bluuebunny/crossref_metadata_2025_split huggingface dataset:
Critical structural fluctuations of proteins upon thermal unfolding challenge the Lindemann criterion
Authors: Katava Marina , Stirnemann Guillaume , Zanatta Marco , Capaccioli Simone , Pachetti Maria , Ngai K. L. , Sterpone Fabio , Paciaroni Alessandro 
Published: August 2017

Significance
In 1910 F. A. Lindemann introduced a practical criterion to predict the melting of crystals on the basis of the relative magnitude of thermal atomic fluctuations and the crystal lattice constant. The idea of a critical threshold for the local motions that would trigger melting also in disordered media like proteins has inspired important subsequent investigations. Here, a common scaling toward a constant value for the local fluctuations of a model protein in different environments is proved when approaching the unfolding temperature. This landmark result not only sheds unique light on the relationship between protein flexibility and stability, but also opens the possibility to predict protein unfolding in special environments (e.g., the cell interior) by following thermal local fluctuations.
Changes in aggregation states of light-harvesting complexes as a mechanism for modulating energy transfer in desert crust cyanobacteria
Authors: Bar Eyal Leeat , Ranjbar Choubeh Reza , Cohen Eyal , Eisenberg Ido , Tamburu Carmen , Dorogi Márta , Ünnep Renata , Appavou Marie-Sousai , Nevo Reinat , Raviv Uri , Reich Ziv , Garab Győző , van Amerongen Herbert , Paltiel Yossi , Keren Nir 
Published: August 2017

Significance
All photosynthetic organisms regulate efficiency of excitation energy transfer (EET) to fit energy supply to biochemical demands. For desiccation-tolerant desert crust cyanobacteria this ability is of the utmost importance. These organisms spend most of the daytime in the desiccated state whence absorbed energy is completely quenched. Based on our observations we propose a model where in the hydrated state the organized rod structure of the light-harvesting phycobilisome supports directional EET to reaction centers with minimal losses to thermal dissipation. In the desiccated state this structure gives way to more random aggregates. The resulting EET path exhibits increased coupling to the environment and enhanced quenching. This energy dissipation mechanism is completely reliant on changes in aggregation state of phycobilisome components.
Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (C
e
3D)
Authors: Li Weizhe , Germain Ronald N. , Gerner Michael Y. 
Published: August 2017

Significance
Major biological processes rely on the precise positioning of diverse cell types in specific anatomical locations. Existing techniques for studying cellular spatial positioning in tissues, especially with robust identification of densely packed cells, have substantial time, cost, resolution, and multiplexing limitations. Here, we describe an easy-to-use and inexpensive tissue clearing technique for attaining high-quality images of cells and diverse molecules of interest in substantial tissue volumes, enabling simultaneous quantitative analysis of 3D organ structure and fine-grained cellular composition. This technology will enhance our capacity for acquiring a quantitative understanding of the relationships between cells and their microenvironments in the context of broader tissue organization and is directly applicable to diverse biological disciplines as well as diagnostic medicine.
A protein complex regulates RNA processing of intronic heterochromatin-containing genes in
Arabidopsis
Authors: Duan Cheng-Guo , Wang Xingang , Zhang Lingrui , Xiong Xiansong , Zhang Zhengjing , Tang Kai , Pan Li , Hsu Chuan-Chih , Xu Huawei , Tao W. Andy , Zhang Heng , Zhu Jian-Kang 
Published: August 2017

Significance
How heterochromatin affects RNA processing is unclear. The chromatin regulators ASI1 and EDM2 function in regulating alternative polyadenylation at genes with intronic heterochromatin. We found that ASI1 and EDM2 are associated in planta through interactions with a putative RNA-binding protein, AIPP1. Protein interaction assays suggest that the RNA Pol II C-terminal domain phosphatase CPL2 and two other proteins (AIPP2 and AIPP3) are associated with the ASI1-AIPP1-EDM2 complex. Like ASI1 and EDM2, AIPP1 also functions in promoting the expression of heterochromatin-containing genes. However, the function of CPL2, AIPP2, and AIPP3 is antagonistic to that of ASI1, EDM2, and AIPP1. Our discovery of the ASI1-AIPP1-EDM2 complex and associated proteins is important for understanding how heterochromatin regulates RNA processing.
A genome Tree of Life for the Fungi kingdom
Authors: Choi JaeJin , Kim Sung-Hou 
Published: August 2017

Significance
Fungi belong to one of the largest and most diverse groups of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information–based trees (“gene trees”) constructed using a small number of genes. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population, depending on the selection of the genes. We present whole-genome information-based trees (“genome trees”) using a variation of a computational algorithm developed to find plagiarism in two books, where we represent a whole-genomic information of an organism as a book of words without spaces.
A conceptual framework for evaluating data suitability for observational studies
Authors: Shang Ning , Weng Chunhua , Hripcsak George 
Published: August 2017

Abstract

Objective
To contribute a conceptual framework for evaluating data suitability to satisfy the research needs of observational studies.

