bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of prostate size on the perioperative and postoperative outcome of transurethral plasmakinetic enucleation of the prostate: Results of 892 patients with 3 years of follow‐up
Authors: Chen Shu‐Shang , Lin Mei‐Jiao , Weng Ming‐Fang , Zhu Ling‐Feng , Deng Zhen , Wu Cheng‐Yao , Cai Jin‐Quan , Wu Wei‐Zhen , Tan Jian‐Ming
Published: March 2018

To explore the influence of prostate size on the outcome of Plasmakinetic enucleation of the prostate (PkEP) for the treatment of benign prostate hyperplasia (BPH), The data of 892 patients with symptomatic BPH who underwent PkEP were retrospectively reviewed. Among them, 199 (22.31%) had the prostate size smaller than 40 g (Group 1), 409 (45.85%) between 40 and 79 g (Group 2), 197 (22.09%) between 80 and 120 g (Group 3), and 87 (9.75%) larger than 120 g (Group 4). Perioperative variables, perioperative and postoperative complications were recorded. Patients were followed up for 36 months postoperatively. The efficiency of the surgery increased as the prostate size increased. Greater decreases in hemoglobin were noted in groups with larger prostates, while the duration of catheterization after the operation was similar across all groups. During the 3‐year follow‐up, the postoperative improvement in International Prostate Symptom Score (IPSS), Quality of Life (QOL), maximal flow rate (Qmax) and post‐void residual urine volume (PVR), as well as longterm complications including urethral stricture and bladder‐neck contracture were comparable across the 4 groups. These findings revealed that PkEP is more efficient for large prostate and can treat all prostates regardless of the size with equivalent symptom relief and micturition improvement.
The creep behavior of a disk superalloy under different stress conditions
Authors: Jia Chonglin , Li Yang , Zhang Fenglin , Lv Shaomin
Published: March 2018

Throughout this project, a candidate nickel-based turbine disk superalloy was prepared by spray forming process. After creep testing, samples were carried out at 705 °C/750 MPa, 705 °C/793 MPa and 705 °C/897 MPa. The microstructure and creep properties of the alloy were investigated using transmission electron microscope (TEM). The results show that the creep rate of the alloy was improved and the creep life decreased significantly when the stress increased from 750 MPa to 793 MPa and 897 MPa. According to the result, the alloy has high stress index. Furthermore, when the stress was as relatively low as 750 MPa or 793 MPa, the creep mechanism of the alloy was dislocation shearing into γ′ phases; when the stress was as high as 897 MPa, the creep mechanism was stacking faults and micro-twins cutting γ′ phases. Under different stress conditions, the tertiary creep has a significant impact on the total deformation quantity and creep life of the alloy and the rafting of γ′ phase is the main reason of the creep acceleration. With the increasing applied stress, rafting of γ′ phase becomes obvious and it accelerates the tertiary creep deformation but reduces the creep properties of the alloy.
Challenging aspects of contemporary cochlear implant electrode array design
Authors: Mistrík Pavel , Jolly Claude , Sieber Daniel , Hochmair Ingeborg
Published: March 2018

Objective

A design comparison of current perimodiolar and lateral wall electrode arrays of the cochlear implant (CI) is provided. The focus is on functional features such as acoustic frequency coverage and tonotopic mapping, battery consumption and dynamic range. A traumacity of their insertion is also evaluated.

Methods

Review of up‐to‐date literature.

Results

Perimodiolar electrode arrays are positioned in the basal turn of the cochlea near the modiolus. They are designed to initiate the action potential in the proximity to the neural soma located in spiral ganglion. On the other hand, lateral wall electrode arrays can be inserted deeper inside the cochlea, as they are located along the lateral wall and such insertion trajectory is less traumatic. This class of arrays targets primarily surviving neural peripheral processes. Due to their larger insertion depth, lateral wall arrays can deliver lower acoustic frequencies in manner better corresponding to cochlear tonotopicity. In fact, spiral ganglion sections containing auditory nerve fibres tuned to low acoustic frequencies are located deeper than 1 and half turn inside the cochlea. For this reason, a significant frequency mismatch might be occurring for apical electrodes in perimodiolar arrays, detrimental to speech perception. Tonal languages such as Mandarin might be therefore better treated with lateral wall arrays. On the other hand, closer proximity to target tissue results in lower psychophysical threshold levels for perimodiolar arrays. However, the maximal comfort level is also lower, paradoxically resulting in narrower dynamic range than that of lateral wall arrays. Battery consumption is comparable for both types of arrays.

