bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of P‐glycoprotein (Pgp) expression in human osteosarcoma by high‐throughput tissue microarray
Authors: Gao Yan , Liao Yunfei , Shen Jacson K. , Feng Yong , Choy Edwin , Cote Gregory , Harmon David , Mankin Henry J. , Hornicek Francis J. , Duan Zhenfeng
Published: January 2016

Survival of osteosarcoma patients is currently limited by the development of metastases and multidrug resistance (MDR). A well‐established cause of MDR involves overexpression of P‐glycoprotein (Pgp) in tumor cells. However, some discrepancies still exist as to the clinical significance of Pgp in osteosarcoma. We sought to elucidate further whether the Pgp expression correlated with clinical behavior in a series of patients with osteosarcoma via high‐throughput tissue microarray (TMA) analysis. Immunohistochemical analysis of Pgp expression in a TMA of 114 specimens with a retrospective review of 70 osteosarcoma patients admitted to the Massachusetts General Hospital (MGH) was performed. High Pgp expression was correlated with metastasis development and poor response to pre‐operative chemotherapy in osteosarcoma patients. Eighteen of the fifty‐seven patients initially admitted with primary osteosarcoma showed high Pgp expression. Among these 18 patients with high Pgp expression, 13 of 18 (72%) patients eventually developed metastases. There was no significant clinical relevance between Pgp expression and osteosarcoma survival. These results support that high expression of Pgp is important, but cannot be assigned as, an individual predictor in the development of human osteosarcoma. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1606–1612, 2016.
Intraoperative navigation in robotically assisted compartmental surgery of uterine cancer by visualisation of embryologically derived lymphatic networks with indocyanine‐green (ICG)
Authors: Kimmig Rainer , Aktas Bahriye , Buderath Paul , Rusch Peter , Heubner Martin
Published: January 2016

Background and Objectives

To evaluate feasibility of intraoperative visualization of embryologically defined organ compartments and their drainage by ICG in uterine cancer.

Methods

Total of 2.5 mg of ICG have been injected into cervix or corpus in uterine cancer patients immediately prior to surgery. Green fluorescence was intermittently detected during robotically assisted laparoscopic surgery (Firefly System®, Intuitve Surgical Inc.). Total of 36 patients with uterine cancer without macroscopically suspicious nodes were evaluated with respect to their compartmental lymphatic network, collecting lymphatic vessels, and the connection to the postponed lymph basins.

Results

Müllerian (sub) compartment and transport of lymph fluid along the lymphatic collectors and connecting vessels to the postponed lymph basins could be visualized invariably in all patients. Cervix drained along the ligamentous and caudal part of vascular mesometria, whereas midcorporal and fundal drainage occurred along the upper part of vascular mesometria and along the mesonephric pathway along the ovarian vessels.

Conclusions

Visualization of lymphatic network and downstream flow of lymphatic fluid to the postponed lymph basins by ICG is feasible; it can be used to navigate along compartment boarders for education, intraoperative orientation, and quality control. It seems to confirm the compartmental order of pelvic organ systems and postponed lymph basins. J. Surg. Oncol. 2016;113:554–559. © 2016 Wiley Periodicals, Inc.
Role of adrenal vein sampling in primary aldosteronism: Impact of imaging, localization, and age
Authors: Wachtel Heather , Zaheer Salman , Shah Parth K. , Trerotola Scott O. , Karakousis Giorgos C. , Roses Robert E. , Cohen Debbie L. , Fraker Douglas L.
Published: January 2016

Background

The role of adrenal vein sampling (AVS) has been debated, with some authorities advocating selective use in younger patients (≤40 years), and those localized by preoperative imaging. We examined our experience to determine the impact of AVS in patients who routinely underwent AVS with a high success rate.

Methods

A retrospective cohort study was performed using a prospectively maintained database of patients referred for evaluation of PA (1997–2013). Patients were classified as localized (L) if a unilateral mass was identified on imaging, and non‐localized (NL) otherwise.

Results

Of 367 patients, 94% (n = 345) underwent successful AVS. Seventy‐two percent (n = 265) were L; AVS was lateralizing 58% (n = 214). AVS changed management in 43% of patients (n = 158). In patients ≤40 years, AVS changed management in 30% (n = 15). In patients ≤40 years with a ≥1 cm adrenal mass, 12% (n = 3) would have undergone unnecessary surgery based on imaging results alone; in patients >40 years with a ≥1 cm adrenal mass, 3% (n = 5) would have undergone wrong‐side surgery, and 30% (n = 50) would have undergone unnecessary surgery based on imaging.