Materials and Methods
Suitability considerations were derived from a systematic literature review on researchers’ common data needs in observational studies and a scoping review on frequent clinical database design considerations, and were harmonized to construct a suitability conceptual framework using a bottom-up approach. The relationships among the suitability categories are explored from the perspective of 4 facets of data: intrinsic, contextual, representational, and accessible. A web-based national survey of domain experts was conducted to validate the framework.

Results
Data suitability for observational studies hinges on the following key categories: Explicitness of Policy and Data Governance, Relevance, Availability of Descriptive Metadata and Provenance Documentation, Usability, and Quality. We describe 16 measures and 33 sub-measures. The survey uncovered the relevance of all categories, with a 5-point Likert importance score of 3.9 ± 1.0 for Explicitness of Policy and Data Governance, 4.1 ± 1.0 for Relevance, 3.9 ± 0.9 for Availability of Descriptive Metadata and Provenance Documentation, 4.2 ± 1.0 for Usability, and 4.0 ± 0.9 for Quality.

Conclusions
The suitability framework evaluates a clinical data source’s fitness for research use. Its construction reflects both researchers’ points of view and data custodians’ design features. The feedback from domain experts rated Usability, Relevance, and Quality categories as the most important considerations.
Wheat breeding for quality: A historical review
Authors: Kiszonas Alecia M. , Morris Craig F. 
Published: August 2017

Background and objectivesWheat (Triticumspp. L.) is a leading cereal contributing to the nourishment of humankind. Since its domestication ca. 12,000 years ago, humans have profoundly influenced its evolution. In the more recent past, breeding via cross‐hybridization and the selection of progeny with superior end‐use quality have moved from solely phenotyping (e.g., bread baking quality), to a more detailed genetic approach of selecting genes, alleles, and whole‐genome structure for desirable traits.FindingsThe present review provides a brief historical summary of wheat improvement for end‐use quality. In the last ~150 years, wheat improvement has benefited from advances in genetics, chemistry and biotechnology. In the past couple decades, rapid advances inDNAand next‐generation sequencing technology have promised a revolution in wheat improvement. The various technologies are reviewed here.ConclusionsThe “future” of wheat improvement may involve the whole‐genome‐based analysis, “genomic selection.” However, to date, the plethora ofQTLgenerated over the recent years have largely remained unused.Significance and noveltyWheat is vital to the survival of humankind, and new cultivars must be continually developed. These cultivars should have high quality for processing and consumer products. An important means of breeding and selecting for high quality is through rapidly evolving genome‐based technologies.
Reduced Field-of-View Diffusion-Weighted Magnetic Resonance Imaging of the Prostate at 3 Tesla: Comparison With Standard Echo-Planar Imaging Technique for Image Quality and Tumor Assessment
Authors: Tamada Tsutomu , Ream Justin M. , Doshi Ankur M. , Taneja Samir S. , Rosenkrantz Andrew B. 
Published: August 2017

Objective
The purpose of this study was to compare image quality and tumor assessment at prostate magnetic resonance imaging (MRI) between reduced field-of-view diffusion-weighted imaging (rFOV-DWI) and standard DWI (st-DWI).

Methods
A total of 49 patients undergoing prostate MRI and MRI/ultrasound fusion–targeted biopsy were included. Examinations included st-DWI (field of view [FOV], 200 × 200 mm) and rFOV-DWI (FOV, 140 × 64 mm) using a 2-dimensional (2D) spatially-selective radiofrequency pulse and parallel transmission. Two readers performed qualitative assessments; a third reader performed quantitative evaluation.

Results
Overall image quality, anatomic distortion, visualization of capsule, and visualization of peripheral/transition zone edge were better for rFOV-DWI for reader 1 (P ≤ 0.002), although not for reader 2 (P ≥ 0.567). For both readers, sensitivity, specificity, and accuracy for tumor with a Gleason Score (GS) of 3 + 4 or higher were not different (P ≥ 0.289). Lesion clarity was higher for st-DWI for reader 2 (P = 0.008), although similar for reader 1 (P = 0.409). Diagnostic confidence was not different for either reader (P ≥ 0.052). Tumor-to-benign apparent diffusion coefficient ratio was not different (P = 0.675).

