

Both MRF and MFU-V led to significant improvement in face and neck laxity. There were no statistical differences between MRF and MFU-V in standardized investigator measures of face and neck laxity, patient satisfaction, and adverse events.
Specific Inhibition of Brain Angiotensin III Formation as a New Strategy for Prevention of Heart Failure After Myocardial Infarction
Authors: Leenen Frans H. H. , Ahmad Monir , Marc Yannick , Llorens-Cortes Catherine
Published: December 2018

Aims:

Inhibition of brain angiotensin III by central infusion of aminopeptidase A (APA) inhibitor firibastat (RB150) inhibits sympathetic hyperactivity and heart failure in rats after myocardial infarction (MI). This study evaluated effectiveness of systemic treatment with firibastat compared with AT1R blocker, losartan.

Methods and Results:

MI was induced by ligation of left coronary artery in male Wistar rats. Rats were treated from 1 to 5 weeks after MI in protocol 1 with vehicle, or firibastat at 50 mg/kg/d subcutaneously (s.c.) or 150 mg/kg/d oral, once daily, and in protocol 2, with vehicle, firibastat 150 mg/kg or losartan 50 mg/kg oral twice daily. At 5 weeks, left ventricle function was evaluated by echocardiography and Millar catheter. After MI, rats developed moderate severe heart failure. Both s.c. and oral firibastat inhibited brain APA and attenuated left ventricle dysfunction. Oral firibastat and losartan similarly improved left ventricular end diastolic pressure. However, whereas firibastat improved dP/dtmax, losartan lowered dP/dtmax and left ventricular peak systolic pressure, and increased plasma creatinine by ~50%. On the other hand, losartan more effectively inhibited cardiac fibrosis.

Conclusion:

Inhibition of the brain renin–angiotensin system by oral APA inhibitor is at least as effective as oral AT1R blocker to inhibit cardiac dysfunction after MI but without hypotension or renal dysfunction.
Feasibility of prehospital freeze-dried plasma administration in a UK Helicopter Emergency Medical Service
Authors: Oakeshott Joanna E. , Griggs Joanne E. , Wareham Gary M. , Lyon Richard M.
Published: December 2018

Background

Early transfusion of patients with major traumatic haemorrhage may improve survival. This study aims to establish the feasibility of freeze-dried plasma transfusion in a Helicopter Emergency Medical Service in the UK.

Patients and methods

A retrospective observational study of major trauma patients attended by Kent, Surrey and Sussex Helicopter Emergency Medical Service and transfused freeze-dried plasma since it was introduced in April 2014.

Results

Of the 1873 patients attended over a 12-month period before its introduction, 79 patients received packed red blood cells (4.2%) with a total of 193 units transfused. Of 1881 patients after the introduction of freeze-dried plasma, 10 patients received packed red blood cells only and 66 received both packed red blood cells and freeze-dried plasma, with a total of 158 units of packed red blood cells transfused, representing an 18% reduction between the two 12-month periods. In the 20 months since its introduction, of 216 patients transfused with at least one unit of freeze-dried plasma, 116 (54.0%) patients received both freeze-dried plasma and packed red blood cells in a 1: 1 ratio. Earlier transfusion was feasible, transferring the patient to the hospital before transfusion would have incurred a delay of 71 min (interquartile range: 59–90 min).

Conclusion

Prehospital freeze-dried plasma and packed red blood cell transfusion is feasible in a 1: 1 ratio in patients with suspected traumatic haemorrhage. The use of freeze-dried plasma as a first-line fluid bolus reduced the number of prehospital packed red blood cell units required and reduced the time to transfusion.
Proton beam therapy in pediatric oncology
Authors: Baliga Sujith , Yock Torunn I.
Published: December 2018

Purpose of review

The advent of proton beam therapy (PBT) has initiated a paradigm shift in the field of pediatric radiation oncology, with increasing promise to alleviate both short-term and long-term toxicities. Given the dramatic rise in proton therapy centers in the United States, a discussion of the quality of evidence supporting its use in pediatric cancers is warranted.

Recent findings

Proton radiotherapy appears to decrease the incidence and severity of late effects with the strongest evidence in pediatric brain tumor cohorts that shows benefits in neurocognitive, hearing, and endocrine outcomes. However, emerging data has shown that more conservative brainstem dose limits with protons compared with photons are required to limit brainstem toxicity; these modified recommendations have been incorporated into national cooperative group studies. Decreased toxicity in tumors outside of the CNS for PBT have also been reported in sarcomas, Hodgkin disease and neuroblastoma. Similarly, QoL outcomes are improved in brain tumor and other cohorts of patients treated with PBT.

