bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methods of fixation used in management of femoral neck fractures in adults: a systematic review
Authors: Abdel Rahman Amr Farouk , Gouda Ayman , Ibrahim Ramy 
Published: May 2018

Background:
Femoral neck fractures in adults younger than 50 yr old are uncommon and often result from high-energy trauma. They account for only 2-3% of all femoral neck fractures. Femoral neck fractures in young adults are associated with a high incidence of femoral head osteonecrosis and nonunion. Dynamic hip screw, multiple cannulated screws, and a Targon® femoral neck (TFN) plate can be used in management. A systematic review of the literature was done to evaluate which technique is best.

Methods:
After literature search, 11 articles were found and were reviewed to evaluate final outcome of fixation of femoral neck fractures using dynamic hip screw, multiple cannulated screws, or a TFN plate.

Results:
After evaluation of all studies, the incidence of nonunion, osteonecrosis of the femoral head, implant failure, and reoperation were almost equal in both dynamic hip screw and TFN plate groups, while it was much higher in the patient group fixed with multiple cannulated screws.

Conclusions:
Dynamic hip screw fixation had a low incidence of complications in the final outcome when compared with multiple cannulated screws. Further study was needed for application of the TFN plate.
Error-correcting DNA barcodes for high-throughput sequencing
Authors: Hawkins John A. , Jones Stephen K. , Finkelstein Ilya J. , Press William H. 
Published: May 2018

ABSTRACTMany large-scale high-throughput experiments use DNA barcodes—short DNA sequences prepended to DNA libraries—for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely-used error-correcting codes borrowed from computer science (e.g., Hamming and Levenshtein codes) do not properly account for insertions and deletions in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate FREE (Filled/truncated Right End Edit) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced GC content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error-correction levels that may be useful in diverse high-throughput applications, including >106 single-error correcting 16-mers that strike a balance between decoding accuracy, barcode length, and library size. Moreover, concatenating two or more FREE codes into a single barcode increases the available barcode space combinatorially, generating lists with > 1015 error-correcting barcodes. The included software for creating barcode libraries and decoding sequenced barcodes is efficient and designed to be user-friendly for the general biology community.SIGNIFICANCE STATEMENTModern high-throughput biological assays study pooled populations of individual members by labeling each member with a unique DNA sequence called a “barcode.” DNA barcodes are frequently corrupted by DNA synthesis and sequencing errors, leading to significant data loss and incorrect data interpretation. Here, we describe a novel error-correction strategy to improve the efficiency and statistical power of DNA barcodes. To our knowledge, this is the first report of an error-correcting method that accurately handles insertions and deletions in DNA barcodes, the most common type of error encountered during DNA synthesis and sequencing, resulting in order-of-magnitude increases in accuracy, efficiency, and signal-to-noise. The accompanying software package makes deployment of these barcodes effortless for the broader experimental scientist community.
Polar targeting and assembly of theLegionellaDot/Icm type IV secretion system (T4SS) by T6SS-related components
Authors: Jeong KwangCheol C. , Gyore Jacob , Teng Lin , Ghosal Debnath , Jensen Grant J. , Vogel Joseph P. 
Published: May 2018

SummaryLegionella pneumophila, the causative agent of Legionnaires’ disease, survives and replicates inside amoebae and macrophages by injecting a large number of protein effectors into the host cells’ cytoplasm via the Dot/Icm type IVB secretion system (T4BSS). Previously, we showed that the Dot/Icm T4BSS is localized to both poles of the bacterium and that polar secretion is necessary for the proper targeting of theLegionellacontaining vacuole (LCV). Here we show that polar targeting of the Dot/Icm core-transmembrane subcomplex (DotC, DotD, DotF, DotG and DotH) is mediated by two Dot/Icm proteins, DotU and IcmF, which are able to localize to the poles ofL. pneumophilaby themselves. Interestingly, DotU and IcmF are homologs of the T6SS components TssL and TssM, which are part of the T6SS membrane complex (MC). We propose thatLegionellaco-opted these T6SS components to a novel function that mediates subcellular localization and assembly of this T4SS. Finally, in depth examination of the biogenesis pathway revealed that polar targeting and assembly of theLegionellaT4BSS apparatus is mediated by an innovative “outside-inside” mechanism.
A computational model of task allocation in social insects – ecology and interactions alone can drive specialisation
Authors: Chen Rui , Meyer Bernd , García Julian 
Published: May 2018