Conclusion

AVS changed management in a significant minority of patients regardless of age and imaging findings. AVS should be routinely recommended in all patients with PA, to direct operative therapy. J. Surg. Oncol. 2016;113:532–537. © 2016 Wiley Periodicals, Inc.
High‐performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications
Authors: Williamson James C. , Edwards Alistair V. G. , Verano‐Braga Thiago , Schwämmle Veit , Kjeldsen Frank , Jensen Ole N. , Larsen Martin R.
Published: January 2016

We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label‐free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3‐based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label‐free approach offers a more linear response with a wider dynamic range than MS/MS‐based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS‐based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation that significantly impacts the choice of instrument.
Morpheus Spectral Counter: A computational tool for label‐free quantitative mass spectrometry using the Morpheus search engine
Authors: Gemperline David C. , Scalf Mark , Smith Lloyd M. , Vierstra Richard D.
Published: January 2016

Label‐free quantitative MS based on the Normalized Spectral Abundance Factor (NSAF) has emerged as a straightforward and robust method to determine the relative abundance of individual proteins within complex mixtures. Here, we present Morpheus Spectral Counter (MSpC) as the first computational tool that directly calculates NSAF values from output obtained from Morpheus, a fast, open‐source, peptide‐MS/MS matching engine compatible with high‐resolution accurate‐mass instruments. NSAF has distinct advantages over other MS‐based quantification methods, including a greater dynamic range as compared to isobaric tags, no requirement to align and re‐extract MS1 peaks, and increased speed. MSpC features an easy‐to‐use graphic user interface that additionally calculates both distributed and unique NSAF values to permit analyses of both protein families and isoforms/proteoforms. MSpC determinations of protein concentration were linear over several orders of magnitude based on the analysis of several high‐mass accuracy datasets either obtained from PRIDE or generated with total cell extracts spiked with purified Arabidopsis 20S proteasomes. The MSpC software was developed in C# and is open sourced under a permissive license with the code made available at http://dcgemperline.github.io/Morpheus_SpC/.
Effects of stem cell therapy on protein profile of parkinsonian rats using an18O‐labeling quantitative proteomic approach
Authors: Liu Yahui , Liu Kefu , Qin Wei , Liu Chenghao , Zheng Xiaowei , Deng Yulin , Qing Hong
Published: January 2016

The application of neural stem cell (NSC) research to neurodegenerative diseases has led to promising clinical trials. Currently, NSC therapy is most promising for Parkinson's disease (PD). We conducted behavioral tests and immunoassays for the profiling of a PD model in rats to assess the therapeutic effects of NSC treatments. Further, using a multiple sample comparison workflow, combined with 18O‐labeled proteome mixtures, we compared the differentially expressed proteins from control, PD, and NSC‐treated PD rats. The results were analyzed bioinformatically and verified by Western blot. Based on our initial findings, we believe that the proteomic approach is a valuable tool in evaluating the therapeutic effects of NSC transplantation on neurodegenerative disorders.
Maternal body mass index before pregnancy is associated with increased bronchodilator dispensing in early childhood: A cross‐sectional study
Authors: MacDonald Kelvin D. , Vesco Kimberly K. , Funk Kristine L. , Donovan Jerena , Nguyen Thuan , Chen Zunqiu , Lapidus Jodi A. , Stevens Victor J. , McEvoy Cindy T.
Published: January 2016

Rationale

Maternal prepregnancy obesity has been associated with early wheeze and childhood asthma in their offspring. Some of these studies have been in minority, urban, and disadvantaged populations using parental recall and questionnaires. The association of maternal prepregnancy obesity with bronchodilator dispensing to their offspring, in a primarily insured, non‐urban, White population in the United States is unknown.

Objectives and Methods

We conducted a retrospective cohort study using pharmacy dispensing data from the electronic medical records of a large United States health maintenance organization to examine the relationship between maternal prepregnancy body mass index (BMI) and inhaled bronchodilator dispensing in the offspring to 4 years of age. We included infants ≥37 weeks' gestation with birth weight ≥2.5 kg which yielded 6,194 mother‐baby pairs. Maternal prepregnancy BMI was categorized as underweight (<18.5 kg/m2), normal (18.5−24.9 kg/m2), overweight (25−29.9 kg/m2), or obese (≥30 kg/m2).

Results

In the entire cohort, 27.6% of the offspring received a bronchodilator dispensing. This ranged from 19.2% in the offspring of underweight mothers to 31.3% of those born to obese mothers. In the fully adjusted model using normal BMI as the referent, children of obese mothers had a 22% higher rate of bronchodilator dispensing (adjusted OR = 1.22; 95%CI 1.05–1.41; P = 0.008).

Conclusions

In this insured, non‐urban, White population, maternal prepregnancy obesity was associated with bronchodilator dispensing in the offspring in early life. These results extend previous data and reaffirm the potential widespread public health impact that prepregnancy obesity may have on subsequent childhood respiratory health. Pediatr Pulmonol. 2016;51:803–811. © 2016 Wiley Periodicals, Inc.
Modeling of heat transfer processes in Ni2MnIn magnetic wires
Authors: Pavlukhina Oksana , Sokolovskiy Vladimir , Buchelnikov Vasiliy
Published: January 2016