The collective findings demonstrate improved understanding and refinement of PBT in pediatric cancers. Data on QOL, toxicity and disease outcomes with PBT should continue to be collected and reported in order to understand the full extent of the risks and benefits associated with PBT.
Potential Drug-drug Interactions at a Referral Pediatric Oncology Ward in Iran: A Cross-sectional Study
Authors: Tavousi Faezeh , Sadeghi Alireza , Darakhshandeh Ali , Moghaddas Azadeh
Published: December 2018

Incidence of drug-drug interactions (DDIs) has been widely reported; however, such reports in pediatric oncology patients still remain scarce. We studied frequency and demographic correlates of moderate and major DDIs at a pediatric oncology ward in Isfahan, Iran. All pediatric oncology patients admitted to the Omid hospital during a 6-month period (2017) who received at least 2 anticancer or non-anticancer drugs concomitantly were included in our study. Potential DDIs between anticancer and non-anticancer drugs during hospitalization was identified using Lexi-Interact on-line software. We detected 194 DDIs with moderate or major severity for our included 115 patients. Mechanistically, most of DDIs (56.4%) were pharmacodynamic. Systematic use of corticosteroids (82.0%), antimetabolites (77.0%), and antiemetic drugs (69.5%) were the most frequent medication classes responsible for detected DDIs. The interaction between aminoglycosides and the third generation cephalosporins was the most common (13.9%) non-anticancer DDI. The only identified interaction between 2 anticancer drugs was doxorubicin with cyclophosphamide. Age, sex, and the number of administered medications were associated with DDIs. Potential moderate or major DDIs occur frequently among pediatric cancer patients. More studies are needed to assess clinical and economic implications of DDIs in pediatric oncology patients.
Predicting Motor Sequence Learning in People With Parkinson Disease
Authors: Olivier Geneviève N. , Paul Serene S. , Lohse Keith R. , Walter Christopher S. , Schaefer Sydney Y. , Dibble Leland E.
Published: December 2018

Background and Purpose:

Skill acquisition (ie, performance changes during practice) occurs in a nonlinear fashion. Despite this, motor learning is typically measured by comparing discrete timepoints. Thus, typical measures of motor learning do not detect skill acquisition characteristics that may be clinically meaningful. Reliable prediction of motor skill learning in people with Parkinson disease (PD) would allow therapists to more effectively individualize practice doses to fit specific patients' needs. The purposes of this study were to (a) characterize postural skill acquisition in people with PD, and identify factors (such as acquisition rate and practice dose to plateau) that predict learning, and (b) investigate whether levodopa medication (l-dopa) status during practice impacted learning.

Methods:

Twenty-seven adults with PD practiced a postural motor task over 3 days, followed by 2 retention tests. Participants were randomized to practice either ON or OFF l-dopa. Data for repeating and random sequences were each analyzed using nonlinear curve-fitting and mixed-effects regressions. Learning was defined as pretest minus retention test performance.

Results:

Participants with less physical impairment demonstrated less learning on the repeating and random sequence tasks compared with participants with more impairment. Participants who improved faster during practice demonstrated less learning on the repeating sequence task compared with participants who improved more slowly. Reaching plateau during practice was not related to learning. l-dopa did not impair learning.

Discussion and Conclusions:

Participants' skill acquisition characteristics were related to learning a postural motor task. Patient-specific factors, such as the rate of skill acquisition, level of physical function, and medication status, may influence how postural motor practice is delivered during balance rehabilitation.

