bluuebunny/crossref_metadata_2025 huggingface dataset:
Immediate extubation after heart transplantation in a child by remifentanil-based ultra-fast anesthesia
Authors: Yao Yong-Xing , Wu Jia-Teng , Zhu Wei-Liu , Zhu Sheng-Mei
Published: January 2019

Rationale:

Ventilator-associated complications comprise important fatal aetiologies during heart transplantation. Ultra-fast anesthesia might provide the most effective measure to prevent this type of complication. Immediate extubation after heart transplantation (IEAHT) has recently been reported in adult patients. However, IEAHT in children is much more challenging due to limitations in anesthesia protocols. Recently, we managed to perform an ultra-fast anesthesia protocol combined with IEAHT during a heart transplant operation in a child, who had an excellent postoperative outcome.

Patient concerns:

A 13-year-old girl had been diagnosed with dilated cardiomyopathy 5 years before this case, due to intractable dyspnoea and cough. She received multiple medical treatments after diagnosis, with minimal effects. Physical examination findings included a bulge in her left chest and pitting edema over both legs. Moist rales could be heard in the lung. Echocardiography revealed very large heart chambers, with an ejection fraction of 17%.

Diagnosis:

The patient was diagnosed with dilated cardiomyopathy and scheduled to undergo an emergent operation for heart transplantation.

Interventions:

The patient underwent an ultra-fast anesthesia protocol and ultra-fast reversal during heart transplantation. General anesthesia was induced with etomidate, fentanyl, and vecuronium; it was then maintained with remifentanil-based total intravenous anesthesia.

Outcomes:

Immediately after the end of the operation, the patient was brought to consciousness with stable breathing and haemodynamics. The patient was successfully extubated on the operating table and transferred to the intensive care unit with spontaneous breathing, without postoperative mechanical ventilation. The recovery period was uneventful and the patient was discharged 1 month later without complications.

Lessons:

Our experience, in this case, revealed that IEAHT in children is achievable if the ultra-fast protocol is performed properly and carefully, in order to prevent ventilator-associated complications.
Are newer insulins always the better option?
Authors: Malkani Samir
Published: January 2019

Purpose of review

Since its discovery almost a century ago, there have been numerous advancements in the formulations of insulin. The newer insulin analogs have structural modifications with the goal of altering pharmacokinetics to achieve either quick onset and offset of action (mealtime bolus analogs), or a prolonged steady action (basal analogs). These analogs offer many advantages over older human insulins but are several-fold more expensive. The aim of this review is to evaluate reasons for the exorbitant price of the newer insulins, to examine the evidence regarding their clinical advantages and to make value-based prescribing recommendations.

Recent findings

The higher cost of newer insulins cannot be justified based on drug development or manufacturing costs. Compared with older insulins, newer analogs do not offer significant advantage in achieving hemoglobin A1c targets, but they reduce risk of hypoglycemia. The reductions in hypoglycemia are relatively modest and most apparent in those with type 1 diabetes, possibly because these individuals are more prone to hypoglycemia.

When cost considerations are important, the older insulins (regular and NPH insulin) can be used safely and effectively for most individuals with type 2 diabetes who have a low risk of hypoglycemia.
Why are hypomethylating agents or low-dose cytarabine and venetoclax so effective?
Authors: Pollyea Daniel A. , Jordan Craig T.
Published: January 2019

Purpose of review

Venetoclax with backbone therapies have shown promising efficacy for newly diagnosed, previously untreated, older, unfit acute myeloid leukemia patients. This review discusses this data and potential reasons for the efficacy of these venetoclax-based combinations.

Recent findings

Venetoclax with hypomethylators and low-dose cytarabine have resulted in high response rates, promising response durations, and significant overall survival in relatively small, uncontrolled studies. There is emerging data that these responses are due to the effective targeting of leukemia stem cells through an alteration of the metabolic environment that is poorly tolerated by this population.

Venetoclax with a backbone therapy in older, untreated patients with acute myeloid leukemia has shown promising efficacy in preliminary clinical trials, and at least partially works through a novel mechanism that can target the leukemia stem cell population. Future investigations will help elucidate the mechanism and the contributions being made by each agent in the regimen.
Diagnostic Performance of Apparent Diffusion Coefficient for Prediction of Grading of Pancreatic Neuroendocrine Tumors
Authors: Zong Rui Long , Geng Li , Wang Xiaohong , Xie Daohai
Published: January 2019

Objectives

The aim of this study was to evaluate the diagnostic value of apparent diffusion coefficient (ADC) for the World Health Organization grade of pancreatic neuroendocrine tumors (pNETs).

Methods

The MEDLINE, Google Scholar, PubMed, and Embase databases were searched to identify relevant original articles investigating the ADC value in predicting the grade of pNETs. The pooled sensitivity (SE), specificity (SP), positive likelihood ratio (PLR), and negative likelihood ratio (NLR) were calculated by using random effects models. Subgroup analysis was performed to discover heterogeneity effects.