Conclusions

Lateral wall arrays are less likely to cause trauma to cochlear structures. As the current trend in cochlear implantation is the maximal protection of residual acoustic hearing, the lateral wall arrays seem more suitable for hearing preservation CI surgeries. Future development could focus on combining the advantages of both types: perimodiolar location in the basal turn extended to lateral wall location for higher turn locations.
Fabrication of paper-based analytical devices optimized by central composite design
Authors: Hamedpour Vahid , Leardi Riccardo , Suzuki Koji , Citterio Daniel
Published: March 2018

In this work, an application of a design of experiments approach for the optimization of an isoniazid assay on a single-area inkjet-printed paper-based analytical device (PAD) is described.
Three-dimensional nitrogen-doped porous carbon anchored CeO2 quantum dots as an efficient catalyst for formaldehyde oxidation
Authors: Luo Dong , Chen Bingbing , Li Xingyun , Liu Zaojin , Liu Xiaowei , Liu Xuehua , Shi Chuan , Zhao Xiu Song
Published: March 2018

A unique 3D structured composite composed of CeO2 quantum dots and CN is successfully constructed by a novel synthesis procedure to serve as an efficient HCHO oxidation catalyst.
Therapeutic nanosystems co-deliver anticancer drugs and oncogene SiRNA to achieve synergetic precise cancer chemo-gene therapy
Authors: Huang Wei , Liang Yuanwei , Sang Chengcheng , Mei Chaoming , Li Xiaoling , Chen Tianfeng
Published: March 2018

Herein we design a therapeutic nanoplatform as carriers of oncogene siRNA and chemotherapeutics to achieve precise cancer therapy.
Simultaneous hydrothermal bioactivation with nano-topographic modulation of porous titanium alloys towards enhanced osteogenic and antimicrobial responses
Authors: Kapat Kausik , Maity Priti Prasanna , Rameshbabu Arun Prabhu , Srivas Pavan Kumar , Majumdar Pallab , Dhara Santanu
Published: March 2018

Post-implantation failure associated with insufficient host tissue integration at the bone–implant interface and aseptic loosening is a major concern in orthopaedics as well as in dentistry.
Identification of activity peaks in time-tagged data with a scan-statistics driven clustering method and its application to gamma-ray data samples
Authors: Pacciani Luigi
Published: March 2018

Context.The investigation of activity periods in time-tagged data samples is a topic of great interest. Among astrophysical samples, gamma-ray sources are widely studied, due to the huge quasi-continuum data set available today fromFermi-LAT (FermiLarge Area Telescope) and the AGILE-GRID (Astro Rivelatore Gamma a Immagini LEggero-Gamma Ray Imaging Detector)

Aims.To reveal flaring episodes of a given gamma-ray source, researchers make use of binned light curves. This method suffers from several drawbacks: the results depend on time-binning and the identification of activity periods is difficult for bins with a low signal-to-noise ratio. A different approach is investigated in this paper.

Methods.We developed a general temporal-unbinned method to identify flaring periods in time-tagged data and discriminate statistically significant flares. We propose an event clustering method in one dimension to identify flaring episodes, and scan statistics to evaluate the flare significance within the whole data sample. This is a photometric algorithm. The comparison of the photometric results (e.g. photometric flux, gamma-ray spatial distribution) for the identified peaks with the standard likelihood analysis for the same period is mandatory to establish if source confusion is spoiling results.

Results.The procedure can be applied to reveal flares in any time-tagged data sample. The result of the proposed method is similar to a photometric light curve, but peaks are resolved, they are statistically significant within the whole period of investigation, and peak detection capability does not suffer time-binning related issues. The study of the gamma ray activity of 3C 454.3 and of the fast variability of the Crab Nebula are shown as examples. The method can be applied for gamma-ray sources of known celestial position, for example, sources taken from a catalogue. Furthermore the method can be used when it is necessary to assess the statistical significance within the whole period of investigation of a flare from an unknown gamma-ray source. Extensive results based on this analysis method for some astrophysical problems are the subject of a forthcoming paper.
Preparation and properties of W-SiC/Cu composites by tape casting and hot-pressing sintering
Authors: Zhang Chengcheng , Zhang Jian , Luo Guoqiang , Liu Yao , Shen Qiang , Zhang Lianmeng
Published: March 2018

In this study, W-SiC/Cu composites were prepared by tape casting and vacuum hot-pressing sintering. The microstructures and properties of the composites were studied by means of X-ray diffraction, X-ray photoelectron spectroscopy, field emission scanning electron microscopy, Vickers hardness test, bending strength test and coefficient of thermal expansion (CTE) test. The results showed that W2C, WC and WSi2 formed in the composites. The effects of SiC particle size on the relative densities, Vickers hardness, bending strength and CTE of composites were investigated. Vickers hardness, bending strength and CTE of the composite with SiC particle size of 6 µm reached the optimal values, which were 445.2 HV, 726.1 MPa, 9.24 ppm K−1.
Joint inhomogeneity in dissimilar friction stir welded martensitic and nanostructured ferritic steels
Authors: Han Wentuo , Wan Farong , Yabuuchi Kiyohiro , Serizawa Hisashi , Kimura Akihiko
Published: March 2018

Dissimilar welding between oxide dispersion strengthened ferritic (ODS) steel and reduced activation martensitic steel would be required for constructing the advanced blanket of progressive fusion reactors. In this study, we achieved dissimilar joints by friction stir welding, and aimed to characterise and ameliorate joint inhomogeneity. Main results reveal that the joint inhomogeneity is generated from discrepant microstructural evolutions within the martensitic and ODS ferritic steels. The ODS steel achieves evolution by the dynamic recrystallisation, while the martensitic steel undergoes phase transformation that drastically hardens the stir zone. By a proper post-weld heat treatment, the joint inhomogeneity can be effectively ameliorated due to carbide reprecipitation and stress relief in the joint.
Management of a Previously Coiled Anterior Cerebral Artery Aneurysm in a Child: 3-Dimensional Operative Video
Authors: Agarwal Vijay , Barrow Daniel L
Published: March 2018