In this work, we study a heat transfer in the three‐dimensional magnetic cooling cell involving microwires of NiMnIn Heusler alloy. Thermophysical properties of microwires such as the heat capacity, magnetic part of entropy, and magnetocaloric effect were investigated by means of Monte Carlo simulations with parameters taken from ab initio calculations as input. The diameter of the magnetic wires was varied from 10 to 50 m while the length was fixed to 1 mm. The system is supplied a coolant water flow at a constant speed and temperature. We have shown that the cooling power depends on the magnetic wire thickness and the coolant flow rate. The relaxation times of the temperature of wires, the temperature distribution in the magnetic wires and coolant, as well as the velocity fields of a coolant in the cell were calculated.
What can molecular simulation do for global warming?
Authors: Tian Ziqi , Dai Sheng , Jiang De‐en
Published: January 2016

Carbon capture is necessary to reduce CO2 emissions from burning fossil fuels, which has led to global warming. Molecular simulations offer chemical insights and design principles for new separation media and for understanding the separation process. In this review, we summarize recent applications of simulation methods from ab initio and density functional theory to classical molecular dynamics and Grand canonical Monte Carlo in understanding ionic liquids and porous carbonaceous materials for CO2 separation, especially the postcombustion CO2/N2 separation. We highlight design and simulation of the porous two‐dimensional (2D) materials as the highly selective membranes for CO2 separation. Simulated structure–property relationships for the materials are discussed in connection to the corresponding chemisorption, physisorption, or membrane process. In chemisorption, the focus is on reducing the heat of reaction with CO2; in physisorption, the key is to increase the binding strength via CO2‐philic groups; in membrane process, the key is to increase solubility for ionic‐liquid membranes and to control pore size for 2D materials. Challenges and opportunities for simulating emerging materials are also discussed. WIREs Comput Mol Sci 2016, 6:173–197. doi: 10.1002/wcms.1241

This article is categorized under:

Structure and Mechanism > Computational Materials Science

Electronic Structure Theory > Density Functional Theory

Molecular and Statistical Mechanics > Molecular Interactions
Group IVB transition metal trichalcogenides: a new class of 2D layered materials beyond graphene
Authors: Dai Jun , Li Ming , Zeng Xiao Cheng
Published: January 2016

The discovery of graphene, a single atomic layer of carbon in a hexagonal lattice, has invigorated enormous research interests in two‐dimensional (2D) layered materials and their one‐dimensional (1D) derivatives not only owing to their extraordinary physical and chemical properties but also their high potential for applications in electronic and photonic devices. A weakness of the graphene however is its lack of a bandgap—a prerequisite for building field‐effect transistors (FETs). A stream of new 2D layered materials have been developed over the past 5 years, including, among many others, silicene, phosphorene, and transition metal dichalcogenides. Monolayers of many of these 2D materials exhibit a bandgap, either direct or indirect. In 2015, a new class of 2D layered materials, namely, group‐IVB transition metal trichalcogenides (TMTCs), has been uncovered. A prototypical representative of this new class of 2D materials is TiS3 whose monolayer is predicted to possess a direct band gap of about 1 eV [close to that (1.17 eV) of bulk silicon], and relatively high carrier mobility. Isolation of the few‐layer TiS3 sheets and TiS3 nanoribbons via mechanical exfoliation has been realized in the laboratory in 2015. The modest 1‐eV band gap, relatively high carrier mobility, as well as high chemical stability in open air render TiS3 monolayer a promising 2D material for nanoelectronic and nanophotonic applications. In this study, we give an overview of the emerging area of 2D and 1D TMTC materials and suggest future research directions related to these novel materials. WIREs Comput Mol Sci 2016, 6:211–222. doi: 10.1002/wcms.1243

This article is categorized under:

Structure and Mechanism > Computational Materials Science
The Stored-Program Universal Computer: Did Zuse Anticipate Turing and von Neumann?
Authors: Copeland B. Jack , Sommaruga Giovanni
Published: January 2016

This chapter sets out the early history of the stored-program concept. The several distinct ‘onion skins’ making up the concept emerged slowly over a ten-year period, giving rise to a number of different programming paradigms. A notation is developed for describing different aspects of the stored-program concept. Theoretical contributions by Turing, Zuse, Eckert, Mauchly, and von Neumann are analysed, followed by a comparative study of the first practical implementations of stored-programming, at the Aberdeen Ballistic Research Laboratory in the US and the University Manchester in the UK. Turing’s concept of universality is also examined, and an assessment is provided of claims that various historic computers—including Babbage’s Analytical Engine, Flowers’ Colossus and Zuse’s Z3—were universal. The chapter begins with a discussion of the work of the great German pioneer of computing, Konrad Zuse.
Clinical analysis of retroperitoneoscopic nephroureterectomy for renal tuberculosis
Authors: Yan Min‐Bo , Lu Jing , Li Xiao‐Feng , Guo Zhen‐Yu
Published: January 2016

Objectives

To explore the feasibility and safety of retroperitoneoscopic nephroureterectomy for kidney tuberculosis.

Methods

Forty‐eight retroperitoneoscopic nephroureterectomies and thirty‐five nephroureterectomies for kidney tuberculosis procedures were performed from June 2008 to December 2014. The patients consisted of 53 males and 30 females with a mean age of 36 years (range: 26–51 years). The patients' data were reviewed and analyzed.