Results

Nine studies with 386 patients met our inclusion criteria. For identifying G1 from G2/3, the pooled SE, SP, PLR, NLR, and area under the curve of the summary receiver operating characteristic curve were 0.84 (95% confidence interval [95% CI], 0.73–0.91), 0.87 (95% CI, 0.72–0.94), 6.3 (95% CI, 2.7–14.6), 0.19 (95% CI, 0.10–0.34), and 0.91 (95% CI, 0.89–0.94), respectively. The summary estimates for ADC in distinguishing G3 from G1/2 were as follows: SE, 0.93 (95% CI, 0.66–0.99); SP, 0.92 (95% CI, 0.86–0.95); PLR, 11.1 (95% CI, 6.6–18.6); NLR, 0.08 (95% CI, 0.01–0.45); and area under the curve, 0.92 (95% CI, 0.85–0.96).

Conclusions

Diffusion-weighted imaging is a reliable tool for predicting the grade of pNETs, especially for G3. Moreover, the combination of 3.0-T device and higher b value can slightly help improve SE and SP.
Comparative Study Between Gemcitabine-Based and Gemcitabine Plus S1–Based Preoperative Chemoradiotherapy for Localized Pancreatic Ductal Adenocarcinoma, With Special Attention to Initially Locally Advanced Unresectable Tumor
Authors: Takeuchi Taijiro , Mizuno Shugo , Murata Yasuhiro , Hayasaki Aoi , Kishiwada Masashi , Fujii Takehiro , Iizawa Yusuke , Kato Hiroyuki , Tanemura Akihiro , Kuriyama Naohisa , Azumi Yoshinori , Usui Masanobu , Sakurai Hiroyuki , Isaji Shuji
Published: January 2019

Objectives

To evaluate clinical/histological response and prognosis between preoperative gemcitabine-based chemoradiation therapy (G-CRT) and gemcitabine plus S1–based CRT (GS-CRT) for localized pancreatic ductal adenocarcinoma patients according to the 3 resectability groups.

Methods

Among 199 patients who had 90% or more relative dose intensity of chemotherapy and completion of radiotherapy preoperatively (G-CRT: 98 and GS-CRT: 101), the subjects were 113 patients (G-CRT: 60 and GS-CRT: 53) who underwent curative-intent resection, and we compared clinical and histological effects between the 2 regimens.

Results

There is a significant improvement in clinical and histological responses as assessed by reduction rate in tumor size, post-CRT serum level of carbohydrate antigen 19-9, and the ratio of histological high responder according to the Evans grading system in GS-CRT, as compared with G-CRT, which in turn significantly increased R0 resection rate (P = 0.013). These effects of GS-CRT resulted in significant improvement of disease-specific survival (median survival time, 36.0 vs 27.2 months; P = 0.042), especially in patients with unresectable locally advanced disease (36.0 vs 18.1 months, P = 0.014).

Conclusions

For localized pancreatic ductal adenocarcinoma patients, GS-CRT, as compared with G-CRT, provides significant improvement in clinical and histological response as well as long-time survival, especially in patients with unresectable locally advanced disease.
Cellular Immunotherapy for Multiple Myeloma
Authors: Rosenblatt Jacalyn , Avigan David
Published: January 2019

Cellular immunotherapy for myeloma has the unique potential both to potently kill the malignant clone and to evoke a memory response to protect from relapse. Understanding the complex interactions between the malignant clone and the microenvironment that promote immune escape is critical to evoke effective antimyeloma immunity. Tremendous progress has been made in the area of cancer vaccines and adoptive T-cell therapy in recent years. Careful study of the mechanisms of response and of immune escape will be critical to developing novel combination therapies and ultimately to improve outcomes for patients with myeloma.
Patient-Reported Outcome Measures for Toe-to-Hand Transfer: A Prospective Longitudinal Study
Authors: Tsai Tzong-Yun , Fries C. Anton , Hsiao Jo-Chun , Hsu Chung-Chen , Lin Yu-Te , Chen Shih-Heng , Lin Chih-Hung , Wei Fu-Chan , Lin Cheng-Hung
Published: January 2019

Background:

Patient-reported outcome measures are an important metric in evaluating treatment efficacy of reconstructive surgery. Toe-to-hand transfer can restore vital prehensile function; however, this surgery is complex, extensive rehabilitation is required, and there are concerns about donor-site morbidity. This study longitudinally explores the benefits of this procedure, from the patient’s perspective, using patient-reported outcome measures.

Methods:

Twenty-three patients who underwent free toe-to-hand transfers from 2012 to 2015 were evaluated preoperatively and postoperatively using the following validated questionnaires: the Michigan Hand Outcomes Questionnaire, the 36-Item Short-Form Health Survey, and the Lower Limb Outcomes Questionnaire. Subgroup analysis was performed between dominant and nondominant reconstructed hands.

Results:

Mechanism of injury was crush in 83 percent; the remainder sustained cutting, avulsion, and burn injuries. Thirty-four toes were transferred: nine great toes, 20 second toes, and five third toes. Michigan Hand Outcomes Questionnaire results showed significant improvement in overall activities of daily living, work, aesthetics, and patient satisfaction (p < 0.05). The results of the 36-Item Short-Form Health Survey showed significant improvements in physical and emotional roles (p < 0.05). The Lower Limb Outcomes Questionnaire showed no deterioration of foot function (p = 0.55). Subgroup analysis showed significant improvement in patient-reported outcome measures for patients undergoing dominant hand reconstruction but no difference between thumb reconstruction and finger-only reconstruction.