Video Abstract available for more insights from the authors (see the Video, Supplemental Digital Content 1, available at: http://links.lww.com/JNPT/A250).
Solving Congestion in the Plastic Surgery Match: A Game Theory Analysis
Authors: Molina Burbano Felipe , Yao Amy , Burish Nikki , Ingargiola Michael , Freeman Matthew , Stock Jeffrey , Taub Peter J.
Published: December 2018

Plastic and reconstructive surgery is among the most competitive specialties in the residency match. Applicants seeking to maximize their chances of a successful match often submit numerous applications to the National Residency Matching Program. It is not uncommon for those applying to plastic and reconstructive surgery to apply to every program. The high application volume imparts significant time and financial burden for applicants and programs alike. Furthermore, it makes distinguishing between applicants with a genuine interest in a specific program and those who are merely hoping to improve their chances vastly more difficult. The authors sought to characterize trends in the match rate, as the number of integrated plastic and reconstructive surgery programs continues to increase. Furthermore, they reviewed the literature on game theory for possible solutions to residency application congestion. The authors propose the use of the game theory model to explain the observed results and show why an application limit is the most reasonable approach to address this issue.
The Utility of Preoperative Arteriography for Free Flap Planning in Patients with Chronic Lower Extremity Wounds
Authors: Janhofer David E. , Lakhiani Chrisovalantis , Kim Paul J. , Akbari Cameron , Naz Iram , Tefera Eshetu A. , Attinger Christopher E. , Evans Karen Kim
Published: December 2018

Background:

In patients with lower extremity wounds, free tissue transfer is often the last option before amputation, making it crucial to optimize preoperative planning to prevent flap breakdown. No consensus exists regarding preoperative vascular workup before lower extremity free tissue transfer. In this study, the authors analyzed the utility of using arteriography for lower extremity free flap planning.

Methods:

A retrospective review was performed of 57 patients who underwent lower extremity arteriography and 59 free flap operations for lower extremity wounds between November of 2014 and August of 2017. Findings were used to guide flap recipient vessel selection. Arterial abnormality was addressed by means of endovascular intervention, where appropriate. Encountered abnormality was described and patient demographics, comorbidities, and outcomes were analyzed for correlation with abnormal angiographic studies.

Results:

Angiographic abnormalities were observed in 40 patients (67.8 percent), including 23 (57.5 percent) with stenosis/occlusion, 20 (50.0 percent) with atretic/nonvisualized vessels, and 11 (27.5 percent) requiring endovascular intervention. Stenosis/occlusion was detected in nine patients (15.3 percent) with no previously known arterial disease, leading to a new diagnosis of peripheral vascular disease. The flap survival rate was 98.3 percent, six patients (10.2 percent) ultimately progressed to amputation, and 53 patients (89.8 percent) were able to continue community ambulation at a mean follow-up time of 15.1 ± 9.51 months (range, 1.67 to 35.2 months). After arteriography, two patients (3.39 percent) suffered contrast-induced acute kidney injury. No other complications were noted.

Conclusion:

Preoperative lower extremity arteriography aids in the diagnosis of peripheral vascular disease, allows for timely endovascular intervention, and allows for optimal flap recipient vessel selection with a low complication rate.

CLINICAL QUESTION/LEVEL OF EVIDENC:

Diagnostic, IV.
An Embodied Neurocomputational Framework for Organically Integrating Biopsychosocial Processes: An Application to the Role of Social Support in Health and Disease
Authors: Smith Ryan , Weihs Karen L. , Alkozei Anna , Killgore William D.S. , Lane Richard D.
Published: December 2018

Objective

Two distinct perspectives—typically referred to as the biopsychosocial and biomedical models—currently guide clinical practice. Although the role of psychosocial factors in contributing to physical and mental health outcomes is widely recognized, the biomedical model remains dominant. This is due in part to (a) the largely nonmechanistic focus of biopsychosocial research and (b) the lack of specificity it currently offers in guiding clinicians to focus on social, psychological, and/or biological factors in individual cases. In this article, our objective is to provide an evidence-based and theoretically sophisticated mechanistic model capable of organically integrating biopsychosocial processes.

Methods

To construct this model, we provide a narrative review of recent advances in embodied cognition and predictive processing within computational neuroscience, which offer mechanisms for understanding individual differences in social perceptions, visceral responses, health-related behaviors, and their interactions. We also review current evidence for bidirectional influences between social support and health as a detailed illustration of the novel conceptual resources offered by our model.

Results

When integrated, these advances highlight multiple mechanistic causal pathways between psychosocial and biological variables.

