bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optic Pathway Gliomas in Neurofibromatosis Type 1: An Update: Surveillance, Treatment Indications, and Biomarkers of Vision
Authors: de Blank Peter M. K. , Fisher Michael J. , Liu Grant T. , Gutmann David H. , Listernick Robert , Ferner Rosalie E. , Avery Robert A. 
Published: August 2017

Abstract
Optic pathway gliomas (OPGs) occur in 15%–20% of children with neurofibromatosis type 1 (NF1), leading to visual deficits in fewer than half of these individuals. The goal of chemotherapy is to preserve vision, but vision loss in NF1-associated OPG can be unpredictable. Determining which child would benefit from chemotherapy and, equally important, which child is better observed without treatment can be difficult. Unfortunately, despite frequent imaging and ophthalmologic evaluations, some children experience progressive vision loss before treatment. Indications for chemotherapy usually are based on a comprehensive, quantitative assessment of vision, but reliable vision evaluation can be challenging in young children with NF1-OPG. The ability to identify and predict impending vision loss could potentially improve management decisions and visual outcomes. To address this challenge, ophthalmologic, electrophysiologic, and imaging biomarkers of vision in NF1-OPG have been proposed. We review current recommendations for the surveillance of children at risk for NF1-OPG, outline guidelines for initiating therapy, and describe the utility of proposed biomarkers for vision.
Pediatric Optic Neuritis: What Is New
Authors: Borchert Mark , Liu Grant T. , Pineles Stacy , Waldman Amy T. 
Published: August 2017

Abstract:
Few diseases blur the margins between their childhood and adult-onset varieties as much as optic neuritis. This report will review our state of knowledge of pediatric optic neuritis, as well as its relationship to the latest consensus definitions of neuroinflammatory disease. Current diagnostic and treatment options will be explored, as well as our potential to uncover an understanding of pediatric optic neuritis through systematic prospective studies. The risk of evolving multiple sclerosis is probably less than in adults, but pediatric optic neuritis is more likely to be an initial manifestation of acute disseminated encephalomyelitis. Steroids may hasten visual recovery, but they do not change visual outcome except in cases because of neuromyelitis optica. The role of puberty in modifying the presentation and risk associations is unknown. Prospective studies are required to resolve these diagnostic and management issues.
Identifying a TFIID interactome via integrated biochemical and high-throughput proteomic studies
Authors: Liu Wei-Li , Song Lihua , Dailey Gina , Piasecka Anna , Coleman Robert A. 
Published: August 2017

AbstractThe core promoter recognition TFIID complex acts as a central regulator for eukaryotic gene expression. To direct transcription initiation, TFIID binds the core promoter DNA and aids recruitment of the transcription machinery (e.g., RNA polymerase II) to the transcription start site. Many transcription factors target TFIID to control vital cellular processes. Current studies on finding TFIID interactors have predominantly focused on transcription factors. Yet, a comprehensive interactome of mammalian TFIID has not been established. Therefore, this study sought to reveal potential TFIID-nucleated networks by identifying likely co-regulatory factors that bind TFIID. By using intact native human TFIID complexes, we have exploited three independent approaches including a high-throughput Next Generation DNA sequencing coupled with proteomic analysis. Among these methods, we found some overlapping and new candidates in which we further assessed three putative interactors (i.e., Sox2, H2A and EMSY) by co-immunoprecipitation assays. Notably, in addition to known TFIID interactors, we identified a number of novel factors that participate either in co-regulatory pathways or non-transcription related functions of TFIID. Overal, these results indicate that, in addition to transcription initiation, mammalian TFIID may be involved in broader regulatory pathways than previous studies suggested.
MERS-CoV spillover at the camel-human interface
Authors: Dudas Gytis , Carvalho Luiz Max , Rambaut Andrew , Bedford Trevor , Somily Ali M. , Barry Mazin , Al Subaie Sarah S. , BinSaeed Abdulaziz A. , Alzamil Fahad A. , Zaher Waleed , Qahtani Theeb Al , Jerian Khaldoon Al , McNabb Scott J.N. , Al-Jahdali Imad A. , Alotaibi Ahmed M. , Batarfi Nahid A. , Cotten Matthew , Watson Simon J. , Binter Spela , Kellam Paul 
Published: August 2017