Conclusions:

Patient-reported outcome measures demonstrate the significant utility of toe-to-hand transfer procedures in both functional and psychosocial domains in that there are relatively greater benefits in reconstructing the dominant hand, and that donor-site morbidity is well tolerated.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Aspiration pneumonia and pneumonitis: a spectrum of infectious/noninfectious diseases affecting the lung
Authors: Neill Sarah , Dean Nathan
Published: January 2019

Purpose of review

Our purpose is to describe aspiration pneumonia/pneumonitis as a spectrum of infectious/noninfectious diseases affecting the lung. We summarize diagnosis, risk factors, treatment, and strategies for prevention of aspiration.

Recent findings

Aspiration is present in normal individuals, and disease manifestation depends on the chemical characteristics, frequency, and volume of inoculum. Anaerobes, though present, are no longer the predominant microbes isolated in aspiration pneumonia. Targets for preventing aspiration including improved oral hygiene and positional feeding have had mixed results. Patients diagnosed by clinicians with aspiration pneumonia experience greater morbidity and mortality than patients with community-acquired pneumonia.

Aspiration pneumonia and pneumonitis are part of the pneumonia continuum and share similarities in pathophysiology, microbiology, and treatment. Modern microbiology demonstrates that the lung is not sterile, and isolates in aspiration pneumonia frequently include aerobes or mixed cultures. Treatment for aspiration pneumonia should include antibiotic coverage for oral anaerobes, aerobes associated with community-acquired pneumonia, and resistant organisms depending on appropriate clinical context. Additional studies targeting prevention of aspiration and investigating the increased morbidity and mortality associated with aspiration pneumonia are warranted.
Why have trials of inhaled antibiotics for ventilator-associated infections failed?
Authors: Palmer Lucy B.
Published: January 2019

Purpose of review

Two recent large randomized placebo-controlled clinical trials of adjunctive inhaled therapy for the treatment of ventilator-associated pneumonia failed to show a mortality effect or more rapid resolution of pneumonia symptoms. Does the failure of these studies to reach their endpoints suggest the end of inhaled therapy? This review will explain why inhaled therapy may still have an important role in the treatment of ventilated patients.

Recent findings

The recent interest in inhaled antimicrobial therapy is driven by the global emergence of increasingly resistant bacteria to systemic therapy. As fast as the pharmaceutical pipeline delivers more powerful systemic antibiotics to the ICU, the bacteria evolve and develop resistance to them. The hypothesis of recent trials has been that adjunctive inhaled therapy will make systemic treatment more effective. This review summarizes the available data from the two recent multisite randomized Phase 2 and Phase 3 trials of inhaled antimicrobials as adjunctive therapy and suggests why they failed to achieve their endpoints. When given properly, these drugs can provide high concentrations of drug in the lung that could not be achieved with intravenous antibiotics without significant systemic toxicity. The results of these trials and the data from many other smaller trials are compelling us to re-examine the indications for inhaled therapy as well as what clinical outcomes are most important.

This review summarizes current evidence describing the use of inhaled antibiotics for the treatment of bacterial ventilator-associated infections. Future investigations need to reevaluate the design and the outcomes that are most important in this era of multidrug-resistant bacteria.
Recovery of Severe Aphasia After Cranioplasty: Considerations on a Case Study
Authors: Corallo Francesco , De Cola Maria Cristina , Lo Buono Viviana , Cammaroto Simona , Marra Angela , Manuli Alfredo , Calabrò Rocco Salvatore
Published: January 2019

Cranioplasty is the main surgical intervention for repairing cranial defects performed in about 80% of the patients following cancer surgery or decompressive craniectomy. Although some works have shown recovery of motor and cognitive function, including memory, attention, and executive functions, until today no studies have focused on language recovery after cranioplasty. A 68-year-old woman came to the Neurorehabilitation Unit of the IRCCS Neurolesi (Messina, Italy) because of a fluent aphasia due to a severe left nucleocapsular hemorrhage and greatly improved her motor and neuropsychological status after cranioplasty. Results confirmed that cranioplasty might significantly improve motor and neuropsychological function, besides aphasia. Healthcare professionals involved in rehabilitation should be aware of the potential role of cranioplasty in improving rehabilitative outcomes to better plan a more personalized rehabilitative program. Moreover, rehabilitation nurses can play a pivotal role within the rehabilitation process, as they are educated to interact and communicate with the patient suffering from aphasia.
A Multimetric Evaluation of Online Spanish Health Resources for Lymphedema
Authors: Johnson Anna Rose , Doval Andres F. , Egeler Sabine A. , Lin Samuel J. , Lee Bernard T. , Singhal Dhruv
Published: January 2019

Background

Breast cancer is a leading cause of death in US Hispanic females. This demographic is more likely to present with later-stage disease and require more extensive surgical treatment, including axillary lymph node dissection, which increases risk of lymphedema. The Spanish-speaking Hispanic population has a lower health literacy level and requires materials contoured to their unique needs. The aim of this study was to evaluate online Spanish lymphedema resources.