Conclusions

By highlighting these pathways, the resulting model has important implications motivating a more psychologically sophisticated, person-specific approach to future research and clinical application in the biopsychosocial domain. It also highlights the potential for quantitative computational modeling and the design of novel interventions. Finally, it should aid in guiding future research in a manner capable of addressing the current criticisms/limitations of the biopsychosocial model and may therefore represent an important step in bridging the gap between it and the biomedical perspective.
Surgical Algorithmic Approach to Facilitate Primary Closure of the Anterolateral Thigh Flap Donor Site in Head and Neck Reconstruction
Authors: Hung Kuo-Shu , Chen Szu-Han , Chen Wei-Chen , Tseng Wan-Ling , Lee Yao-Chou
Published: December 2018

Background

Use of the anterolateral thigh (ALT) flap has gained popularity in head and neck reconstruction. However, donor sites that cannot achieve primary closure are reported to have poorer functional and aesthetic outcomes. Therefore, we propose an algorithm to facilitate primary closure of the donor site.

Methods

Since May 2013, when an attempt at donor site direct closure failed, we have used a VY advancement flap or a propeller flap for primary closure of the donor site, using the remnant lateral thigh perforator or nearby medial thigh perforator. Otherwise, a skin graft was used. A total of 91 patients were enrolled in this algorithmic approach. We retrospectively reviewed patients with head and neck cancer who underwent cancer ablation and immediate ALT flap reconstruction since August 2010. The patients were then categorized into a “before” group and an “after” group according to the application time of the algorithm. Their demographics, intraoperative findings, and postoperative outcomes were analyzed.

Results

A total of 321 patients (309 men, 12 women) were enrolled, with 230 patients in the before group and 91 patients in the after group, with a mean age of 52.9 years. The mean size of the flap was 130 cm2, with a mean width of 8.1 cm. No statistical difference existed between the groups. The donor site was directly closed in 82 patients (35.7%) in the before group. Using the perforator-based flap in 21 patients (23.1%), the donor site was closed primarily in 72 patients (79.1%) in the after group, contributing to a significantly higher donor site closure rate (P < 0.001). The average operative time was 348.7 minutes. The overall flap survival rate was 97.2%, donor-site complication rate was 6.9%, and hospitalization length was 23.5 days. None showed statistical differences between the groups.

Conclusions

The proposed algorithm may considerably increase the primary closure rate of the ALT flap donor site.
Reduced Awareness of Memory Deficit is Associated With Increased Medicare Home Health Care Use in Dementia
Authors: DeFeis Brittany , Chapman Silvia , Zhu Carolyn , Azar Martina , Sunderaraman Preeti , Ornstein Katherine , Gu Yian , Cosentino Stephanie
Published: December 2018

Objective:

The objective of this study was to examine whether reduced awareness of memory deficits in individuals with dementia is associated with more frequent need for Medicare home health care services.

Methods:

Cross-sectional analyses were conducted in a multicenter, clinic-based cohort. In total, 192 participants diagnosed with dementia and their informants were independently asked whether or not the participant demonstrated cognitive symptoms of dementia related to memory and word-finding. Participant self-awareness was measured as the discrepancy between participant and caregiver report of these symptoms. Annual Medicare home health benefit use data was obtained from Medicare claims matched by year to the Predictors study visit.

Results:

Participants that used home health services had lower awareness scores than those who did not. Awareness remained independently associated with home health use in a logistic regression adjusted for age, gender, education, caregiver relationship, global cognition, dementia subtype, and medical comorbidities.

Implications:

Reduced self-awareness of memory deficits in individuals with dementia is associated with more frequent use of Medicare home health services. The disproportionate use of in-home assistance as a function of awareness level may reflect dangers faced by patients, and challenges faced by caregivers, when patients have limited awareness of their memory deficits. Current results have implications for clinical care, caregiver education, and models of health care utilization.
The role of African buffalo in the epidemiology of foot-and-mouth disease in sympatric cattle and buffalo populations in Kenya
Authors: Omondi George , Gakuya Francis , Arzt Jonathan , Sangula Abraham , Hartwig Ethan , Pauszek Steven , Smoliga George , Brito Barbara , Perez Andres , Obanda Vincent , VanderWaal Kimberly
Published: December 2018