We present the case of an 11-yr-old male who originally presented to an outside hospital with subarachnoid hemorrhage. He was discovered at that time to have a ruptured right A1-A2 junction anterior cerebral artery aneurysm just proximal to the anterior communicating artery. He underwent endovascular coiling at the outside center. While recovering at a rehabilitation center, he had a rehemorrhage and acute neurological decline. He was transferred to our service, where he underwent surgical exploration and clip reconstruction of what appeared to be a pseudoaneurysm. After a frontotemporal exposure, the right A1 segment was identified at the carotid bifurcation and followed medially. The aneurysm was significantly larger than on the original angiogram and the wall of the aneurysm was extraordinarily thin, consistent with a pseudoaneurysm. A small portion of the gyrus rectus was removed to expose the A2 segments and the remainder of the large, partially thrombosed and coiled sac of the aneurysm. Thrombus and the previously placed coils were removed in a piecemeal fashion. Two fenestrated clips were used to reconstruct the right A1, with the blades used to bring together normal tissue on the ventral surface to create a new lumen. A Doppler ultrasound was used to insunate both A1s and A2s to confirm patency. Intraoperative cerebral angiogram showed complete obliteration of the aneurysm and excellent reconstruction of the anterior cerebral complex.

The patient did very well and was neurologically intact on discharge.

All appropriate patient consents were obtained for this submission.
Microsurgical Resection of a Large Intraventricular Trigonal Tumor: 3-Dimensional Operative Video
Authors: Cheng Chun-Yu , Shetty Rakshith , Sekhar Laligam N
Published: March 2018

A 62-yr-old woman presented with incidentally detected left trigonal mass by magnetic resonance imaging (MRI) performed during workup for left-sided hearing loss and vertigo of 5-yr duration. Due to persistent dizziness, headache, and progressive enlargement of the tumor in follow-up scans, operation was planned. Because the tumor extended superiorly, a superior parietal lobule approach was selected.

She underwent a left parietal craniotomy. A strip electrode was used to localize the motor and sensory regions, and neuronavigation was used to confirm the entry site. A small transsulcal corticotomy was performed posterior to a large cortical vein. The tumor was pinkish in color with a well-defined capsule. It was centrally debulked by using curettes, pituitary forceps, and the ultrasonic aspirator. Tumoral blood supply from the choroid plexus and the posterior choroidal vessels were cauterized and divided. Additional blood supply coming from the anterior choroidal vessels was also found and cauterized. After circumferential dissection of the tumor capsule, the tumor was removed completely. The pathology indicated WHO Grade I meningioma. The patient had mild expressive and receptive aphasia postoperatively, but improved progressively. The postoperative MRI showed total resection with no evidence of brain injury. At 3-mo follow-up, the speech was normal; she was independent for all daily activities, but had not yet returned to work (Karnofsky score 80).

This 3-D video shows the technical nuances of microsurgical resection of an intraventricular tumor through a narrow brain corridor.

Informed consent was obtained from the patient prior to the surgery that included videotaping of the procedure and its distribution for educational purposes. All relevant patient identifiers have also been removed from the video and accompanying radiology slides.
Sex differences in gene expression in response to ischemia in the human myocardium
Authors: Stone Gregory , Choi Ashley , Oliva Meritxell , Gorham Joshua , Heydarpour Mahyar , Seidman Christine E. , Seidman Jon G. , Aranki Sary F. , Body Simon C. , Carey Vincent J. , Raby Benjamin A. , Stranger Barbara E. , Muehlschlegel Jochen D.
Published: March 2018

Abstract and Keywords

Background

Sex differences exist in the prevalence, presentation, and outcomes of ischemic heart disease. Females have higher risk of heart failure post myocardial infarction relative to males and the female sex is an independent risk factor for hospital and operative mortality after cardiac surgery. However, the mechanisms underlying this sexual dimorphism remain unclear. We examined sex differences in human myocardial gene expression in response to ischemia.

Methods

Left ventricular biopsies from 68 male and 46 female patients undergoing aortic valve replacement surgery were obtained at baseline and after a median 74 minutes of cold cardioplegic arrest/ischemia and respective transcriptomes were quantified by RNA-Seq. Sex-specific responses to ischemia were quantified by differential gene expression, expression quantitative trait loci (eQTL) and pathway and functional analysis. Cell-type enrichment analysis. was used to obtain an estimate of the identity and relative proportions of different cell types present in each sample.

Results

A sex-specific response to ischemia was observed for 271 genes. Functional annotation analysis revealed sex-specific modulation of the oxytocin signaling pathway and common pathway of fibrin clot formation. The eQTL analysis identified variant-by-sex interaction eQTLs at baseline and post-ischemia, indicative of sex differences in the genotypic effects on gene expression, and cell-type enrichment analysis showed sex-bias in proportion of specific cell types.