Methods

A web search using the Spanish term “linfedema” was performed, and the top 10 websites were identified. Each was analyzed using validated metrics to assess readability, understandability, actionability, and cultural sensitivity using the SOL (Simplified Measure of Gobbledygook, Spanish), Patient Education and Materials Assessment for Understandability and Actionability (Patient Education and Assessment Tool), and Cultural Sensitivity and Assessment Tool (CSAT), respectively. Online materials were assessed by 2 independent evaluators, and interrater reliability was determined.

Results

Online lymphedema material in Spanish had a mean reading grade level of 9.8 (SOL). Average understandability and actionability scores were low at 52% and 36%, respectively. The mean CSAT was 2.27, below the recommended value of 2.5. Cohen κ for interrater reliability was greater than 0.81 for the Patient Education and Assessment Tool and CSAT, suggesting excellent agreement between raters.

Conclusions

Available online Spanish lymphedema resources are written at an elevated reading level and are inappropriate for a population with lower health literacy levels. As patients continue to use the internet as their primary source for health information, health care entities must improve the quality of provided Spanish resources in order to optimize patient comprehension.
Behavioral interventions in epilepsy
Authors: Haut Sheryl R. , Gursky Jonathan M. , Privitera Michael
Published: January 2019

Purpose of review

Behavioral intervention describes multiple modalities of treatments which are of increasing interest in epilepsy. This review addresses recent behavioral clinical trials in epilepsy including cognitive behavioral therapy (CBT), mindfulness, progressive muscle relaxation (PMR), and self-management. Results and conclusions from updated Cochrane reviews and the recent International League Against Epilepsy Psychology task force are presented.

Recent findings

Two recent large randomized controlled trials (mindfulness and progressive muscle relaxation) reported improved seizure frequency with behavioral treatments. In both studies, participants in both the active and the attentional control arms showed significant seizure reduction, whereas quality of life and stress reduction were better noted in the active arms. Additional behavioral modalities have reported improved seizure control including yoga, bio/neurofeedback, and music therapy.

Significant improvements in multiple quality of life, cognitive domains, and medication adherence have been reported from randomized and open label trials of cognitive behavioral therapy, and self-management programs. Multiple promising self-management programs have been recently reported, often utilizing the power of web-based apps, and digitally delivered group therapy. In 2018, the International League Against Epilepsy Psychology task force recommended that ‘psychological interventions should be incorporated into comprehensive epilepsy care.’

Behavioral treatments are successful and likely underutilized in the treatment of epilepsy. Given the challenge of conducting randomized clinical trials of behavioral therapy, much remains to be studied. However, for motivated and interested patients, appropriately chosen behavioral therapies appear to be important adjuncts to standard therapy. The timing is currently optimal to take best advantage of smartphone apps and web-based delivery systems, both for research and therapeutic purposes.
Laser interstitial thermal therapy in drug-resistant epilepsy
Authors: Shimamoto Shoichi , Wu Chengyuan , Sperling Michael R.
Published: January 2019

Purpose of review

MRI-guided stereotactic laser interstitial thermal therapy (LiTT) has been utilized in the surgical treatment of discrete, small epileptogenic lesions. This review summarizes the current literature and addresses the clinical application of this technique.

Recent findings

LiTT has the potential to reduce the morbidity and discomfort of epilepsy surgery. Review of data from retrospective, uncontrolled studies suggests that LiTT may offer benefit when treating drug-resistant epilepsy because of mesial temporal sclerosis, hypothalamic hamartoma, cavernous hemangioma, and small cortical dysplasias and malformations. It is now being offered as initial therapy in place of anterior temporal lobectomy in many centers, and a prospective study is underway to compare it with historical temporal lobectomy reports.

LiTT appears promising and has potential for reduced morbidity and improved tolerability compared with open surgery. Studies must be done to compare efficacy and safety of LiTT with open surgery, and further investigation is needed to optimize this technique.
Nonparaneoplastic autoimmune cerebellar ataxias
Authors: Joubert Bastien , Honnorat Jerome
Published: January 2019

Purpose of review

The current review develops the clinical presentations of nonparaneoplastic autoimmune cerebellar ataxia (ACA) and analyzes the association with autoantibodies.

Recent findings

Emerging evidence suggests that autoimmunity is involved in a significant proportion of sporadic ataxia cases. Moreover, numerous autoantibodies have recently been described in association with sporadic cerebellar ataxia, improving diagnosis and patient categorization.