AbstractSocial insect colonies are capable of allocating their workforce in a decentralised fashion; addressing a variety of tasks and responding effectively to changes in the environment. This process is fundamental to their ecological success, but the mechanisms behind it remain poorly understood. While most models focus on internal and individual factors, empirical evidence highlights the importance of ecology and social interactions. To address this gap we propose a game theoretical model of task allocation. Individuals are characterised by a trait that determines how they split their energy between two prototypical tasks: foraging and regulation. To be viable, a colony needs to learn to adequately allocate its workforce between these two tasks. We study two different processes: individuals can learn relying exclusively on their own experience, or by using the experiences of others via social learning. We find that social organisation can be determined by the ecology alone, irrespective of interaction details. Weakly specialised colonies in which all individuals tend to both tasks emerge when foraging is cheap; harsher environments, on the other hand, lead to strongly specialised colonies in which each individual fully engages in a single task. We compare the outcomes of self-organised task allocation with optimal group performance. Counter to intuition, strongly specialised colonies perform suboptimally, whereas the group performance of weakly specialised colonies is closer to optimal. Social interactions lead to important differences when the colony deals with dynamic environments. Colonies whose individuals rely on their own experience are more exible when dealing with change. Our computational model is aligned with mathematical predictions in tractable limits. This different kind of model is useful in framing relevant and important empirical questions, where ecology and interactions are key elements of hypotheses and predictions.
Single-neuron interactions between the somatosensory thalamo-cortical circuits during perception
Authors: Tauste Campo Adrià , Vázquez Yuriria , Álvarez Manuel , Zainos Antonio , Rossi-Pool Román , Deco Gustavo , Romo Ranulfo 
Published: May 2018

SUMMARYSensory thalamo-cortical interactions are key components of the neuronal chains associated with stimulus perception, but surprisingly, they are poorly understood. We addressed this problem by evaluating a directional measure between simultaneously recorded neurons from somatosensory thalamus (VPL) and somatosensory cortex (S1) sharing the same cutaneous receptive field, while monkeys judged the presence or absence of a tactile stimulus. During the stimulus-presence, feedforward (VPL→S1) interactions increased, while pure feedback (S1→VPL) interactions were unaffected. Remarkably, bidirectional interactions (VPL↔S1) emerged with high stimulus amplitude, establishing a functional thalamo-cortical loop. Furthermore, feedforward interactions were modulated by task context and error trials. Additionally, significant stimulus modulations were found on intra-cortical (S1→S1) interactions, but not on intra-thalamic (VPL→VPL) interactions. Thus, these results show the directionality of the information flow between the thalamo-cortical circuits during tactile perception. We suggest that these interactions may contribute to stimulus perception during the detection task used here.
Selection of horizontal gene transfer through public good production
Authors: Dimitriu Tatiana , Misevic Dusan , Capelle Julien Benard , Lindner Ariel B , Brown Sam P , Taddei Francois 
Published: May 2018

AbstractIn bacteria, cooperative genes encoding public good molecules are preferentially located on mobile genetic elements (MGEs), and horizontal transfer of MGEs favours the maintenance of public good cooperation. The rate of horizontal transfer itself can evolve in response to selective pressures acting on both MGEs and bacterial hosts: benefits and costs of infectious spread, but also indirect effects of MGE genes to the host. We show here that carriage of public good genes on MGEs can generate another indirect selection for MGE transfer. Transfer increases public good production and, when relatedness is sufficiently high, public goods benefit preferentially genotypes with high transfer ability. Both our simulations and experiments indicate that transfer is not required to occur among kin, provided that public goods still benefit kin. Public good gene mobility thus aligns the interests of chromosomes and MGEs concerning transfer, promoting gene exchange among bacteria.
The development of individual differences in cooperative behaviour: maternal glucocorticoid hormones alter helping behaviour of offspring in wild meerkats
Authors: Dantzer Ben , Dubuc Constance , Goncalves Ines Braga , Cram Dominic L. , Bennett Nigel C. , Ganswindt Andre , Heistermann Michael , Duncan Chris , Gaynor David , Clutton-Brock Tim H. 
Published: May 2018

AbstractThe phenotype of parents can have long-lasting effects on the development of offspring as well as on their behaviour, physiology, and morphology as adults. In some cases, these changes may increase offspring fitness but, in others, they can elevate parental fitness at a cost to the fitness of their offspring. We show that in Kalahari meerkats (Suricata suricatta), the circulating glucocorticoid (GC) hormones of pregnant females affect the growth and cooperative behaviour of their offspring. We performed a 3-year experiment in wild meerkats to test the hypothesis that GC-mediated maternal effects reduce the potential for offspring to reproduce directly and therefore cause them to exhibit more cooperative behaviour. Daughters (but not sons) born to mothers treated with cortisol during pregnancy grew more slowly early in life and exhibited significantly more of two types of cooperative behaviour (pup rearing and feeding) once they were adults compared to offspring from control mothers. They also had lower measures of GCs as they aged, which could explain the observed increases in cooperative behaviour. Because early life growth is a crucial determinant of fitness in female meerkats, our results indicate that GC-mediated maternal effects may reduce the fitness of offspring, but may elevate parental fitness as a consequence of increasing the cooperative behaviour of their daughters.
Bayesian Estimation of 3D Chromosomal Structure from Single Cell Hi-C Data
Authors: Rosenthal Michael , Bryner Darshan , Huffer Fred , Evans Shane , Srivastava Anuj , Neretti Nicola 
Published: May 2018