Conclusion

In response to myocardial ischemia, the human left ventricle demonstrates changes in gene expression that differ between the sexes. These differences provide insight into the sexual dimorphism of ischemic heart disease and may aid in the development of sex-specific therapies that reduce myocardial injury.
Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots
Authors: Dashti A. , Shekhar M.S. , Hail D. Ben , Mashayekhi G. , Schwander P. , Georges A. des , Frank J. , Singharoy A. , Ourmazd A.
Published: March 2018

We present a new approach to determining the conformational changes associated with biological function, and demonstrate its capabilities in the context of experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca2+-channel involved in skeletal muscle excitation/contraction coupling. These results include the detailed conformational motions associated with functional paths including transitions between energy landscapes. The functional motions differ substantially from those inferred from discrete structures, shedding new light on the gating mechanism in RyR1. The differences include the conformationally active structural domains, the nature, sequence, and extent of conformational motions involved in function, and the way allosteric signals are transduced within and between domains. The approach is general, and applicable to a wide range of systems and processes.
Endogenous miRNA sponges mediate the generation of oscillatory dynamics for a non-coding RNA network
Authors: Dhawan Andrew , Harris Adrian L. , Buffa Francesca M. , Scott Jacob G.
Published: March 2018

Oscillations are crucial to the sustenance of living organisms, across a wide variety of biological processes. In eukaryotes, oscillatory dynamics are thought to arise from interactions at the protein and RNA levels; however, the role of non-coding RNA in regulating these dynamics remains understudied. In this work, using a mathematical model, we show how non-coding RNA acting as microRNA (miRNA) sponges in a conserved miRNA - transcription factor feedback motif, can give rise to oscillatory behaviour. Control of these non-coding RNA can dynamically create oscillations or stability, and we show how this behaviour predisposes to oscillations in the stochastic limit. These results, supported by emerging evidence for the role of miRNA sponges in development, point towards key roles of different species of miRNA sponges, such as circular RNA, potentially in the maintenance of yet unexplained oscillatory behaviour. These results help to provide a paradigm for understanding functional differences between the many redundant, but distinct RNA species thought to act as miRNA sponges in nature, such as long non-coding RNA, pseudogenes, competing mRNA, circular RNA, and 3’ UTRs.

Author summary

We analyze the effects of a newly discovered species of non-coding RNA, acting as microRNA (miRNA) sponges, on intracellular signalling dynamics. We show that oscillatory behaviour can arise in a time-varying manner in an over-represented transcriptional feedback network. These results point towards novel hypotheses for the roles of different species of miRNA sponges, such as their increasingly understood role in neural development.
Chemotaxis model for human breast cancer cells based on signal-to-noise ratio
Authors: Lim S. , Nam H. , Jeon J.S.
Published: March 2018

Chemotaxis, a biased migration of cells under a chemical gradient, plays a significant role in diverse biological phenomena including cancer metastasis. Stromal cells release signaling proteins to induce chemotaxis, which further causes organ-specific metastasis. Epidermal growth factor (EGF) is an example of the chemical attractants, and its gradient stimulates metastasis of breast cancer cells. Hence, the interactions between EGF and breast cancer cells have long been a subject of interest for oncologists and clinicians. However, most current approaches do not systematically separate the effects of gradient and absolute concentration of EGF on chemotaxis of breast cancer cells. In this work, we develop a theoretical model based on signal-to-noise ratio to represent stochastic properties and report our microfluidic experiments to verify the analytical predictions from the model. The results demonstrate that even under the same EGF concentration gradients, breast cancer cells can reveal distinct chemotaxis patterns at different absolute concentrations. Moreover, we found that addition of EGF receptor antibody can promote chemotaxis at a low EGF level. This apparently counterintuitive finding suggests that EGF receptor-targeted therapy may stimulate metastasis of breast cancer at a particular condition, which should be considered in anticancer drug design.
Dimerization of rhomboid protease RHBDL2 in lipid membranes addressed by FRET with MC simulations
Authors: Škerle J. , Humpolíčková J. , Rampírová P. , Poláchová E. , Adámková L. , Suchánková A. , Jakubec D. , Strisovsky K.
Published: March 2018

Many membrane proteins are thought to function as oligomers, but measuring membrane protein dimerization in native lipid membranes is particularly challenging. Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) are non-invasive, optical methods of choice that have been applied to the analysis of dimerization of single-spanning membrane proteins. The effects inherent to such two-dimensional systems, such as excluded volume of polytopic transmembrane proteins, proximity FRET, and rotational diffusion of fluorophore dipoles, complicate interpretation of FRET data and have not been typically accounted for. Here, using FRET and FCS we introduce methods to measure surface protein density and to estimate kappa squared, and we use Monte Carlo simulations of the FRET data to account for the proximity FRET effect occurring in confined 2D environments. We then use FRET and FCS to analyze the dimerization of human rhomboid protease RHBDL2 in its native lipid membranes. While previous reports have proposed that rhomboid proteases dimerize and this allosterically activates them, we find no evidence for stable oligomers of RHBDL2 in lipid membranes of human cells. This indicates that the rhomboid transmembrane core may be intrinsically monomeric. Finally, our findings will find use in the application of FRET and FCS for the analysis of oligomerization of transmembrane proteins in lipid membranes.
Monitoring Unfolding of Titin I27 single- and bi-Domain with High-Pressure NMR Spectroscopy
Authors: Herrada I. , Barthe P. , Van Heusden M. , DeGuillen K , Mammri L , Delbecq S. , Rico F. , Roumestand C.
Published: March 2018