Nonparaneoplastic ACA encompasses postinfectious acute cerebellar ataxia, opsoclonus-myoclonus-ataxia syndrome, and pure cerebellar ataxia with or without autoantibodies. There is still confusion about how to diagnose and classify the patients, and retrospective data suggest that these very rare entities are in fact largely underrecognized. Numerous autoantibodies have been found associated with sporadic ataxia, improving diagnosis accuracy, and patient categorization. However, although anti-glutamate decarboxylase isotype 65 (GAD65), anti-contactin-associated protein 2 (CASPR2), and anti metabotropic glutamate receptor (mGluR1) antibodies are well recognized biomarkers, many other autoantibodies have been described in very small numbers of patients and their specificity is unknown. Efficient biomarkers for ACA are still lacking and in many cases the diagnosis has to rely on a body of converging evidence.
Supranormal Sensory Nerve Action Potential Amplitude Correlates of Sensory Symptoms
Authors: Tipton Philip W. , Rubin Devon I.
Published: January 2019

Purpose:

Patients presenting with pain, numbness, or paresthesias frequently have normal electrodiagnostic studies. Supranormal sensory nerve action potential amplitudes may be a potential biomarker of sensory nerve hyperexcitability.

Methods:

A retrospective chart review of 400 consecutive patients with normal electromyography reports between July and November 2016 was performed. Patients were divided into tertiles based on the degree of sensory nerve action potential amplitudes above lower limits of normal (<2×, 2–3×, and >3×). Patient demographics and sensory symptom quality were assessed. Multivariate analysis assessed for an association between sensory symptoms and sensory nerve action potential amplitudes, age, or gender.

Results:

After controlling for age and gender, subjects in the 2–3× and >3× normal tertiles had a higher association with multifocal symptoms, whereas those in the >3× normal tertile had a lower association with distal symptoms compared with the <2× normal tertile.

Conclusion:

The association of supranormal sensory nerve action potential amplitudes with multifocal symptoms may be an indicator of diffuse hyperexcitability.
Attitudes Toward Electroconvulsive Therapy Among Involuntary and Voluntary Patients
Authors: Takamiya Akihiro , Sawada Kyosuke , Mimura Masaru , Kishimoto Taishiro
Published: January 2019

Objective

We aimed to examine attitudes toward electroconvulsive therapy (ECT) among involuntary patients, voluntary patients, and their relatives.

Methods

Patients experiencing a major depressive episode and receiving ECT and their relatives were recruited for the survey. Patients and their relatives answered the self-rating questionnaires with a 7-point Likert scale. We explored differences in the survey results between involuntary and voluntary patients, as well as differences in the survey results between patients and their relatives.

Results

We recruited 97 participants (53 patients and 44 relatives) for the survey. Approximately 80% of the patients showed positive attitudes toward ECT. There were no statistically significant differences between involuntary (n = 23) and voluntary (n = 30) patients across multiple aspects of the ECT experience, including treatment satisfaction, positive or adverse effects of ECT, and treatment preference in the future. Relatives were more satisfied with the positive effects of ECT and with the information offered before ECT treatment than the patients themselves.

Conclusions

Approximately 80% of the patients showed overall satisfaction with ECT irrespective of consent status. Relatives were more satisfied with ECT than patients. Electroconvulsive therapy can be a lifesaving treatment for severely depressed patients, and the subjective experience of involuntary patients should be taken into consideration when discussing involuntary ECT treatment.
A brief history of thylakoid biogenesis
Authors: Mechela Annabel , Schwenkert Serena , Soll Jürgen
Published: January 2019

The thylakoid membrane network inside chloroplasts harbours the protein complexes that are necessary for the light-dependent reactions of photosynthesis. Cellular processes for building and altering this membrane network are therefore essential for life on Earth. Nevertheless, detailed molecular processes concerning the origin and synthesis of the thylakoids remain elusive. Thylakoid biogenesis is strongly coupled to the processes of chloroplast differentiation. Chloroplasts develop from special progenitors called proplastids. As many of the needed building blocks such as lipids and pigments derive from the inner envelope, the question arises how these components are recruited to their target membrane. This review travels back in time to the beginnings of thylakoid membrane research to summarize findings, facts and fictions on thylakoid biogenesis and structure up to the present state, including new insights and future developments in this field.
Construction of layered hierarchical CoMoO
4
nanostructured arrays for supercapacitors with enhanced areal capacitance
Authors: Hu XiaoYan , Wang Hai , Jin SanMei , Wang Heng
Published: January 2019

Layered hierarchical CoMoO
4
nano-structured arrays grown on nickel foam were designed and synthesized by a two-step hydrothermal method following by annealing. With the increase in the nearly three times loading mass of active materials, the specific capacitance of the layered hierarchical CoMoO
4
nano-structured arrays only shows a slight loss compared with the single-layer CoMoO
4
nano-structured arrays, which dramatically improved the areal capacitance from 2.47 to 6.79 F cm
−2
. Also, the layered hierarchical CoMoO
4
nano-structured arrays showed 94.8% capacitance retention after 2500 cycles, which is mainly due to the well-designed layered hierarchical structure and good conductivity.
Photodegradation of naphthalene over Fe
3
O
4
under visible light irradiation
Authors: Zhang Jiawei , Fan Shanshan , Lu Bin , Cai Qinghai , Zhao Jingxiang , Zang Shuying
Published: January 2019