Results

The retroperitoneoscopic nephroureterectomy procedures were completed successfully in 48 cases with no conversions to open surgery. The mean operating time was 170 minutes (range: 121–258 minutes), the mean blood loss was 110 ml (range: 70–250 ml), and the mean hospital stay was 5.70 days (range: 5–14 days); these were all much less than nephroureterectomy procedures (P < 0.05). A total of five minor complications (10.4%) occurred, injury to the peritoneum was observed in three patients, and infection at the incision site was observed in two patients, there were no obvious difference between the two surgical methods (P > 0.05). Seventy‐five patients were followed up, and the average follow‐up time was 12.5 months (range: 6–20 months). All the patients recovered without any lesions remaining.

Conclusions

The results of this study indicate that retroperitoneoscopic nephroureterectomy is a feasible, safe, effective, and less invasive treatment modality for treating renal tuberculosis.
Burnout syndrome among psychiatric trainees in 22 countries: Risk increased by long working hours, lack of supervision, and psychiatry not being first career choice
Authors: Jovanović N. , Podlesek A. , Volpe U. , Barrett E. , Ferrari S. , Rojnic Kuzman M. , Wuyts P. , Papp S. , Nawka A. , Vaida A. , Moscoso A. , Andlauer O. , Tateno M. , Lydall G. , Wong V. , Rujevic J. , Platz Clausen N. , Psaras R. , Delic A. , Losevich M.A. , Flegar S. , Crépin P. , Shmunk E. , Kuvshinov I. , Loibl-Weiß E. , Beezhold J.
Published: January 2016

Background

Postgraduate medical trainees experience high rates of burnout, but evidence regarding psychiatric trainees is missing. We aim to determine burnout rates among psychiatric trainees, and identify individual, educational and work-related factors associated with severe burnout.

Methods

In an online survey psychiatric trainees from 22 countries were asked to complete the Maslach Burnout Inventory (MBI-GS) and provide information on individual, educational and work-related parameters. Linear mixed models were used to predict the MBI-GS scores, and a generalized linear mixed model to predict severe burnout.

Results

This is the largest study on burnout and training conditions among psychiatric trainees to date. Complete data were obtained from 1980 out of 7625 approached trainees (26%; range 17.8–65.6%). Participants were 31.9 (SD 5.3) years old with 2.8 (SD 1.9) years of training. Severe burnout was found in 726 (36.7%) trainees. The risk was higher for trainees who were younger (P < 0.001), without children (P = 0.010), and had not opted for psychiatry as a first career choice (P = 0.043). After adjustment for socio-demographic characteristics, years in training and country differences in burnout, severe burnout remained associated with long working hours (P < 0.001), lack of supervision (P < 0.001), and not having regular time to rest (P = 0.001). Main findings were replicated in a sensitivity analysis with countries with response rate above 50%.

Conclusions

Besides previously described risk factors such as working hours and younger age, this is the first evidence of negative influence of lack of supervision and not opting for psychiatry as a first career choice on trainees’ burnout.
Relationship between body mass index and depression in women: A 7-year prospective cohort study. The APNA study
Authors: Martin-Rodriguez E. , Guillen-Grima F. , Aubá E. , Martí A. , Brugos-Larumbe A.
Published: January 2016

Background

The association between body mass index (BMI) and depression is complex and controversial. The present study examined the relationship between BMI and new-onset depression during 7 years of follow-up in 20,212 adult women attending Primary Health Care Centres in Navarra, Spain.

Methods

The Atención Primaria de Navarra (APNA) study is a dynamic prospective cohort study. A total of 20,212 women aged 18–99 years (mean age: 50.7 ± 18.5 years) without depression at baseline were selected from 2004 to 2011. We estimated the incidence of depression. We used the Kaplan-Meier analysis to predict the survival curve. The risk of depression onset according to different measures of BMI at baseline was assessed using Cox regression analyses.

Results

During the 7 years of follow-up, depression appeared in 8.9% (95% CI 8.5–9.3). The highest rates of depression incidence at follow-up occurred in underweight and obese women (9.8% [95% CI 7.3–12.9] and 10.3% [95% CI 9.5–11.1] respectively). The distribution of depression incidence by weight category was U-shaped. The risk of depression increased over time with an observed Kaplan-Meier estimation of 6.67. After adjusting for age, underweight and obese women at baseline have increased risk of depression onset during the follow-up period compared with normal weight women (HR = 1.48, 95% CI = 1.09–2.00 and HR = 1.14, 95% CI = 1.01–1.29 respectively).

Conclusions

In this 7-year prospective study in the APNA women population, depression emerged in 8.9%. Being underweight or obese (not overweight) at baseline is significantly associated with future onset of depression.
The Survey of Pain Attitudes: A revised version of its pediatric form
Authors: Miró Jordi , Solé Ester , Castarlenas Elena , Jensen Mark P.
Published: January 2016

Background and aims

Valid and reliable measures of patients’ pain beliefs are needed by clinicians and researchers to better understand the efficacy and mechanisms of pain treatments. The objective of this work was to address this need by further developing the pediatric version of the Survey of Pain Attitudes (Peds-SOPA), one of the most commonly used measures of pain beliefs.