A complete description of the pathways and mechanisms of protein folding requires a detailed structural and energetic characterization of the folding energy landscape. Simulations, when corroborated by experimental data yielding global information on the folding process, can provide this level of insight. Molecular Dynamics (MD) has been associated often to force spectroscopy experiments to decipher the unfolding mechanism of titin Ig-like single- or multi-domain, the giant multi-modular protein from sarcomere, yielding information on the sequential events during titin unfolding under stretching. Here, we used high-pressure NMR to monitor the unfolding of titin I27 Ig-like single-domain and tandem. Since this method brings residue-specific information on the folding process, it can provide quasi-atomic details on this process, without the help of MD simulations. Globally, the results of our high-pressure analysis are in agreement with previous results obtained by the association of experimental measurements and MD simulation and/or protein engineering, although the intermediate folding state caused by the early detachment of the AB ß-sheet, often reported in previous works based on MD or force spectroscopy, cannot be detected. On the other hand, the A’G parallel ß-sheet of the ß-sandwich has been confirmed as the Achilles heel of the 3D scaffold: its disruption yields complete unfolding, with very similar characteristics (free energy, unfolding volume, kinetics constant rates) for the two constructs.
Plus-end directionality is present in the catalytic core of kinesin-14 minus-end directed motors
Authors: Yamagishi M. , Yajima J.
Published: March 2018

Molecular motors move along microtubules unidirectionally. However, the origin of directionality is not clear. Here kinesin-14 monomers were engineered such that they could be anchored via either their N- or C-termini, leaving the opposite terminal regions mechanically disconnected from the surface. We find that the conserved catalytic motor core of kinesin-14 has intrinsic plus-end directionality and that the proper function of the neck-helix region is required to achieve minus-end directionality.
Beta diversity patterns derived from island biogeography theory
Authors: Lu Muyang , Vasseur David , Jetz Walter
Published: March 2018

The Theory of Island Biogeography (TIB) has been successful in predicting alpha diversity patterns such as species-area relationships and species-abundance distributions. Although beta diversity (i.e. the dissimilarity of community composition) has long been recognized as an important element of the TIB and is crucial for understanding community assembly processes, it has never been formally incorporated into the theory. Here we derive theoretical predictions for the expected pairwise beta diversity values under a species-level neutral scenario where all species have equal colonization and extinction rates. We test these predictions for the avian community composition of 42 islands (and 93 species) in the Thousand Island Lake, China. We find that alpha diversity patterns alone do not distinguish a species-level neutral model from a non-neutral model. In contrast, beta diversity patterns clearly reject a species-level neutral model. We suggest that the presented theoretical integration beta diversity offers a powerful path for testing the presence of neutral processes in ecology and biogeography.
Adaptation to local climate in a multi-trait space: evidence from silver fir (Abies albaMill.) populations across a heterogeneous environment
Authors: Csilléry Katalin , Ovaskainen Otso , Sperisen Christoph , Widmer Alex , Gugerli Felix
Published: March 2018

Attempts to identify and understand selection pressures responsible for local adaptation are central to evolutionary research. We tested whether populations of silver fir (Abies albaMill.), sampled across a heterogeneous environment, have more strongly diverged at quantitative traits than expected from genetic drift. We genotyped 387 trees from 19 Swiss populations at 374 single-nucleotide polymorphisms (SNPs) to estimate their demographic distances, and used these to generate a null expectation for divergence in a multi-trait space including morphology and life-history traits obtained from a published common garden trial. Local soil and historical climate data were used to identify the selective environment of the source populations. Our results revealed a strong selection on height driven by temperature: trees from warm sites evolved to become taller than those from cooler sites. The evolution of growth rate, growth duration and bud break were correlated, and populations evolved towards two extreme strategies, “start early and grow slow” or “start late and grow fast”, driven by precipitation seasonality. We conclude that local climate has shaped the morphology and life-history of silver fir populations since they recolonized the Alps. Our methodology provides a show-case for empirical evaluation of adaptive evolutionary strategies combining genetic data and common gardens.
Reductions in Retrieval Competition Predict the Benefit of Repeated Testing
Authors: Rafidi Nicole S. , Hulbert Justin C. , Pacheco Paula , Norman Kenneth A.
Published: March 2018