Using FeCl
3
and FeSO
4
as precursors, Fe
3
O
4
were prepared by co-precipitation method via FeCl
3
and FeSO
4
aqueous solutions successively added to NaOH solution. The sample was proved by X-ray powder diffraction, transmission electron microscope, ultraviolet–visible spectrophotometry and magnetic measurement. The results showed that the prepared Fe
3
O
4
material was composed of an average diameter of about 15 nm particles and nano rods with well-crystallized magnetite and stronger superparamagnetic, getting a saturation magnetization of 49.5 emu g
−1
. This Fe
3
O
4
material was found to be an effective catalyst for photodegradation of naphthalene with or without H
2
O
2
under visible light irradiation, getting 81.1% and 74.3% degradation rate in these two cases, respectively. The degradation pathway in the absence and presence of H
2
O
2
was analysed via measurement of the distribution of degradation products by GC-MS and adsorption of reactants on the surface of the catalyst by
in situ
DRIFTS spectra.
Weighted recurrence networks for the analysis of time-series data
Authors: Jacob Rinku , Harikrishnan K. P. , Misra R. , Ambika G.
Published: January 2019

Recurrence networks (RNs) have become very popular tools for the nonlinear analysis of time-series data. They are unweighted and undirected complex networks constructed with specific criteria from time series. In this work, we propose a method to construct a ‘weighted recurrence network’ from a time series and show that it can reveal useful information regarding the structure of a chaotic attractor which the usual unweighted RN cannot provide. Especially, a network measure, the node strength distribution, from every chaotic attractor follows a power law (with exponential cut off at the tail) with an index characteristic to the fractal structure of the attractor. This provides a new class among complex networks to which networks from all standard chaotic attractors are found to belong. Two other prominent network measures, clustering coefficient and characteristic path length, are generalized and their utility in discriminating chaotic dynamics from noise is highlighted. As an application of the proposed measure, we present an analysis of variable star light curves whose behaviour has been reported to be strange non-chaotic in a recent study. Our numerical results indicate that the weighted recurrence network and the associated measures can become potentially important tools for the analysis of short and noisy time series from the real world.
Influence of the composition gradient on the propagation of heat pulses in functionally graded nanomaterials
Authors: Cao B.-Y. , Di Domenico M. , Nie B.-D. , Sellitto A.
Published: January 2019

A theoretical model to describe heat transport in functionally graded nanomaterials is developed in the framework of extended thermodynamics. The heat-transport equation used in our theoretical model is of the Maxwell–Cattaneo type. We study the propagation of acceleration waves in functionally graded materials (FGMs). In the special case of functionally graded Si

1−
c

Ge

c

thin layers, we point out the influence of the composition gradient on the propagation of heat pulses. A possible use of heat pulses as exploring tool to infer the inner composition of FGMs is suggested.
Pausing for arbitrarily long times in dynamical systems
Authors: Webber Simon , Glendinning Paul , Jeffrey Mike R.
Published: January 2019

It is well known that continuity in dynamical systems is not sufficient to guarantee uniqueness of solutions, but less obvious is that non-uniqueness can carry internal structure useful to characterize a system's dynamics. The non-uniqueness that concerns us here arises when an isolated non-differentiability of a flow results in spatial or temporal ambiguity of solutions. Spatial ambiguity can render a flow set valued after a specific event, and non-trivial examples are increasingly being seen in models of switching occurring in electronic or biological systems. Temporal ambiguity can mean that the same spatial trajectory may be traversed in different times, making an arbitrarily long pause at the non-differentiable point. We focus here on temporal indeterminacy and the extent to which it can be resolved. To investigate the typical forms, we take representative examples of the different conditions (non-differentiability, discontinuity or singularity) under which it occurs.
Evolution of self-limited cell division of symbionts
Authors: Uchiumi Yu , Ohtsuki Hisashi , Sasaki Akira
Published: January 2019

In mutualism between unicellular hosts and their endosymbionts, symbiont's cell division is often synchronized with its host's, ensuring the permanent relationship between endosymbionts and their hosts. The evolution of synchronized cell division thus has been considered to be an essential step in the evolutionary transition from symbionts to organelles. However, if symbionts would accelerate their cell division without regard for the synchronization with the host, they would proliferate more efficiently. Thus, it is paradoxical that symbionts evolve to limit their own division for synchronized cell division. Here, we theoretically explore the condition for the evolution of self-limited cell division of symbionts, by assuming that symbionts control their division rate and that hosts control symbionts' death rate by intracellular digestion and nutrient supply. Our analysis shows that symbionts can evolve to limit their own cell division. Such evolution occurs if not only symbiont's but also host's benefit through symbiosis is large. Moreover, the coevolution of hosts and symbionts leads to either permanent symbiosis where symbionts proliferate to keep pace with their host, or the arms race between symbionts that behave as lytic parasites and hosts that resist them by rapid digestion.
Is neurogenesis in two songbird species related to their song sequence variability?
Authors: Polomova Justina , Lukacova Kristina , Bilcik Boris , Kubikova Lubica
Published: January 2019