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic virus from camels causing significant mortality and morbidity in humans in the Arabian Peninsula. The epidemiology of the virus remains poorly understood, and while case-based and seroepidemiological studies have been employed extensively throughout the epidemic, viral sequence data have not been utilised to their full potential. Here we use existing MERS-CoV sequence data to explore its phylodynamics in two of its known major hosts, humans and camels. We employ structured coalescent models to show that long-term MERS-CoV evolution occurs exclusively in camels, whereas humans act as a transient, and ultimately terminal host. By analysing the distribution of human outbreak cluster sizes and zoonotic introduction times we show that human outbreaks in the Arabian peninsula are driven by seasonally varying zoonotic transfer of viruses from camels. Without heretofore unseen evolution of host tropism, MERS-CoV is unlikely to become endemic in humans.
Evolution of chalcone isomerase from a non-catalytic ancestor
Authors: Kaltenbach Miriam , Burke Jason R. , Dindo Mirco , Pabis Anna , Munsberg Fabian S. , Rabin Avigayel , Kamerlin Shina C. L. , Noel Joseph P. , Tawfik Dan S. 
Published: August 2017

AbstractThe emergence of catalysis in a non-catalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a non-enzymatic ancestor related to the widely-distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs for “CHI-like”). Ancestral inference confirmed that CHI evolved from a protein lacking isomerase activity. We also identified four alternative founder mutations, i.e. mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI’s laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity can readily emerge despite a catalytically inactive starting point. X-ray crystallography, NMR, and MD simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.
Genome downsizing, physiological novelty, and the global dominance of flowering plants
Authors: Simonin Kevin A. , Roddy Adam B. 
Published: August 2017

SummaryDuring the Cretaceous (145-66 Ma), early angiosperms rapidly diversified, eventually outcompeting the ferns and gymnosperms previously dominating most ecosystems. Heightened competitive abilities of angiosperms are often attributed to higher rates of transpiration facilitating faster growth. This hypothesis does not explain how angiosperms were able to develop leaves with smaller, but densely packed stomata and highly branched venation networks needed to support increased gas exchange rates. Although genome duplication and reorganization have likely facilitated angiosperm diversification, here we show that genome downsizing facilitated reductions in cell size necessary to construct leaves with a high density stomata and veins. Rapid genome downsizing during the early Cretaceous allowed angiosperms to push the frontiers of anatomical trait space. In contrast, during the same time period ferns and gymnosperms exhibited no such changes in genome size, stomatal size, or vein density. Further reinforcing the effect of genome downsizing on increased gas exchange rates, we found that species employing water-loss limiting crassulacean acid metabolism (CAM) photosynthesis, have significantly larger genomes than C3 and C4 species. By directly affecting cell size and gas exchange capacity, genome downsizing brought actual primary productivity closer to its maximum potential. These results suggest species with small genomes, exhibiting a larger range of final cell size, can more finely tune their leaf physiology to environmental conditions and inhabit a broader range of habitats.
A subset of sweet-sensing neurons identified by IR56d are necessaryand sufficient for fatty acid taste
Authors: Tauber John M. , Brown Elizabeth , Li Yuanyuan , Yurgel Maria E. , Masek Pavel , Keene Alex C. 
Published: August 2017