Repeated testing leads to improved long-term memory retention compared to repeated study, but the mechanism underlying this improvement remains controversial. In this work, we test the hypothesis that retrieval practice benefits subsequent recall by reducing competition from related memories. This hypothesis implies that the degree of reduction in competition between retrieval practice attempts should predict subsequent memory for practiced items. To test this prediction, we collected electroencephalography (EEG) data across two sessions. In the first session, participants practiced selectively retrieving exemplars from superordinate semantic categories (high competition), as well as retrieving the names of the superordinate categories from exemplars (low competition). In the second session, participants repeatedly studied and were tested on Swahili-English vocabulary. One week after session two, participants were again tested on the vocabulary. We trained a within-subject classifier on the data from session one to distinguish high and low competition states.We then used this classifier to measure competition across multiple retrieval practice attempts in the second session. The degree to which competition decreased for a given vocabulary word predicted whether that item was subsequently remembered in the third session. These results are consistent with the hypothesis that repeated testing improves retention by reducing competition.
Peptidoglycan precursor synthesis along the sidewall of pole-growing mycobacteria
Authors: García-Heredia Alam , Pohane Amol Arunrao , Melzer Emily S. , Carr Caleb R. , Fiolek Taylor J. , Rundell Sarah R. , Lim Hoong Chuin , Wagner Jeffrey , Morita Yasu S. , Swarts Benjamin M. , Carr Caleb R. , Siegrist M. Sloan
Published: March 2018

d-amino acid probes label cell wall peptidoglycan at both the poles and sidewall of pole-growing mycobacteria. Since peptidoglycan assembly along the cell periphery could provide a rapid, growth-independent means by which to edit the cell wall, we sought to clarify the precise metabolic fates of these probes.d-amino acid monopeptides were incorporated into peptidoglycan byl,d-transpeptidase remodeling enzymes to varying extents. Dipeptides were incorporated into cytoplasmic precursors. While dipeptide-marked peptidoglycan synthesis at the poles was associated with cell elongation, synthesis along the periphery was highly responsive to cell wall damage. Our observations suggest a post-expansion role for peptidoglycan assembly along the mycobacterial sidewall and provide a conceptual framework for understanding cell wall robustness in the face of polar growth.
Glucocorticoid receptor gene polymorhisms and breast cancer: significant association in cancerous tissue samples from Turkish patients
Authors: Akyildiz Gürkan , Akkіprіk Mustafa , Özer Ayşe , Kaya Handan , Güllüoğlu Bahadіr M. , Aral Cenk
Published: March 2018

Background and Aims: Glucocorticoid receptor (GR) has been postulated to serve an important role in normal breast and breast carcinoma. On the other hand, studies on its common polymorphisms with breast cancer are very limited. In this study, we aimed to assess the presence and frequency of 4 common polymorphisms of the GR gene in the cancerous tissue samples from breast cancer patients in the Turkish population and compare them with healthy individuals. Methods: DNA samples from 86 Turkish female breast cancer patients and 86 healthy controls analysed for BclI, Tth111I, N363S and ER22/23EK polymorphisms of GR gene by PCR-RFLP. Results: N363S polymorphism was not observed in study samples. Frequency of BclI polymorphism did not differ between cases and controls but it associated with family history of cancer. The polymorphic allele frequency of Tth111I and ER22/23EK was found to be higher in cases compared to healthy samples (p<0.05). Also, a haplotype containing polymorphic variants of these two polymorphisms found to be associated with breast cancer. Conclusion: The data presented here suggest that polymorphisms of GR gene may be an important risk factor for breast cancer predisposition.
A unifying framework for summary statistic imputation
Authors: Wu Yue , Eskin Eleazar , Sankararaman Sriram
Published: March 2018

Imputation has been widely utilized to aid and interpret the results of Genome-Wide Association Studies(GWAS). Imputation can increase the power to identify associations when the causal variant was not directly observed or typed in the GWAS. There are two broad classes of methods for imputation. The first class imputes the genotypes at the untyped variants given the genotypes at the typed variants and then performs a statistical test of association at the imputed variants. The second class of methods, summary statistic imputation, directly imputes the association statics at the untyped variants given the association statistics observed at the typed variants. This second class of methods is appealing as it tends to be computationally efficient while only requiring the summary statistics from a study while the former class requires access to individual-level data that can be difficult to obtain. The statistical properties of these two classes of imputation methods have not been fully understood. In this paper, we show that the two classes of imputation methods are equivalent,i.e., have identical asymptotic multivariate normal distributions with zero mean and minor variations in the covariance matrix, under some reasonable assumptions. Using this equivalence, we can understand the effect of imputation methods on power. We show that a commonly employed modification of summary statistic imputation that we term summary statistic imputation with variance re-weighting generally leads to a loss in power. On the other hand, our proposed method, summary statistic imputation without performing variance re-weighting, fully accounts for imputation uncertainty while achieving better power.
Surveillance of CKD epidemiology in the US – a joint analysis of NHANES and KEEP
Authors: Myers OB , Pankratz VS , Norris KC , Vassalotti JA , Unruh M , Argyropoulos C
Published: March 2018