Neurogenesis takes part in the adult songbird brain and new neurons are integrated into the forebrain including defined areas involved in the control of song learning and production. It has been suggested that the new neurons in the song system might enable vocal variability. Here, we examined the basal levels of neurogenesis in two songbird species, zebra finch (
Taeniopygia guttata
) and Bengalese finch (
Lonchura striata var. domestica
), which do not learn new song elements as adults but differ in the level of song sequence variability. We found that Bengalese finches had less linear and stereotyped song sequence and a higher number of newborn cells in the neurogenic subventricular zone (SVZ) as well as the number of newly born neurons incorporated into the vocal nucleus HVC (used as a proper name) in comparison to zebra finches. Importantly, this vocal sequence variability in Bengalese finches correlated with the number of new neurons in the vocal nucleus HVC and more plastic song was associated with higher neuronal incorporation. In summary, our data support the hypothesis that newly generated neurons facilitate behavioural variability.
Using genomics to understand antimicrobial resistance and transmission in Neisseria gonorrhoeae
Authors: Sánchez-Busó Leonor , Harris Simon R.
Published: January 2019

Gonorrhoea infections are on the increase and strains that are resistant to all antimicrobials used to treat the disease have been found worldwide. These observations encouraged the World Health Organization to include

Neisseria gonorrhoeae

on their list of high-priority organisms in need of new treatments. Fortunately, concurrent resistance to both antimicrobials used in dual therapy is still rare. The fight against antimicrobial resistance (AMR) must begin from an understanding of how it evolves and spreads in sexual networks. Genome-based analyses have allowed the study of the gonococcal population dynamics and transmission, giving a novel perspective on AMR gonorrhoea. Here, we will review past, present and future treatment options for gonorrhoea and explain how genomics is helping to increase our understanding of the changing AMR and transmission landscape. This article contains data hosted by Microreact.
lncRNA Neat1 drives neuronal histone methylation and age-related memory impairments
Authors: Butler Anderson A. , Johnston Daniel R. , Kaur Simranjit , Lubin Farah D.
Published: January 2019

Histone methylation is critical for the formation and maintenance of long-term memories. Long noncoding RNAs (lncRNAs) are regulators of histone methyltransferases and other chromatin modifying enzymes (CMEs). We investigated how lncRNA Neat1-mediated histone methylation contributes to hippocampus-dependent long-term memory formation, using a combination of transcriptomics, RNA binding protein immunoprecipitation, CRISPR mediated gene activation, and behavioral approaches. Suppression of the lncRNA Neat1 revealed widespread changes in gene transcription as well as perturbations of histone 3 lysine 9 dimethylation (H3K9me2), a repressive histone modification mark that is dysregulated in the aging hippocampus. We identified a Neat1-dependent mechanism of transcriptional repression via H3K9me2 at the c-Fos promoter corresponding with observed changes in c-Fos mRNA levels. Overexpression of hippocampal Neat1 via CRISPRa is sufficient to impair memory formation in young adults, recapitulating observed memory deficits in old adults, while Neat1 suppression in both young and old adult mice improves memory. These results suggest that lncRNA Neat1 is a potent epigenetic regulator of hippocampus-dependent long-term memory formation.
G4-iM Grinder: DNA and RNA G-Quadruplex, i-Motif and higher order structure search and analyser tool
Authors: Belmonte-Reche Efres , Morales Juan Carlos
Published: January 2019

Herein, we present G4-iM Grinder as a system for potential G4, i-Motif and higher-order structure identification and characterization. Several grading tools of biological relevance and G4 in vitro formation probability are included in this highly modulable and robust engine. G4-iM Grinder improves other current quadruplex search engines when compared in capabilities and processing time. We used G4-iM Grinder in the analysis of the complete human genome whilst focusing on frequency and score of G-based structures. We studied the most recurrent potential quadruplex sequences (PQS) and the longest highest scoring potential higher order quadruplex sequences (PHOQS) in our genome. As proof of the analytical capabilities of G4-iM Grinder, we also analysed a new PHOQS and predicted the most probable PQS subunits to form it. Taking the human average PQS density as reference, we examined the genomes of organisms that cause leishmaniosis, diphtheria, brucellosis, meningitis, pneumonia, toxoplasmosis, tuberculosis, leprosy, AIDS, dengue fever and hepatitis C, and found they are very rich in PQS. G4-iM Grinder identified within many of these organisms several already known-to-form G4 sequences. Together, this suggests that G4-quadruplexes may potentially be important therapeutic targets against many of these organisms that currently kill millions worldwide.

GRAPHICAL ABSTRACT
Magnetic Ultrathin Tissue Sections for Ease of Light and Electron Microscopy
Authors: Koestinger German , During Daniel , Rickauer Simone , Leite Vanessa , Yamahachi Homare , Csucs Gabor , Hahnloser Richard HR
Published: January 2019

This manuscript has been removed as the result of a ruling by ETH Zurich.
Completing the ENCODE3 compendium yields accurate imputations across a variety of assays and human biosamples
Authors: Schreiber Jacob , Bilmes Jeffrey , Stafford Noble William
Published: January 2019

Motivation

Recent efforts to describe the human epigenome have yielded thousands of uniformly processed epigenomic and transcriptomic data sets. These data sets characterize a rich variety of biological activity in hundreds of human cell lines and tissues (“biosamples”). Understanding these data sets, and specifically how they differ across biosamples, can help explain many cellular mechanisms, particularly those driving development and disease. However, due primarily to cost, the total number of assays that can be performed is limited. Previously described imputation approaches, such as Avocado, have sought to overcome this limitation by predicting genome-wide epigenomics experiments using learned associations among available epigenomic data sets. However, these previous imputations have focused primarily on measurements of histone modification and chromatin accessibility, despite other biological activity being crucially important.