Transmission of pathogens at wildlife-livestock interfaces poses a substantial challenge to the control of infectious diseases, including for foot-and-mouth disease virus (FMDV) in African buffalo and cattle. The extent to which buffalo play a role in the epidemiology of this virus in livestock populations remains unresolved in East Africa. Here, we show that FMDV occurs at high seroprevalence (~77%) in Kenyan buffalo. In addition, we recovered 80 FMDV VP1 sequences from buffalo, all of which were serotype SAT1 and SAT2, and seventeen FMDV VP1 sequences from cattle, which included serotypes A, O, SAT1 and SAT2. Notably, six individual buffalo were co-infected with both SAT1 and SAT2 serotypes. Our results suggest that transmission of FMDV between sympatric cattle and buffalo is rare. However, viruses from FMDV outbreaks in cattle elsewhere in Kenya were caused by viruses closely related to SAT1 and SAT2 viruses found in buffalo. We also show that the circulation of FMDV in buffalo is influenced by fine-scale geographic features, such as rivers, and that social segregation amongst sympatric herds may limit between-herd transmission. Our results significantly advance knowledge of the ecology and molecular epidemiology of FMDV at wildlife-livestock interfaces in Eastern Africa, and will help to inform the design of control and surveillance strategies for this disease in the region.
Geographical Distributions and Spatial Equilibrium in Historical Epidemics of the United States
Authors: Coleman Stephen
Published: December 2018

This research examines the geographical distributions of several historical epidemics in the United States and investigates whether they reached a geographical equilibrium, however briefly. An equilibrium distribution over a geographical area, as the end state of a diffusion or spatial contagion process, has definitive mathematical properties. These permit qualitative and quantitative tests that may confirm an equilibrium and identify its characteristics. The analysis uses United States state-level data for several common infectious diseases of the 1950s, and results show geographical equilibrium distributions for several epidemics. These are not predicted by the most commonly used epidemiological models but are consistent with observed geographical disparities in disease prevalence that continued over a number of years in spite of recurrent epidemic cycles and long-term trends.
Spirometric indices in primary ciliary dyskinesia: systematic review and meta-analysis
Authors: Halbeisen Florian S. , Jose Anu , de Jong Carmen , Nyilas Sylvia , Latzin Philipp , Kuehni Claudia E. , Goutaki Myrofora
Published: December 2018

Primary ciliary dyskinesia (PCD) is a genetic, heterogeneous disease caused by dysfunction of cilia. Evidence is sparse and reports of lung function of PCD patients ranges from normal to severe impairment. This systematic review and meta-analysis of studies of lung function of PCD patients examines the spirometric indices of PCD patients and differences by age group and sex.

We searched PubMed, Embase, and Scopus for studies that described lung function in ≥10 patients with PCD. We performed meta-analyses and metaregression to explain heterogeneity. We included 24 studies, ranging from 13-158 patients per study. The most commonly reported spirometric indices were forced expiratory volume in 1 sec (FEV1) and forced vital capacity (FVC) presented as mean and standard deviation of percent of predicted values. We found considerable heterogeneity for both parameters (I2range 94-96%). The heterogeneity remained when we stratified the analysis by age; however, FEV1 in adult patients was lower. Even after taking into account explanatory factors, the largest part of the between-studies variance remained unexplained. Heterogeneity could be explained by genetic differences between study populations, methodological factors related to the variability of study inclusion criteria, or details on the performance and evaluation of lung function measurements that we could not account for. Prospective studies therefore need to use standardised protocols and international reference values. These results underline the possibility of distinct PCD phenotypes as in other chronic respiratory diseases. Detailed characterisation of these phenotypes and related genotypes is needed in order to better understand the natural history of PCD.
Comparing the functional structure of neural networks from representational similarity analysis with those from functional connectivity and univariate analyses
Authors: Pillet Ineke , de Beeck Hans Op , Masson Haemy Lee
Published: December 2018

The invention of representational similarity analysis (RSA, following multi-voxel pattern analysis (MVPA)) has allowed cognitive neuroscientists to identify the representational structure of multiple brain regions, moving beyond functional localization. By comparing these structures, cognitive neuroscientists can characterize how brain areas form functional networks. Univariate analysis (UNIVAR) and functional connectivity analysis (FCA) are two other popular methods to identify the functional structure of brain networks. Despite their popularity, few studies have examined the relationship between the structure of the networks from RSA with those from UNIVAR and FCA. Thus, the aim of the current study is to examine the similarities between neural networks derived from RSA with those from UNIVAR and FCA to explore how these methods relate to each other. We analyzed the data of a previously published study with the three methods and compared the results by performing (partial) correlation and multiple regression analysis. Our findings reveal that neural networks resulting from RSA, UNIVAR, and FCA methods are highly similar to each other even after ruling out the effect of anatomical proximity between the network nodes. Nevertheless, the neural network from each method shows idiosyncratic structure that cannot be explained by any of the other methods. Thus, we conclude that the RSA, UNIVAR and FCA methods provide similar but not identical information on how brain regions are organized in functional networks.
Surrogate R-spondins for tissue-specific potentiation of Wnt signaling
Authors: Luca Vincent C. , Miao Yi , Li Xingnan , Hollander Michael J. , Kuo Calvin J. , Garcia K. Christopher
Published: December 2018