Conclusions
Potentially improved image quality of rFOV-DWI did not yield improved tumor assessment. Continued optimization is warranted.
Lymphoma Causing Gastrosplenic Fistula Revealed by FDG PET/CT
Authors: Wang Trent P. , Doss Mohan , Tokar Jeffrey L. , Reddy Sanjay , Barta Stefan K. , Yu Jian Q. 
Published: August 2017

Abstract
A 73-year-old man presented with fatigue and weight loss. He had CT-proven splenic mass with fistulous connection to the greater curvature of the stomach, which suggested abscess. FDG PET/CT confirmed gastrosplenic fistula in addition to active lymph nodes in the gastrohepatic ligament and epigastric region. Pathological examination after the biopsy of the spleen was consistent with diffuse large B-cell lymphoma. Chemotherapy was administered with close clinical follow-up and resulted in the resolution of fistula without requirement for surgery.
Photosynthesis solutions to enhance productivity
Authors: Foyer Christine H. , Ruban Alexander V. , Nixon Peter J. 
Published: August 2017

The concept that photosynthesis is a highly inefficient process in terms of conversion of light energy into biomass is embedded in the literature. It is only in the past decade that the processes limiting photosynthetic efficiency have been understood to an extent that allows a step change in our ability to manipulate light energy assimilation into carbon gain. We can therefore envisage that future increases in the grain yield potential of our major crops may depend largely on increasing the efficiency of photosynthesis. The papers in this issue provide new insights into the nature of current limitations on photosynthesis and identify new targets that can be used for crop improvement, together with information on the impacts of a changing environment on the productivity of photosynthesis on land and in our oceans.
This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
What limits photosynthetic energy conversion efficiency in nature? Lessons from the oceans
Authors: Falkowski Paul G. , Lin Hanzhi , Gorbunov Maxim Y. 
Published: August 2017

Constraining photosynthetic energy conversion efficiency in nature is challenging. In principle, two yield measurements must be made simultaneously: photochemistry, fluorescence and/or thermal dissipation. We constructed two different, extremely sensitive and precise active fluorometers: one measures the quantum yield of photochemistry from changes in variable fluorescence, the other measures fluorescence lifetimes in the picosecond time domain. By deploying the pair of instruments on eight transoceanic cruises over six years, we obtained over 200 000 measurements of fluorescence yields and lifetimes from surface waters in five ocean basins. Our results revealed that the average quantum yield of photochemistry was approximately 0.35 while the average quantum yield of fluorescence was approximately 0.07. Thus, closure on the energy budget suggests that, on average, approximately 58% of the photons absorbed by phytoplankton in the world oceans are dissipated as heat. This extraordinary inefficiency is associated with the paucity of nutrients in the upper ocean, especially dissolved inorganic nitrogen and iron. Our results strongly suggest that, in nature, most of the time, most of the phytoplankton community operates at approximately half of its maximal photosynthetic energy conversion efficiency because nutrients limit the synthesis or function of essential components in the photosynthetic apparatus.
This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Strategies and tools to improve crop productivity by targeting photosynthesis
Authors: Nuccio Michael L. , Potter Laura , Stiegelmeyer Suzy M. , Curley Joseph , Cohn Jonathan , Wittich Peter E. , Tan Xiaoping , Davis Jimena , Ni Junjian , Trullinger Jon , Hall Rick , Bate Nicholas J. 
Published: August 2017

Crop productivity needs to substantially increase to meet global food and feed demand for a rapidly growing world population. Agricultural technology developers are pursuing a variety of approaches based on both traditional technologies such as genetic improvement, pest control and mechanization as well as new technologies such as genomics, gene manipulation and environmental modelling to develop crops that are capable of meeting growing demand. Photosynthesis is a key biochemical process that, many suggest, is not yet optimized for industrial agriculture or the modern global environment. We are interested in identifying control points in maize photoassimilation that are amenable to gene manipulation to improve overall productivity. Our approach encompasses: developing and using novel gene discovery techniques, translating our discoveries into traits and evaluating each trait in a stepwise manner that reflects a modern production environment. Our aim is to provide step change advancement in overall crop productivity and deliver this new technology into the hands of growers.This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
Enhancing (crop) plant photosynthesis by introducing novel genetic diversity
Authors: Dann Marcel , Leister Dario 
Published: August 2017