Results

We applied Avocado to a data set of 3,814 tracks of data derived from the ENCODE compendium, spanning 400 human biosamples and 84 assays. The resulting imputations cover measurements of chromatin accessibility, histone modification, transcription, and protein binding. We demonstrate the quality of these imputations by comprehensively evaluating the model’s predictions and by showing significant improvements in protein binding performance compared to the top models in an ENCODE-DREAM challenge. Additionally, we show that the Avocado model allows for efficient addition of new assays and biosamples to a pre-trained model, achieving high accuracy at predicting protein binding, even with only a single track of training data.

Availability

Tutorials and source code are available under an Apache 2.0 license at https://github.com/jmschrei/avocado.

Contact

william-noble@uw.edu or jmschr@cs.washington.edu
A novel plasmid-transcribed regulatory sRNA, QfsR, controls chromosomal polycistronic mRNAs in Agrobacterium tumefaciens
Authors: Diel Benjamin , Dequivre Magali , Wisniewski-Dyé Florence , Vial Ludovic , Hommais Florence
Published: January 2019

Plasmids are mobile DNAs that adjust host cell functions for their own amplification and dissemination. We identified QfsR, a small RNA, transcribed from the Ti plasmid in the phytopathogen Agrobacterium fabrum. QfsR is widely conserved throughout RepABC plasmids carried by Rhizobiaceae. Target prediction, expression analysis and site-direct mutagenesis experiments show that QfsR directly pairs within polycistronic mRNAs transcribed from chromosomes (involved in flagella apparatus and succinoglycan biosynthesis) and Ti plasmid (involved in conjugative transfer). QfsR leads to a coordinated expression of whole polycistronic mRNA molecules. Whereas a lack of QfsR induces motility and reduces succinoglycan production, its overproduction increases the quorum sensing signal accumulation and the Ti plasmid conjugative transfer. Based on these observations, we propose QfsR as a hub connecting regulatory networks of motility, succinoglycan biosynthesis and plasmid conjugative transfer. To our knowledge, QfsR is the first example of a plasmid-encoded sRNA that controls chromosomal polycistronic mRNAs.

Significance

Plasmids represent an important cost for the hosting cell although some are beneficial under certain circumstances. Agrobacterium tumefaciens harboring Tumor inducing plasmid (pTi) are able to infect plants and to use specific resources produced by the infected cells. We characterized QfsR, a novel small RNA (sRNA) from pTi, that directly regulates plasmid polycistronic mRNA but also chromosomal ones. QfsR contributes to a fine-tuned regulation of bacterial motility, exopolysaccharide biosynthesis and conjugative dissemination of pTi. Our results report the first plasmid-encoded sRNA able to modify and coordinate cellular behaviour probably for the benefit of the plasmid dissemination and tight crosstalk between plasmid and chromosome. This could be widespread since QfsR homologs were predicted in other plasmids of Rhizobiaceae symbionts and pathogens.
The International Space Station selects for microorganisms adapted to the extreme environment, but does not induce genomic and physiological changes relevant for human health
Authors: Mora Maximilian , Wink Lisa , Kögler Ines , Mahnert Alexander , Rettberg Petra , Schwendner Petra , Demets René , Cockell Charles , Alekhova Tatiana , Klingl Andreas , Alexandrova Alina , Moissl-Eichinger Christine
Published: January 2019

The International Space Station (ISS) is a unique, completely confined habitat for the human crew and co-inhabiting microorganisms. Here, we report on the results of the ISS experiment “EXTREMOPHILES”. We aimed to exploit the microbial information obtained from three surface and air sampling events aboard the International Space Station during increments 51 and 52 (2017) with respect to: i) microbial sources, diversity and distribution within the ISS, ii) functional capacity of microbiome and microbial isolates, iii) extremotolerance and antibiotics-resistance (compared to ground controls), and iv) microbial behavior towards ISS-relevant materials such as biofilm formation, or potential for degradation. We used wipe samples and analyzed them by amplicon and metagenomics sequencing, cultivation, comparative physiological studies, antibiotic resistance tests, genome analysis of isolates and co-incubation experiments with ISS-relevant materials. The major findings were: i) the ISS microbiome profile is highly similar to ground-based confined indoor environments, ii) the ISS microbiome is subject to fluctuations and indicative for the (functional) location, although a core microbiome was present over time and independent from location, iii) the ISS selects for microorganisms adapted to the extreme environment, but does not necessarily induce genomic and physiological changes which might be relevant for human health, iv) cleanrooms and cargo seems to be a minor source of microbial contamination aboard, and v) microorganisms can attach to and grow on ISS-relevant materials. Biofilm formation might be a threat for spacecraft materials with the potential to induce instrument malfunctioning with consequences for mission success. We conclude that our data do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards biofilm formation and material integrity in moist areas.