Secreted R-spondin1-4 proteins (RSPO1-4) orchestrate stem cell renewal and tissue homeostasis by potentiating Wnt/β-catenin signaling. RSPOs induce the turnover of negative Wnt regulators RNF43 and ZNRF3 through a process that requires RSPO interactions with either Leucine-rich repeat containing G-protein coupled receptors (LGRs) or heparin sulfate proteoglycans (HSPGs). Here, we describe the engineering of ‘surrogate RSPOs’ that function independently of LGRs and HSPGs to enhance Wnt signaling on cell types expressing a target surface marker. These bispecific proteins were generated by fusing an RNF43- or ZNRF3-specific single chain antibody variable fragment (scFv) to the immune cytokine IL-2. Surrogate RSPOs mimic the function of natural RSPOs by crosslinking the extracellular domain (ECD) of RNF43 or ZNRF3 to the ECD of the IL-2 receptor CD25, which sequesters the complex and results in highly selective amplification of Wnt signaling on CD25+ cells. Furthermore, surrogate RSPOs were able substitute for wild type RSPO in a colon organoid growth assay when intestinal stem cells were transduced to express CD25. Our results provide proof-of-concept for a technology that may be adapted for use on a broad range of cell- or tissue-types and will open new avenues for the development of Wnt-based therapeutics for regenerative medicine.
Dark aerobic sulfide oxidation by anoxygenic phototrophs in anoxic waters
Authors: Berg Jasmine S. , Pjevac Petra , Sommer Tobias , Buckner Caroline R.T. , Philippi Miriam , Hach Philipp F. , Liebeke Manuel , Holtappels Moritz , Danza Francesco , Tonolla Mauro , Sengupta Anupam , Schubert Carsten J. , Milucka Jana , Kuypers Marcel M.M.
Published: December 2018

Anoxygenic phototrophic sulfide oxidation by green and purple sulfur bacteria (PSB) plays a key role in sulfide removal from anoxic shallow sediments and stratified waters. Although some PSB can also oxidize sulfide with nitrate and oxygen, little is known about the prevalence of this chemolithotrophic lifestyle in the environment. In this study, we investigated the role of these phototrophs in light-independent sulfide removal in the chemocline of Lake Cadagno. Our temporally resolved, high-resolution chemical profiles indicated that dark sulfide oxidation was coupled to high oxygen consumption rates of ~9 μM O2·h−1. Single-cell analyses of lake water incubated with13CO2in the dark revealed thatChr. okeniiwas to a large extent responsible for aerobic sulfide oxidation and it accounted for up to 40 % of total dark carbon fixation. The genome ofChr. okeniireconstructed from the Lake Cadagno metagenome confirms its capacity for microaerophilic growth and provides further insights into its metabolic capabilities. Moreover, our genomic and single-cell data indicated that other PSB grow microaerobically in these apparently anoxic waters. Altogether, our observations suggest that aerobic respiration may not only play an underappreciated role in anoxic environments, but also that organisms typically considered strict anaerobes may be involved.

ORIGINALITY-SIGNIFICANCE STATEMENT

This study reveals that dark aerobic sulfide oxidation within an anoxic layer dominated by anoxygenic phototrophic bacteria in the stratified water column of Lake Cadagno is to a large extent carried out by the anoxygenic phototrophic bacteriumChromatium okenii. Our findings imply that aerobic metabolisms may be more prevalent in anoxic zones than previously thought. We also present an environmental metagenome-assembled genome ofChr. okeniiwhich is the first genome sequence for the genusChromatiumand reveals new interesting physiological features of this environmentally relevant organism, including its capacity for aerobic respiration.
Podoplanin interaction with caveolin-1 promotes tumour cell migration and invasion
Authors: Pedro Luisa , Shields Jacqueline D.
Published: December 2018