Methods

A convenience sample of three hundred and seven adolescents (mean age= 14.35; SD = 1.62; 59% girls) participated in the study. They rated the intensity of their worst pain experienced in the 3 months prior to the assessment and completed both the Functional Disability Inventory and a revised version of a pediatric version of the Survey of Pain Attitudes (Peds-SOPA-R).

Results

Factor analyses confirmed a seven-factor solution of the questionnaire, and the revised version demonstrated improvements in the internal consistency of several of the scales (values ranged between adequate and good: 0.71–0.87), except for the Medical Cure scale which showed an internal consistency value of 0.65. The results support the validity of the Peds-SOPA-R scale scores by showing, as predicted, positive relationships between beliefs thought to be maladaptive (e.g., the belief that one is unable to function because of pain) and pain intensity and disability, and negative relationships with beliefs thought to be adaptive (e.g., the belief that exercise is beneficial for pain management) and these criterion variables.

Conclusions

These findings will be helpful to researchers who wish to study the role that pain beliefs play in adjustment to pain in youth.

Implications

The results provide critical psychometric information about a revised version of one of the most used questionnaires to assess pain beliefs. The evidence presented will be helpful to researchers who want to study the role that pain beliefs play in adjustment to chronic pain in young people.
Co-occurrence of mylodontid sloths and insights on their potential distributions during the late Pleistocene
Authors: Varela Luciano , Fariña Richard A.
Published: January 2016

Species distribution models (SDMs) for the last interglacial (LIG), the global last glacial maximum (LGM) and the Holocene climatic optimum (HCO) were generated for three extinct South American Pleistocene mylodontid giant sloths,Glossotherium robustum,Lestodon armatusandMylodon darwinii. They are recorded co-occurring in some localities including Arroyo del Vizcaíno site (AdV) in Uruguay. Co-occurrence records were studied based on the overlap of their generated areas of potential distributions, and compared with the available biome reconstructions of South America during the LGM to analyze their distribution patterns, ecological requirements and possible interactions between them. Our results suggest that these sloths could have co-existed mainly in the Chaco-Paraná Basin and the plains in the Río de la Plata area. Areas of high suitability were observed for submerged parts of the continental shelf that were exposed during the LGM showing an overall increase in potential habitat compared to the LIG and HCO. This suggests that there was a drastic reduction in total available areas of preferred habitat at the end of the Pleistocene. The co-occurrence of these sloths at the AdV site suggests the presence of vegetation indicative of mainly open, cold to temperate habitats but with mixed patches typical of humid climates.
On the Kapitza instability and the generation of capillary waves
Authors: Dietze Georg F.
Published: January 2016

We revisit the classical problem of a liquid film falling along a vertical wall due to the action of gravity, i.e. the Kapitza paradigm (Kapitza,Zh. Eksp. Teor. Fiz., vol. 18, 1948, pp. 3–28). The free surface of such a flow is typically deformed into a train of solitary pulses that consists of large asymmetric wave humps preceded by small precursory ripples, designated as ‘capillary waves’. We set out to answer four fundamental questions. (i) By what mechanism do the precursory ripples form? (ii) How can they travel at the same celerity as the large-amplitude main humps? (iii) Why are they designated as ‘capillary waves’? (iv) What determines their wavelength and number and why do they attenuate in space? Asymptotic expansion as well as direct numerical simulations and calculations with a low-dimensional integral boundary-layer model have yielded the following conclusions. (i) Precursory ripples form due to an inertia-based mechanism at the foot of the leading front of the main humps, where the local free-surface curvature is large. (ii) The celerity of capillary waves is matched to that of the large humps due to the action of surface tension, which speeds up the former and slows down the latter. (iii) They are justly designated as ‘capillary waves’ because their wavelength is systematically shorter than the visco-capillary cutoff wavelength of the Kapitza instability. Due to a nonlinear effect, namely that their celerity decreases with decreasing amplitude, they nonetheless attain/maintain a finite amplitude because of being continuously compressed by the pursuing large humps. (iv) The number and degree of compression of capillary waves is governed by the amplitude of the main wave humps as well as the Kapitza number. Large-amplitude main humps travel fast and strongly compress the capillary waves in order for these to speed up sufficiently. Also, the more pronounced the first capillary wave becomes, the more (spatially attenuating) capillary waves are needed to allow a smooth transition to the back of the next main hump. These effects are amplified by decreasing the Kapitza number, whereby, at very small values, streamwise viscous diffusion increasingly attenuates the amplitude of the capillary waves.
Combined use of real-time PCR and nested sequence-based typing in survey of humanLegionellainfection
Authors: QIN T. , ZHOU H. , REN H. , SHI W. , JIN H. , JIANG X. , XU Y. , ZHOU M. , LI J. , WANG J. , SHAO Z. , XU X.
Published: January 2016