Chronic Kidney Disease (CKD), is highly prevalent in the United States. Epidemiological systems for surveillance of CKD rely on data that are based solely on the NHANES survey, which does not include many patients with the most severe and less frequent forms of CKD. We investigated the feasibility of estimating CKD prevalence from the large-scale community disease detection Kidney Early Evaluation and Program (KEEP, n = 127,149). We adopted methodologies from the field of web surveys to address the self-selection bias inherent in KEEP. Primary outcomes studied were CKD Stage 3-5 (estimated glomerular filtration rate [eGFR] <60 mL/min/1.73m2, and CKD Stage 4-5 (eGFR <30 mL/min/1.73m2). The unweighted prevalence of Stage 4-5 CKD was higher in KEEP (1.00%, 95%CI: 0.94-1.05%) than in NHANES (0.51%, 95% CI: 0.43-0.59%). Application of a selection model with IPW of variables related to demographics, recruitment and socio-economic factors resulted in estimates similar to NHANES (0.55%, 95% CI: 0.50-0.60%). Weighted prevalence of Stages 3-5 CKD in KEEP was 6.45% (95% CI: 5.70 7.28%) compared to 6.73% (95% CI: 6.30-7.19%) for NHANES. Application of methodologies that address the self-selection bias in the KEEP program may allow the use of this large, geographically diverse dataset for CKD surveillance.
Effects of exclusive breastfeeding on infant gut microbiota: a meta-analysis across studies and populations
Authors: Ho Nhan T. , Li Fan , Lee-Sarwar Kathleen A. , Tun Hein M. , Brown Bryan , Pannaraj Pia S. , Bender Jeffrey M. , Azad Meghan B. , Thompson Amanda L. , Weiss Scott T. , Azcarate-Peril M. Andrea , Litonjua Augusto A. , Kozyrskyj Anita L. , Jaspan Heather B. , Aldrovandi Grace M. , Kuhn Louise
Published: March 2018

Literature regarding the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants is meager with large variation in methods and results. We performed a meta-analysis of seven studies (a total of 1825 stool samples from 684 infants) to investigate effects of EBF compared to non-EBF on infant gut microbiota across different populations. In the first 6 months of life, overall bacterial diversity, gut microbiota age, relative abundances of Bacteroidetes and Firmicutes and microbial-predicted pathways related to carbohydrate metabolism were consistently increased; while relative abundances of pathways related to lipid, vitamin metabolism and detoxification were decreased in non-EBF vs. EBF infants. The perturbation in microbial-predicted pathways associated with non-EBF was larger in infants delivered by C-section than delivered vaginally. Longer duration of EBF mitigated diarrhea-associated gut microbiota dysbiosis and the effects of EBF persisted after 6 months of age. These consistent findings across vastly different populations suggest that one of the mechanisms of short and long-term benefits of EBF may be alteration in gut microbes.
Classification of early and late stage Liver Hepatocellular Carcinoma patients from their genomics and epigenomics profiles
Authors: Kaur Harpreet , Bhalla Sherry , Raghava GPS
Published: March 2018

Background

Liver Hepatocellular Carcinoma (LIHC) is the second major cancer worldwide, responsible for millions of premature deaths every year. Prediction of clinical staging is vital to implement optimal therapeutic strategy and prognostic prediction in cancer patients. However, to date, no method has been developed for predicting stage of LIHC from genomic profile of samples.

Results

In current study, in silico models have been developed for classifying LIHC patients in early and late stage using RNA expression and DNA methylation data. The Cancer Genome Atlas (TCGA) dataset contains 173 early and 177 late stage samples of LIHC, was extensively analysed to identify differentially expressed RNA transcripts and methylated CpG sites that can discriminate early and late stages of LIHC samples with high precision. Naive Bayes model developed using 51 features that combine 21 CpG methylation sites and 30 RNA transcripts achieved maximum MCC 0.58 with accuracy 78.87% on validation dataset. Further, we also analysed genomics and epigenomics profiles of normal and LIHC samples and developed model to classify LIHC samples with AUROC 0.99. In addition, multiclass models developed for classifying samples in normal, early and late stage of cancer and achieved accuracy of 76.54% and AUROC of 0.86.

Conclusion

Our study reveals stage prediction of LIHC samples with high accuracy based on genomics and epigenomics profiling is a challenging task in comparison to classification of LIHC and normal samples. Comprehensive analysis, differentially expressed RNA transcripts, methylated CpG sites in LIHC samples and prediction models are available from CancerLSP ( http://webs.iiitd.edu.in/raghava/cancerlsp/).
Complementary responses of morphology and physiology enhance the stand‐scale production of a model invasive species under elevated CO2 and nitrogen
Authors: Mozdzer Thomas J. , Caplan Joshua S.
Published: March 2018

Elevated atmospheric carbon dioxide (eCO2) concentrations and nitrogen (N) enrichment are known to enhance plant productivity and invasion. However, the implications of their interactive effects for plant productivity are not well understood, especially at the stand scale, presumably because morphological and physiological responses to these global change factors are rarely studied together in the field or assessed at the stand level.

We first determined how leaf‐level morphological and physiological traits responded to factorial combinations of ambient and elevated CO2 and N. We collected trait data from the model invasive species Phragmites australis (common reed) that were measured over 3 years in a long‐term global change field experiment. We then combined the trait data and additional descriptions of P. australis canopies in a simulation model of carbon assimilation to determine how morphology and physiology contribute to P. australis’ stand‐scale productivity.