Podoplanin, a highly O-glycosylated type-1 transmembrane glycoprotein, found in lymphatic endothelial cells, podocytes, alveolar epithelial cells and lymph node fibroblasts is also expressed by tumour cells, and is correlated with more aggressive disease. Despite numerous studies documenting podoplanin expression, the mechanisms underlying its tumour-promoting functions remain unclear. Using a murine melanoma cell line that endogenously expresses podoplanin, we demonstrate interactions with proteins necessary for cytoskeleton reorganization, adhesion and matrix degradation, and endocytosis/receptor recycling but also identify a novel interaction with caveolin-1. We generated a panel of podoplanin and caveolin-1 variants to determine the molecular interactions and functional consequences of these interactions. Complementaryin vitroandin vivosystems confirmed the existence of a functional cooperation in which surface expression of both full length, signalling competent podoplanin and caveolin-1 are necessary to induce directional migration and invasion, which is executed via PAK1 and ERK1 pathways. Our findings establish that podoplanin signalling mediates the invasive properties of melanoma cells in a caveolin-1 dependent manner.

Summary Statement

This manuscript describes a new interaction and functional cooperation between podoplanin and caveolin1 that drives tumour cell invasion into surrounding tissues.
Galaxy-Kubernetes integration: scaling bioinformatics workflows in the cloud
Authors: Moreno Pablo , Pireddu Luca , Roger Pierrick , Goonasekera Nuwan , Afgan Enis , van den Beek Marius , He Sijin , Larsson Anders , Schober Daniel , Ruttkies Christoph , Johnson David , Rocca-Serra Philippe , Weber Ralf JM , Gruening Björn , Salek Reza M , Kale Namrata , Perez-Riverol Yasset , Papatheodorou Irene , Spjuth Ola , Neumann Steffen
Published: December 2018

Making reproducible, auditable and scalable data-processing analysis workflows is an important challenge in the field of bioinformatics. Recently, software containers and cloud computing introduced a novel solution to address these challenges. They simplify software installation, management and reproducibility by packaging tools and their dependencies. In this work we implemented a cloud provider agnostic and scalable container orchestration setup for the popular Galaxy workflow environment. This solution enables Galaxy to run on and offload jobs to most cloud providers (e.g. Amazon Web Services, Google Cloud or OpenStack, among others) through the Kubernetes container orchestrator.

Availability

All code has been contributed to the Galaxy Project and is available (since Galaxy 17.05) at https://github.com/galaxyproject/ in the galaxy and galaxy-kubernetes repositories. https://public.phenomenal-h2020.eu/ is an example deployment.

Suppl. Information

Supplementary Files are available online.

Contact

pmoreno@ebi.ac.uk, European Molecular Biology Laboratory, EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, Tel: +44-1223-494267, Fax: +44-1223-484696.
Parent and offspring genotypes influence gene expression in early life
Authors: Newhouse Daniel J. , Barcelo-Serra Margarida , Tuttle Elaina M. , Gonser Rusty A. , Balakrishnan Christopher N.
Published: December 2018

Parents can have profound effects on offspring fitness. Little, however, is known about the mechanisms through which parental care variation influences offspring physiology in natural systems. White-throated sparrows Zonotrichia albicollis (WTSPs) exist in two genetic morphs, tan and white, controlled by a large polymorphic supergene. Morphs mate disassortatively, resulting in two pair types: tan male x white female (TxW) pairs, which provide biparental care and white male x tan female (WxT) pairs, which provide female-biased care. To investigate the effects of parental care variation, we performed RNA-seq on WTSP nestlings sampled from nests of both pair types. Pair type had the largest effect on nestling gene expression, with 881 genes differentially expressed (DE) and seven correlated gene co-expression modules. The DE genes and modules up-regulated in nests with female-biased parental care primarily function in metabolism and stress-related pathways resulting from the overrepresentation of stress response and proteolysis genes. These results show that parental genotypes, a proxy for parental care in this system, alter nestling physiology and highlight avenues of further research investigating the ultimate implications of alternative parental care strategies. Nestlings also exhibited morph-specific gene expression, driven by innate immunity genes and co-expression of genes located in the supergene. Remarkably, we identified the same regulatory hub genes in these blood-derived expression networks as were previously identified in WTSP brains (EPM2A, BPNT1, TAF5L). These hub genes were located within the supergene, highlighting the importance of this gene complex in structuring regulatory networks across diverse tissues.