AbstractFat represents a calorically potent food source that yields approximately twice the amount of energy as carbohydrates or proteins per unit of mass. The highly palatable taste of FAs promotes food consumption, activates reward circuitry, and is thought to contribute to hedonic feeding underlying many metabolism-related disorders. Despite a role in the etiology of metabolic diseases, little is known about how dietary fats are detected by the gustatory system to promote feeding. Previously, we showed that a broad population of sugar-sensitive taste neurons expressing Gustatory Receptor 64f (Gr64f), is required for reflexive feeding responses to both FAs and sugars. Here, we report a genetic silencing screen to identify specific populations of taste neurons that mediate fatty acid taste. We find neurons identified by expression of Ionotropic Receptor 56d (IR56d) are necessary and sufficient for reflexive feeding response to FAs. Functional imaging reveals thatIR56d-expressing neurons are responsive to short- and medium-chain FAs. SilencingIR56dneurons selectively abolishes fatty acid taste, while their activation is sufficient to drive feeding responses. Analysis of co-expression withGr64fidentifies two subpopulations ofIR56d-expressing neurons. While physiological imaging reveals that both populations are responsive to FAs,IR56d/Gr64fneurons are activated by medium-chain FAs and are sufficient for reflexive feeding responses to FA. Moreover, flies can discriminate between sugar and FAs in an aversive taste memory assay, indicating that FA taste is a unique modality inDrosophila. Taken together, these findings localize fatty acid taste within theDrosophilagustatory center and provide an opportunity to investigate discrimination between different categories of appetitive tastants.Authors SummaryFat represents a calorically potent food source that yields approximately twice the amount of energy as carbohydrates or proteins per unit of mass. Dietary lipids are comprised of both triacylglycerides and FAs, and growing evidence suggests that it is the free FAs that are detected by the gustatory system. The highly palatable taste of FAs promotes food consumption, activates reward centers in mammals, and is thought to contribute to hedonic feeding that underlies many metabolism-related disorders. Despite a role in the etiology of metabolic diseases, little is known about how dietary fats are detected by the gustatory system to promote feeding. We have identified a subset of sugar-sensing neurons in the fly that also respond to medium-chain FAs and are necessary and sufficient for behavioral responses to FAs. Further, we find that despite being sensed by shared neuron populations, flies can differentiate between the taste of sugar and FAs, fortifying the notion that FAs and sugar represent distinct taste modalities in flies.
Mitotic chromosomes fold by condensin-dependent helical winding of chromatin loop arrays
Authors: Gibcus Johan H. , Samejima Kumiko , Goloborodko Anton , Samejima Itaru , Naumova Natalia , Kanemaki Masato , Xie Linfeng , Paulson James R. , Earnshaw William C. , Mirny Leonid A. , Dekker Job 
Published: August 2017

AbstractDuring mitosis, chromosomes fold into compacted rod shaped structures. We combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations to determine how interphase chromosomes are converted into compressed arrays of loops characteristic of mitotic chromosomes. We found that the interphase organization is disassembled within minutes of prophase entry and by late prophase chromosomes are already folded as arrays of consecutive loops. During prometaphase, this array reorganizes to form a helical arrangement of nested loops. Polymer simulations reveal that Hi-C data are inconsistent with solenoidal coiling of the entire chromatid, but instead suggest a centrally located helically twisted axis from which consecutive loops emanate as in a spiral staircase. Chromosomes subsequently shorten through progressive helical winding, with the numbers of loops per turn increasing so that the size of a helical turn grows from around 3 Mb (~40 loops) to ~12 Mb (~150 loops) in fully condensed metaphase chromosomes. Condensin is essential to disassemble the interphase chromatin conformation. Analysis of mutants revealed differing roles for condensin I and II during these processes. Either condensin can mediate formation of loop arrays. However, condensin II was required for helical winding during prometaphase, whereas condensin I modulated the size and arrangement of loops inside the helical turns. These observations identify a mitotic chromosome morphogenesis pathway in which folding of linear loop arrays produces long thin chromosomes during prophase that then shorten by progressive growth of loops and helical winding during prometaphase.One Sentence SummaryMitotic chromosome morphogenesis occurs through condensin-mediated disassembly of the interphase conformation and formation of extended prophase loop arrays that then shorten by loop growth and condensin-dependent helical winding.
A Linear Algebra Approach to Fast DNA Mixture Analysis Using GPUs
Authors: Samsi Siddharth , Helfer Brian , Kepner Jeremy , Reuther Albert , Ricke Darrell O. 
Published: August 2017