Although some elements of the photosynthetic light reactions might appear to be ideal, the overall efficiency of light conversion to biomass has not been optimized during evolution. Because crop plants are depleted of genetic diversity for photosynthesis, efforts to enhance its efficiency with respect to light conversion to yield must generate new variation. In principle, three sources of natural variation are available: (i) rare diversity within extant higher plant species, (ii) photosynthetic variants from algae, and (iii) reconstruction of no longer extant types of plant photosynthesis. Here, we argue for a novel approach that outsources crop photosynthesis to a cyanobacterium that is amenable to adaptive evolution. This system offers numerous advantages, including a short generation time, virtually unlimited population sizes and high mutation rates, together with a versatile toolbox for genetic manipulation. On such a synthetic bacterial platform, 10 000 years of (crop) plant evolution can be recapitulated within weeks. Limitations of this system arise from its unicellular nature, which cannot reproduce all aspects of crop photosynthesis. But successful establishment of such a bacterial host for crop photosynthesis promises not only to enhance the performance of eukaryotic photosynthesis but will also reveal novel facets of the molecular basis of photosynthetic flexibility.
This article is part of the themed issue ‘Enhancing photosynthesis in crop plants: targets for improvement’.
scPipe: a flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
Authors: Tian Luyi , Su Shian , Dong Xueyi , Amann-Zalcenstein Daniela , Biben Christine , Seidi Azadeh , Hilton Douglas J. , Naik Shalin H. , Ritchie Matthew E. 
Published: August 2017

AbstractSingle-cell RNA sequencing (scRNA-seq) technology allows researchers to profile the transcriptomes of thousands of cells simultaneously. Protocols that incorpo-rate both designed and random barcodes have greatly increased the throughput of scRNA-seq, but give rise to a more complex data structure. There is a need for new tools that can handle the various barcoding strategies used by different protocols and exploit this information for quality assessment at the sample-level and provide effective visualization of these results in preparation for higher-level analyses.To this end, we developedscPipe, a R/Bioconductor package that integrates barcode demultiplexing, read alignment, UMI-aware gene-level quantification and quality control of raw sequencing data generated by multiple 3-prime-end sequencing protocols that include CEL-seq, MARS-seq, Chromium 10X and Drop-seq.scPipeproduces a count matrix that is essential for downstream analysis along with an HTML report that summarises data quality. These results can be used as input for downstream analyses including normalization, visualization and statistical testing.scPipeperforms this processing in a few simple R commands, promoting reproducible analysis of single-cell data that is compatible with the emerging suite of scRNA-seq analysis tools available in R/Bioconductor. ThescPipeR package is available for download fromhttps://www.bioconductor.org/packages/scPipe.
SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site
Authors: Zhang Liyang , Martini Gabriella D. , Rube H. Tomas , Kribelbauer Judith F. , Rastogi Chaitanya , FitzPatrick Vincent D. , Houtman Jon C. , Bussemaker Harmen J. , Pufall Miles A. 
Published: August 2017

ABSTRACTThe DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA binding domains using a refined version ofSELEX-seq. We developed an algorithm,SelexGLM, that quantifies binding specificity over a large (31 bp) binding-site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA binding preferences of AR and GR homodimers differ significantly, both within and outside the 15bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly-A sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding, and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.
Transcriptome wide analysis of natural antisense transcripts shows their potential role in breast cancer
Authors: Wenric Stephane , ElGuendi Sonia , Caberg Jean-Hubert , Bezzaou Warda , Fasquelle Corinne , Charloteaux Benoit , Karim Latifa , Hennuy Benoit , Freres Pièrre , Collignon Joëlle , Boukerroucha Meriem , Schroeder Hélène , Olivier Fabrice , Jossa Véronique , Jerusalem Guy , Josse Claire , Bours Vincent 
Published: August 2017

AbstractNon-coding RNAs (ncRNA) represent at least 1/5 of the mammalian transcript amount, and about 90% of the genome length is actively transcribed. Many ncRNAs have been demonstrated to play a role in cancer. Among them, natural antisense transcripts (NAT) are RNA sequences which are complementary and overlapping to those of protein-coding transcripts (PCT). NATs were punctually described as regulating gene expression, and are expected to act more frequently incisthan other ncRNAs that commonly function intrans. In this work, 22 breast cancers expressing estrogen receptors and their paired healthy tissues were analyzed by strand-specific RNA sequencing. To highlight the potential role of NATs in gene regulations occurring in breast cancer, three different gene extraction methods were used: differential expression analysis of NATs between tumor and healthy tissues, differential correlation analysis of paired NAT/PCT between tumor and healthy tissues, and NAT/PCT read count ratio variation between tumor and healthy tissues. Each of these methods yielded lists of NAT/PCT pairs that were demonstrated to be enriched in survival-associated genes on an independent cohort (TCGA). This work allows to highlight NAT lists that display a strong potential to affect the expression of genes involved in the breast cancer pathology.