AbstractThe problem of 3D chromosome structure inference from Hi-C datasets is important and challenging. While bulk Hi-C datasets contain contact information derived from millions of cells, and can capture major structural features shared by the majority of cells in the sample, they do not provide information about local variability between cells. Single cell Hi-C can overcome this problem, but contact matrices are generally very sparse, making structural inference more problematic. We have developed a Bayesian multiscale approach, named SIMBA3D, to infer 3D structures of chromosomes from single cell Hi-C while including the bulk Hi-C data and some regularization terms as a prior. We study the landscape of solutions for each single-cell Hi-C dataset as a function of prior strength and demonstrate clustering of solutions using data from the same cell.
Embryo timelapses can be compiled and quantified to understand canonical histone dynamics across multiple cell cycles
Authors: Smith Lydia , Maddox Paul 
Published: May 2018

AbstractIn the last decade, computational analysis of big datasets has facilitated the processing of unprecedented quantities of collected biological data. Thus, automations and big data analyses have been revolutionary in detecting and quantifying subtle phenotypes in cell biological contexts. Analyzing similar quantities of data in larger and more complicated biological systems such as live embryos has been more challenging due to experimental necessities impeding both compilations of data collection and informative analysis. Here we present a streamlined workflow that can quantify cell cycle dynamics in early developing embryos using fluorescently labeled proteins. We benchmark this pipeline usingCaenorhabditis elegans(nematode) embryonic development and a fluorescently labeled histone. Using our pipeline, we find that histone proteins are broadly stable in early embryonic development. In sum, we have utilized the large biological and experimental variation associated with quantification of fluorescent proteins in embryonic systems, to quantify nuclear accumulation rate, chromatin incorporation, and turnover/stability of canonical histones during early development.
Evaluation of current and emerging anti-malarial medicines for inhibition ofToxoplasma gondiigrowth in vitro
Authors: Radke Joshua B. , Burrows Jeremy N. , Goldberg Daniel E. , Sibley L. David 
Published: May 2018

AbstractToxoplasma gondiiis a common zoonotic infection of humans and estimates indicate that 1-2 billion people are chronically infected. Although largely asymptomatic, chronic infection poses risk of serious disease due to reactivation should immunity decline. Current therapies for toxoplasmosis only control acute infection caused by actively proliferating tachyzoites but do not eradicate the chronic tissue cyst stages. As well, there are considerable adverse side effects of the most commonly used therapy of combined sulfadiazine and pyrimethamine. Targeting the folate pathway is also an effective treatment for malaria, caused by the related parasitesPlasmodiumspp., suggesting common agents might be used to treat both infections. Here we evaluated currently approved and newly emerging medicines for malaria to determine if such compounds might also prove useful for treating toxoplasmosis. Surprisingly, the majority of anti-malarial compounds being used currently or in development for treatment of malaria were only modestly effective at inhibiting in vitro growth ofT. gondiitachyzoites. These findings suggest that many essential processes inP. falciparumthat are targeted by anti-malarial compounds are either divergent, or non-essential inT. gondii, thus limiting options for repurposing of current antimalarial medicines for toxoplasmosis.
Engineering Nitrogen Fixation Activity in an Oxygenic Phototroph
Authors: Liu Deng , Liberton Michelle , Yu Jingjie , Pakrasi Himadri B. , Bhattacharyya-Pakrasi Maitrayee 
Published: May 2018

ABSTRACTBiological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N2fixation is energetically highly expensive, and an energy generating process such as photosynthesis can meet the energy demand of N2fixation. However, synthesis and expression of nitrogenase is exquisitely sensitive to oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N2. Here, we demonstrate a feasible way to engineer nitrogenase activity in the non-diazotrophic cyanobacteriumSynechocystissp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacteriumCyanothecesp. ATCC 51142. In addition, we have identified the minimalnifcluster required for such activity inSynechocystis6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels ofnifgenes. Importantly, the O2tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineeredSynechocystis6803 strains that remarkably have more than 30% N2-fixation activity compared to that inCyanothece51142, the highest such activity established in any non-diazotrophic oxygenic photosynthetic organism. This study establishes a baseline towards the ultimate goal of engineering nitrogen fixation ability in crop plants.IMPORTANCEApplication of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes as well as the wide spread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow crop plants the ability to fix atmospheric N2in situ. One long-term approach is to transfer allnifgenes from a prokaryote to plant cells, and express nitrogenase in an energy-producing organelle, chloroplast or mitochondrion. In this context,Synechocystis6803, the non-diazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.
The chloroplast 2-cysteine peroxiredoxin functions as thioredoxin oxidase in redox regulation of chloroplast metabolism
Authors: Vaseghi Mohamad-Javad , Chibani Kamel , Telman Wilena , Liebthal Michael , Gerken Melanie , Müller Sara Mareike , Dietz Karl-Josef 
Published: May 2018