Legionnaires’ disease (LD) is a globally distributed systemic infectious disease. The burden of LD in many regions is still unclear, especially in Asian countries including China. A survey ofLegionellainfection using real-time PCR and nested sequence-based typing (SBT) was performed in two hospitals in Shanghai, China. A total of 265 bronchoalveolar lavage fluid (BALF) specimens were collected from hospital A between January 2012 and December 2013, and 359 sputum specimens were collected from hospital B throughout 2012. A total of 71 specimens were positive forLegionellaaccording to real-time PCR focusing on the 5S rRNA gene. Seventy of these specimens were identified asLegionella pneumophilaas a result of real-time PCR amplification of thedotA gene. Results of nested SBT revealed high genetic polymorphism in theseL. pneumophilaand ST1 was the predominant sequence type. These data revealed that the burden of LD in China is much greater than that recognized previously, and real-time PCR may be a suitable monitoring technology for LD in large sample surveys in regions lacking the economic and technical resources to perform other methods, such as urinary antigen tests and culture methods.
Genetic diversity and population structure of core watermelon (Citrullus lanatus) genotypes using DArTseq-based SNPs
Authors: Yang Xingping , Ren Runsheng , Ray Rumiana , Xu Jinhua , Li Pingfang , Zhang Man , Liu Guang , Yao Xiefeng , Kilian Andrzej
Published: January 2016

Watermelon [Citrullus lanatus(Thunb.) Matsum. & Nakai var.lanatus] is an economically important vegetable belonging to theCucurbitaceaefamily. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.
Nearing the cold-arid limits of microbial life in permafrost of an upper dry valley, Antarctica
Authors: Goordial Jacqueline , Davila Alfonso , Lacelle Denis , Pollard Wayne , Marinova Margarita M , Greer Charles W , DiRuggiero Jocelyn , McKay Christopher P , Whyte Lyle G
Published: January 2016

Some of the coldest and driest permafrost soils on Earth are located in the high-elevation McMurdo Dry Valleys (MDVs) of Antarctica, but little is known about the permafrost microbial communities other than that microorganisms are present in these valleys. Here, we describe the microbiology and habitable conditions of highly unique dry and ice-cemented permafrost in University Valley, one of the coldest and driest regions in the MDVs (1700 m above sea level; mean temperature −23 °C; no degree days above freezing), where the ice in permafrost originates from vapour deposition rather than liquid water. We found that culturable and total microbial biomass in University Valley was extremely low, and microbial activity under ambient conditions was undetectable. Our results contrast with reports from the lower-elevation Dry Valleys and Arctic permafrost soils where active microbial populations are found, suggesting that the combination of severe cold, aridity, oligotrophy of University Valley permafrost soils severely limit microbial activity and survival.
4π-periodic Josephson supercurrent in HgTe-based topological Josephson junctions
Authors: Wiedenmann J. , Bocquillon E. , Deacon R. S. , Hartinger S. , Herrmann O. , Klapwijk T. M. , Maier L. , Ames C. , Brüne C. , Gould C. , Oiwa A. , Ishibashi K. , Tarucha S. , Buhmann H. , Molenkamp L. W.
Published: January 2016

The Josephson effect describes the generic appearance of a supercurrent in a weak link between two superconductors. Its exact physical nature deeply influences the properties of the supercurrent. In recent years, considerable efforts have focused on the coupling of superconductors to the surface states of a three-dimensional topological insulator. In such a material, an unconventional induced p-wave superconductivity should occur, with a doublet of topologically protected gapless Andreev bound states, whose energies vary 4π-periodically with the superconducting phase difference across the junction. In this article, we report the observation of an anomalous response to rf irradiation in a Josephson junction made of a HgTe weak link. The response is understood as due to a 4π-periodic contribution to the supercurrent, and its amplitude is compatible with the expected contribution of a gapless Andreev doublet. Our work opens the way to more elaborate experiments to investigate the induced superconductivity in a three-dimensional insulator.
Manipulating Majorana zero modes on atomic rings with an external magnetic field
Authors: Li Jian , Neupert Titus , Bernevig B. Andrei , Yazdani Ali
Published: January 2016

Non-Abelian quasiparticles have been predicted to exist in a variety of condensed matter systems. Their defining property is that an adiabatic braid between two of them results in a non-trivial change of the quantum state of the system. The simplest non-Abelian quasiparticles—the Majorana bound states—can occur in one-dimensional electronic nano-structures proximity-coupled to a bulk superconductor. Here we propose a set-up, based on chains of magnetic adatoms on the surface of a thin-film superconductor, in which the control over an externally applied magnetic field suffices to create and manipulate Majorana bound states. We consider specifically rings of adatoms and show that they allow for the creation, annihilation, adiabatic motion and braiding of pairs of Majorana bound states by varying the magnitude and orientation of the external magnetic field.
Peptides in headlock – a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy
Authors: Braun Michael B. , Traenkle Bjoern , Koch Philipp A. , Emele Felix , Weiss Frederik , Poetz Oliver , Stehle Thilo , Rothbauer Ulrich
Published: January 2016

Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a β-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once bound, the peptide is fastened by two nanobody side chains that clamp it in a headlock fashion. Exploiting this unusual binding mode, we generated a novel nanobody-derived capture and detection system. Matrix-coupled nanobody enables the fast and efficient isolation of epitope-tagged proteins from prokaryotic and eukaryotic expression systems. Additionally, the fluorescently labeled nanobody visualizes subcellular structures in different cellular compartments. The high-affinity-binding and modifiable peptide tag of this system renders it a versatile and robust tool to combine biochemical analysis with microscopic studies.
Tuning and Freezing Disorder in Photonic Crystals using Percolation Lithography
Authors: Burgess Ian B. , Abedzadeh Navid , Kay Theresa M. , Shneidman Anna V. , Cranshaw Derek J. , Lončar Marko , Aizenberg Joanna
Published: January 2016

Although common in biological systems, synthetic self-assembly routes to complex 3D photonic structures with tailored degrees of disorder remain elusive. Here we show how liquids can be used to finely control disorder in porous 3D photonic crystals, leading to complex and hierarchical geometries. In these optofluidic crystals, dynamically tunable disorder is superimposed onto the periodic optical structure through partial wetting or evaporation. In both cases, macroscopic symmetry breaking is driven by subtle sub-wavelength variations in the pore geometry. These variations direct site-selective infiltration of liquids through capillary interactions. Incorporating cross-linkable resins into our liquids, we developed methods to freeze in place the filling patterns at arbitrary degrees of partial wetting and intermediate stages of drying. These percolation lithography techniques produced permanent photonic structures with adjustable disorder. By coupling strong changes in optical properties to subtle differences in fluid behavior, optofluidic crystals may also prove useful in rapid analysis of liquids.
Tyrannosaurs as long-lived species
Authors: Weon Byung Mook
Published: January 2016

Biodemographic analysis would be essential to understand population ecology and aging of tyrannosaurs. Here we address a methodology that quantifies tyrannosaur survival and mortality curves by utilizing modified stretched exponential survival functions. Our analysis clearly shows that mortality patterns for tyrannosaurs are seemingly analogous to those for 18th-century humans. This result suggests that tyrannosaurs would live long to undergo aging before maximum lifespans, while their longevity strategy is more alike to big birds rather than 18th-century humans.
Different human vaccine adjuvants promote distinct antigen-independent immunological signatures tailored to different pathogens
Authors: Knudsen Niels Peter H. , Olsen Anja , Buonsanti Cecilia , Follmann Frank , Zhang Yuan , Coler Rhea N. , Fox Christopher B. , Meinke Andreas , D´Oro Ugo , Casini Daniele , Bonci Alessandra , Billeskov Rolf , De Gregorio Ennio , Rappuoli Rino , Harandi Ali M. , Andersen Peter , Agger Else Marie
Published: January 2016

The majority of vaccine candidates in clinical development are highly purified proteins and peptides relying on adjuvants to enhance and/or direct immune responses. Despite the acknowledged need for novel adjuvants, there are still very few adjuvants in licensed human vaccines. A vast number of adjuvants have been tested pre-clinically using different experimental conditions, rendering it impossible to directly compare their activity. We performed a head-to-head comparison of five different adjuvants Alum, MF59®, GLA-SE, IC31® and CAF01 in mice and combined these with antigens from M. tuberculosis, influenza and chlamydia to test immune-profiles and efficacy in infection models using standardized protocols. Regardless of antigen, each adjuvant had a unique immunological signature suggesting that the adjuvants have potential for different disease targets. Alum increased antibody titers; MF59® induced strong antibody and IL-5 responses; GLA-SE induced antibodies and Th1; CAF01 showed a mixed Th1/Th17 profile and IC31® induced strong Th1 responses. MF59® and GLA-SE were strong inducers of influenza HI titers while CAF01, GLA-SE and IC31® enhanced protection to TB and chlamydia. Importantly, this is the first extensive attempt to categorize clinical-grade adjuvants based on their immune profiles and protective efficacy to inform a rational development of next generation vaccines for human use.
Homeodomain-Interacting Protein Kinase (HPK-1) regulates stress responses and ageing in C. elegans
Authors: Berber Slavica , Wood Mallory , Llamosas Estelle , Thaivalappil Priya , Lee Karen , Liao Bing Mana , Chew Yee Lian , Rhodes Aaron , Yucel Duygu , Crossley Merlin , Nicholas Hannah R
Published: January 2016

Proteins of the Homeodomain-Interacting Protein Kinase (HIPK) family regulate an array of processes in mammalian systems, such as the DNA damage response, cellular proliferation and apoptosis. The nematodeCaenorhabditis eleganshas a single HIPK homologue called HPK-1. Previous studies have implicated HPK-1 in longevity control and suggested that this protein may be regulated in a stress-dependent manner. Here we set out to expand these observations by investigating the role of HPK-1 in longevity and in the response to heat and oxidative stress. We find that levels of HPK-1 are regulated by heat stress and that HPK-1 contributes to survival following heat or oxidative stress. Additionally, we show that HPK-1 is required for normal longevity, with loss of HPK-1 function leading to a faster decline of physiological processes that reflect premature ageing. Through microarray analysis, we have found that HPK-1-regulated genes include those encoding proteins that serve important functions in stress responses such as Phase I and Phase II detoxification enzymes. Consistent with a role in longevity assurance, HPK-1 also regulates the expression of age-regulated genes. Lastly, we show that HPK-1 functions in the same pathway as DAF-16 to regulate longevity and reveal a new role for HPK-1 in development.
H2AX deficiency is associated with erythroid dysplasia and compromised haematopoietic stem cell function
Authors: Zhao Baobing , Tan Timothy L. , Mei Yang , Yang Jing , Yu Yiting , Verma Amit , Liang Ying , Gao Juehua , Ji Peng
Published: January 2016