AbstractAnalysis of DNA samples is an important tool in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base pairs. Current forensics approaches use 20 STR loci for analysis. The use of single nucleotide polymorphisms (SNPs) has utility for analysis of complex DNA mixtures. The use of tens of thousands of SNPs loci for analysis poses significant computational challenges because the forensic analysis scales by the product of the loci count and number of DNA samples to be analyzed. In this paper, we discuss the implementation of a DNA sequence comparison algorithm by re-casting the algorithm in terms of linear algebra primitives. By developing an overloaded matrix multiplication approach to DNA comparisons, we can leverage advances in GPU hardware and algoithms for dense matrix multiplication (DGEMM) to speed up DNA sample comparisons. We show that it is possible to compare 2048 unknown DNA samples with 20 million known samples in under 6 seconds using a NVIDIA K80 GPU.
Deciphering Transcriptional Regulation of Human Core Promoters
Authors: Weingarten-Gabbay Shira , Nir Ronit , Lubliner Shai , Sharon Eilon , Kalma Yael , Weinberger Adina , Segal Eran 
Published: August 2017

ABSTRACTDespite its pivotal role in regulating transcription, our understanding of core promoter function, architecture, and cis-regulatory elements is lacking. Here, we devised a highthroughput assay to quantify the activity of ∼15,000 fully designed core promoters that we integrated and expressed from a fixed location within the human genome. We find that core promoters drive transcription unidirectionally, and that sequences originating from promoters exhibit stronger activity than sequences originating from enhancers. Testing multiple combinations and distances of core promoter elements, we observe a positive effect of TATA and Initiator, a negative effect of BREu and BREd, and a 10bp periodicity in the optimal distance between the TATA and the Initiator. By comprehensively screening TF binding-sites, we show that site orientation has little effect, that the effect of binding site number on expression is factor-specific, and that there is a striking agreement between the effect of binding site multiplicity in our assay and the tendency of the TF to appear in homotypic clusters throughout the genome. Overall, our results systematically assay the elements that drive expression in core- and proximal-promoter regions and shed light on organization principles of regulatory regions in the human genome.
Multi-Transition Systems: A theory for neural spatial navigation
Authors: Waniek Nicolai 
Published: August 2017

AbstractSpatial navigation is considered fundamental for animals and is attributed primarily to place and grid cells in the rodent brain. Commonly believed to either perform path integration or localization, the true objective of grid cells, their hexagonal grid fields, and especially their discrete scales remain puzzling. Here it is proposed that grid cells efficiently encode transitions in sequences. A biologically plausible model for dendritic computation in grid cells is presented. A network of competitive cells shows positive gridness scores early in simulations and realigns the orientation of all cells over time. Then, a scale-space model of grid cells is introduced. It improves behaviorally questionable run-times of a single scale significantly by look-ahead in multiple scales, and it is shown that the optimal scale-increment between consecutive scales is√2. Finally, a formal theory for sequences and transitions is stated. It is demonstrated that hexagonal transition encoders are optimal to encode transitions in Euclidean space and emerge due to the sampling theorem. The paper concludes with a discussion about the suggested purpose, makes testable predictions, and highlights relevant connections to computational neuroscience as well as computer science and robotics.
Humans incorporate attention-dependent uncertainty into perceptual decisions and confidence
Authors: Denison Rachel N. , Adler William T. , Carrasco Marisa , Ma Wei Ji 
Published: August 2017