At the leaf level, we found that light‐saturated rates of photosynthesis were strongly stimulated by eCO2 (37%) and that this effect was enhanced by increasing salinity. N had a smaller effect (17% stimulation) on physiological responses than eCO2, but leaf morphological traits responded primarily to N; plant height increased by 27% and leaf area increased by 47%.

Stand‐scale simulations demonstrated that that morphological and physiological adjustments induced approximately additive responses when P. australis experienced both eCO2 and N enrichment. The simulations also indicated that morphological changes (which were primarily associated with canopy size) influenced stand‐scale carbon assimilation more than physiological changes. Moreover, 97% of the N response was due to changes in morphology, whereas 62% of the eCO2 response was caused by physiological shifts.

Our analysis indicates that morphological and physiological trait responses to elevated CO2 and nitrogen are likely to enhance the productivity of P. australis in complementary ways, potentially accelerating its invasion in North America. Furthermore, our data suggest that changes in morphological traits may have a greater influence on carbon gain than leaf‐level physiology under near‐future environmental conditions. Our study also highlights the importance of accounting for both morphological and physiological responses when attempting to infer global change responses from leaf‐level data.

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Variation in home‐field advantage and ability in leaf litter decomposition across successional gradients
Authors: Veen G. F. (Ciska) , Keiser Ashley D. , van der Putten Wim H. , Wardle David A.
Published: March 2018

It is increasingly recognized that interactions between plants and soil (a)biotic conditions can influence local decomposition processes. For example, decomposer communities may become specialized in breaking down litter of plant species that they are associated with, resulting in accelerated decomposition, known as “home‐field advantage” (HFA). Also, soils can vary inherently in their capacity to degrade organic compounds, known as “ability.” However, we have a poor understanding how environmental conditions drive the occurrence of HFA and ability.

Here, we studied how HFA and ability change across three types of successional gradients: coastal sand dunes (primary succession), inland drift sands (primary succession) and ex‐arable fields (secondary succession). Across these gradients, litter quality (i.e. nutrient, carbon and lignin contents) increases with successional time for coastal dunes and decreases for the other two gradients.

We performed a 12‐months reciprocal litter transplant experiment under greenhouse conditions using soils and litters collected from early‐, mid‐ and late‐successional stages of each gradient.

We found that HFA and ability did not consistently shift with successional stage for all gradients, but were instead specific for each type of successional gradient. In coastal dunes, HFA was positive for early‐successional litter, in drift, sands it was negative for mid‐successional litter, and for ex‐arable fields, HFA increased with successional time. Ability of decomposer communities was highest in mid‐successional stages for coastal dunes and drift sands, but for ex‐arable fields, ability decreased throughout with successional time. High HFA was related to high litter C content and soil and organic matter content in soils and to low litter and soil nutrient concentrations. Ability did not consistently occur in successional stages with high or low litter quality.

Synthesis. Our findings show that specific environmental conditions, such as changes in litter or soil quality, along environmental gradients can shape the influence of HFA and ability on decomposition. In sites with strong HFA or ability, interactions between plants, litter and decomposer communities will be important drivers of nutrient cycling and hence have the potential to feedback to plant growth.

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Contrasting plant water‐use responses to groundwater depth in coastal dune ecosystems
Authors: Antunes Cristina , Díaz Barradas Mari Cruz , Zunzunegui Maria , Vieira Simone , Pereira Ângela , Anjos Andreia , Correia Otília , Pereira Maria João , Máguas Cristina
Published: March 2018

Groundwater lowering can produce dramatic changes in the physiological performance and survival of plant species. The impact of decreasing water availability due to climate change and anthropogenic groundwater extraction on coastal dune ecosystems has become of increasing concern, with uncertainties about how vegetation will respond in both the short and long terms.

We aimed to evaluate the water‐use responses of different plant functional types to increasing groundwater table depth and how this would affect their physiology in Mediterranean coastal dune systems differing in aridity.

We modelled water‐table depth, quantified the contribution of different soil layers to plant water through Bayesian isotope mixing models and used a combination of spectral and isotope data to characterize plant ecophysiology. We found that increasing depth to groundwater triggered water uptake adjustments towards deeper soil layers only in the dry season. These adjustments in water source use were made by conifer trees (Pinus pinea,P. pinaster) and hygrophytic shrubs (Erica scoparia, Salix repens) but not by the xerophytic shrubCorema album. Moreover, we observed a greater use of groundwater under semi‐arid conditions. Accompanying the greater use of water from deep soil layers as a response to increasing groundwater depth, the semi‐arid dimorphic‐rooted conifer treeP. pineaand hygrophytic shrubE. scopariadeclined their water content (WI), without implications on photosynthetic parameters, such as chlorophyll content (CHL), photochemical index (PRI) and δ13C. Unexpectedly, under semi‐arid conditions, the shallow‐rooted xerophytic shrubC. album, associated with an absence of water source use adjustments, showed a decline inWI,CHLandPRIwith groundwater table lowering.

We provide insight into how different species, belonging to different functional types, are acclimating to groundwater changes in a region experiencing climatic drought and a scarcity in groundwater due to anthropogenic exploitation. Greater depth to groundwater combined with limited precipitation can have a significant effect on plants’ water source use and ecophysiology in semi‐arid coastal dune ecosystems.

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