Myelodysplastic syndromes (MDS) are clonal disorders of haematopoiesis characterised by dysplastic changes of major myeloid cell lines. However, the mechanisms underlying these dysplastic changes are poorly understood. Here, we used a genetically modified mouse model and human patient data to examine the physiological roles of H2AX in haematopoiesis and how the loss of H2AX contributes to dyserythropoiesis in MDS. H2AX knockout mice showed cell-autonomous anaemia and erythroid dysplasia, mimicking dyserythropoiesis in MDS. Also, dyserythropoiesis was increased in MDS patients with the deletion of chromosome 11q23, where H2AX is located. Although loss of H2AX did not affect the early stage of terminal erythropoiesis, enucleation was decreased. H2AX deficiency also led to the loss of quiescence of hematopoietic stem and progenitor cells, which dramatically compromised their bone marrow engraftment. These results reveal important roles of H2AX in late-stage terminal erythropoiesis and hematopoietic stem cell function.
Revealing the Dynamics of Thylakoid Membranes in Living Cyanobacterial Cells
Authors: Stingaciu Laura-Roxana , O’Neill Hugh , Liberton Michelle , Urban Volker S. , Pakrasi Himadri B. , Ohl Michael
Published: January 2016

Cyanobacteria are photosynthetic prokaryotes that make major contributions to the production of the oxygen in the Earth atmosphere. The photosynthetic machinery in cyanobacterial cells is housed in flattened membrane structures called thylakoids. The structural organization of cyanobacterial cells and the arrangement of the thylakoid membranes in response to environmental conditions have been widely investigated. However, there is limited knowledge about the internal dynamics of these membranes in terms of their flexibility and motion during the photosynthetic process. We present a direct observation of thylakoid membrane undulatory motion in vivo and show a connection between membrane mobility and photosynthetic activity. High-resolution inelastic neutron scattering experiments on the cyanobacterium Synechocystis sp. PCC 6803 assessed the flexibility of cyanobacterial thylakoid membrane sheets and the dependence of the membranes on illumination conditions. We observed softer thylakoid membranes in the dark that have three-to four fold excess mobility compared to membranes under high light conditions. Our analysis indicates that electron transfer between photosynthetic reaction centers and the associated electrochemical proton gradient across the thylakoid membrane result in a significant driving force for excess membrane dynamics. These observations provide a deeper understanding of the relationship between photosynthesis and cellular architecture.
Dual strain mechanisms in a lead-free morphotropic phase boundary ferroelectric
Authors: Walker Julian , Simons Hugh , Alikin Denis O. , Turygin Anton P. , Shur Vladimir Y. , Kholkin Andrei L. , Ursic Hana , Bencan Andreja , Malic Barbara , Nagarajan Valanoor , Rojac Tadej
Published: January 2016

Electromechanical properties such as d33 and strain are significantly enhanced at morphotropic phase boundaries (MPBs) between two or more different crystal structures. Many actuators, sensors and MEMS devices are therefore systems with MPBs, usually between polar phases in lead (Pb)-based ferroelectric ceramics. In the search for Pb-free alternatives, systems with MPBs between polar and non-polar phases have recently been theorized as having great promise. While such an MPB was identified in rare-earth (RE) modified bismuth ferrite (BFO) thin films, synthesis challenges have prevented its realization in ceramics. Overcoming these, we demonstrate a comparable electromechanical response to Pb-based materials at the polar-to-non-polar MPB in Sm modified BFO. This arises from ‘dual’ strain mechanisms: ferroelectric/ferroelastic switching and a previously unreported electric-field induced transition of an anti-polar intermediate phase. We show that intermediate phases play an important role in the macroscopic strain response and may have potential to enhance electromechanical properties at polar-to-non-polar MPBs.
Vocal complexity influences female responses to gelada male calls
Authors: Gustison Morgan L. , Bergman Thore J.
Published: January 2016

Extensive research indicates that inter-sexual selection drives the evolution of complex vocal communication in birds, but parallel lines of evidence are almost entirely absent in mammals. This dearth of evidence, particularly among primates, limits our understanding of the link between sociality and vocal complexity. Here, we use a playback experiment to quantify how wild female geladas (Theropithecus gelada) respond to three call types that are ‘derived’ (i.e., unique to geladas) and made by males during various affiliative contexts. These derived calls appeared to be highly salient and preferable to females: they looked longer towards and spent more time in proximity to playbacks of male vocal sequences containing one of the derived calls than to sequences containing only common and less elaborate ‘grunt’ calls. Our results provide the first experimental evidence for vocal elaboration as a male-specific strategy to maintain social bonds with females in non-human primates.