AbstractPerceptual decisions are better when they take uncertainty into account. Uncertainty arises not only from the properties of sensory input but also from cognitive sources, such as different levels of attention. However, it is unknown whether humans appropriately adjust for such cognitive sources of uncertainty during perceptual decision making. Here we show that human categorization and confidence decisions take into account uncertainty related to attention. We manipulated uncertainty in an orientation categorization task from trial to trial using only an attentional cue. The categorization task was designed to disambiguate decision rules that did or did not depend on attention. Using formal model comparison to evaluate decision behavior, we found that category and confidence decision boundaries shifted as a function of attention in an approximately Bayesian fashion. This means that the observer’s attentional state on each trial contributed probabilistically to the decision computation. This responsiveness of an observer’s decisions to attention-dependent uncertainty should improve perceptual decisions in natural vision, in which attention is unevenly distributed across a scene.
Development of fresh cheese made from coconut milk in combination with cow’s milk
Authors: Tipvarakarnkoon Tatsawan , Sornsa-ard Sangrawee , Imcha Wutcharee 
Published: August 2017

Purpose
The purpose of this paper is to develop fresh cheese made from different types of coconut milk (fresh, UHT, and reconstituted coconut milk) mixed with pasteurized cow’s milk (50:50) by rennet coagulation. The main aim of this study was to achieve successful formation of cheese curd with fully coconut milk aroma and flavor.

Design/methodology/approach
Fresh cheese made from different types of coconut milk mixed with cow’s milk (50:50) were developed and compared to fresh cheese made from cow’s milk (100:0). Physicochemical analysis including pH, acidity, percentage of yield, protein and fat content, texture analysis and sensory evaluation has been performed. The nine-point hedonic preference test (n=35) and consumer testing (n=235) were conducted.

Findings
In comparison, fresh cheese made with the presence of coconut milk (50:50) had higher fat content, lower crude protein content, higher firmness, and adhesiveness than those made from cow’s milk alone (0:100). The cheese with the presence of coconut milk was liked better by consumers (7.35 out of 9). Rehydrated coconut milk was mostly preferred to use among all three types of coconut milk which showed firmer texture and admired flavor. The texture of the developed product was proved to be similar to commercial cottage cheese. Using the rehydrated coconut milk in the formulation gave successful results for making fresh coconut milk cheese, which has also not been used previously in any research.

Research limitations/implications
In this paper, the effect of process conditions on the quality of cheese curd formation was not yet investigated and discussed. The process parameters including heat treatment and renneting time should be further studied.

Originality/value
A novel fresh cheese made from coconut milk mixed with pasteurized cow’s milk was successfully developed. The cheese curd was formed with fully coconut milk aroma and flavor.
The product development of Thai fermented sausage with mixed Tomyum ingredients
Authors: Panjapiyakul Pornpen , Srinin Tongsuk , Kitsawad Kamolnate 
Published: August 2017

Purpose
The purpose of this paper is to study for the product development of Sai Krok Isan or Thai fermented sausage with Tomyum ingredients (TFS-TY) such as kaffir lime leaves, lemon grass, galangal root and chili.

Design/methodology/approach
To study the proper formula of TFS-TY in order to obtain certain characteristics of both fermented sausage and Tomyum attributes by varying the ratio of cooked glutinous rice to cooked rice of total rice content and Tomyum ingredients content. The nine-point hedonic preference method was conducted to evaluate TFS-TY with 30 untrained panelists. Consumer survey from 200 respondents were asked about their behaviors on fermented sausage and opinions to the new products.

Findings
The preference score of the 3:1 (cooked glutinous rice: cooked rice) gained the highest score in all sensory attributes as same as 16 percent of Tomyum ingredients. According to the consumer survey, the TFS-TY was accepted by 90 percent of the total 200 respondents and gained an overall score equal to 7.30±1.11.

Research limitations/implications
The varied preference of Thai respondents has affected on the acceptance of the new products. For example, some preferred very strong tastes either in sourness or spiciness, and some may be disliked.

Originality/value
The balancing characteristics of both products were very important. The new product should be identified by certain attributes in Thai fermented sausage and Tomyum. Over or less in any products gained lower preference attributes scores.