AbstractThiol-dependent redox regulation controls central processes in plant cells including photosynthesis. Thioredoxins reductively activate e.g. Calvin-Benson cycle enzymes. However the mechanism of oxidative inactivation is unknown despite its importance for efficient regulation. Here, the abundant 2-cysteine peroxiredoxin (2-CysPrx), but not its site-directed variants, mediates rapid inactivation of reductively activated fructose-1,6-bisphosphatase and NADPH-dependent malate dehydrogenase (MDH) in the presence of the proper thioredoxins. Deactivation of phosphoribulokinase and MDH was compromised in 2cysprxAB mutants plants upon light/dark transition compared to wildtype. The decisive role of 2cysprxAB in regulating photosynthesis was evident from reoxidation kinetics of ferredoxin upon darkening of intact leaves since its half time decreased 3.5-times in 2cysprxAB. The disadvantage of inefficient deactivation turned into an advantage in fluctuating light. The results show that the 2-CysPrx serves as electron sink in the thiol network important to oxidize reductively activated proteins and represents the missing link in the reversal of thioredoxin-dependent regulation.
Epigenetic regulation affects fertility inDrosophila: toward the production of infertile models
Authors: Kohzaki Hidetsugu , Asano Maki , Murakami Yota , Mazo Alexander 
Published: May 2018

AbstractWe have revealed that the chorion gene clusters amplify by repeatedly initiating DNA replication from chorion gene amplification origins in the response to developmental signals, through the transcription factors inDrosophilaovarian follicle cells. Orc1, Orc2, and Cdc6 are forms of DNA replication machinery, which are conserved from yeast to humans; and Orc1 and Orc2 mutants are lethal. Overexpression of Orc1 or Orc2 (subunits of the origin recognition complex) led to female sterility, but overexpression of Cdc6 (an Orc family member) or GFP did not. We propose that DNA replication machinery contributes to development.Recently, we found that H3K4 was trimethylated at chorion gene amplification origins, but not at the Act1 locus. Overexpression of Lsd1H3K4 dimethylase and Lid H3K4 trimethylase are female sterile but not a Lid mutant. These results showed that epigenetic regulation affected fertility. Screening strategies usingDrosophilaflies could also lead to the development of drugs that reduce sterility and epigenetic effects related histone modification.Summary statementThere are approximately 470,000 infertile individuals in Japan. We knockowned the prereplicative complex components and demethlases duringDrosophilaovary development. In these drospohila, we could be the model of infertile.
‘In plaque-mass spectrometry imaging’ reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions
Authors: Schleyer Guy , Shahaf Nir , Ziv Carmit , Dong Yonghui , Meoded Roy A. , Helfrich Eric J. N. , Schatz Daniella , Rosenwasser Shilo , Rogachev Ilana , Aharoni Asaph , Piel Jörn , Vardi Assaf 
Published: May 2018

AbstractTapping into the metabolic cross-talk between a host and its virus can reveal unique strategies employed during infection. Viral infection is a dynamic process that generates an evolving metabolic landscape. Gaining a continuous view into the infection process is highly challenging and is limited by current metabolomics approaches, which typically measure the average of the entire population at various stages of infection. Here, we took a novel approach to study the metabolic basis of host-virus interactions between the bloom-forming algaEmiliania huxleyiand its specific virus. We combined a classical method in virology, plaque assay, with advanced mass spectrometry imaging (MSI), an approach we termed ‘in plaque-MSI’. Taking advantage of the spatial characteristics of the plaque, we mapped the metabolic landscape induced during infection in a high spatiotemporal resolution, unfolding the infection process in a continuous manner. Further unsupervised spatially-aware clustering, combined with known lipid biomarkers, revealed a systematic metabolic shift towards lipids containing the odd-chain fatty acid pentadecanoic acid (C15:0) induced during infection. Applying ‘in plaque-MSI’ might pave the way for the discovery of novel bioactive compounds that mediate the chemical arms race of host-virus interactions in diverse model systems.