bluuebunny/crossref_metadata_2025_split huggingface dataset:
Severe Community-Acquired Pneumonia due to Acinetobacter baumannii in North America: Case Report and Review of the Literature
Authors: Serota David P , Sexton Mary Elizabeth , Kraft Colleen S , Palacio Federico 
Published: March 2018

Abstract
Acinetobacter baumannii is a rare but emerging cause of fulminant community-acquired pneumonia (CAP-AB). We describe a patient from a rural area who developed acute respiratory distress syndrome and septic shock. We describe risk factors and characteristics of this syndrome and review published cases of CAP-AB from North America.
Effects of dietary chlortetracycline, Origanum essential oil, and pharmacological Cu and Zn on growth performance of nursery pigs
Authors: Feldpausch J A , Amachawadi R G , Tokach M D , Scott H M , Dritz S S , Goodband R D , Woodworth J C , DeRouchey J M 
Published: March 2018

Abstract
Two 47-d experiments were conducted with 21-d-old weaned pigs (PIC 1050, initially 6.1 kg) to determine the effects of feeding low or high doses of chlortetracycline (CTC) and antibiotic alternatives (Cu, Zn, and essential oil [EO]), alone or in combination, on growth performance. On d 5 postweaning, pens of 5 pigs were allotted to diet treatments with 8 (exp. 1) or 7 (exp. 2) replicate pens per treatment. In exp. 1, treatments were fed from d 5 to 26 postweaning and arranged in a 2 × 3 factorial with main effects of added ZnO (0 vs. 2,500 ppm of Zn) and CTC (0, 55, or 441 ppm). In exp. 2, treatments were fed from d 5 to 33 and structured in a (2 × 2 × 2) + 2 factorial with main effects of added CuSO4 (0 vs. 125 ppm Cu), added ZnO (0 vs. 3,000 ppm Zn from d 5 to 12 and 2,000 ppm Zn from d 12 to 33), and Regano EX (0 vs. 0.1% Regano EX containing 5% Origanum oil). The 2 additional treatments were subtherapeutic (55 ppm) and therapeutic (441 ppm) levels of CTC. Following the treatment period, a common diet without antimicrobial was fed until d 47. All diets contained 16.5 ppm Cu and 110 ppm Zn from the trace mineral premix. In exp. 1, no ZnO × CTC interactions were observed. Feeding ZnO increased (P &lt; 0.05) ADG, ADFI, and BW during the treatment period and increased (P &lt; 0.05) ADG and ADFI overall (d 5 to 47). Pigs fed CTC had increased (linear, P &lt; 0.05) ADG, ADFI, and BW during the treatment period and had marginally significant increases (linear, P &lt; 0.10) in overall ADG and ADFI, but overall G:F tended (quadratic, P = 0.070) to increase then decrease as CTC increased. During the treatment period in exp. 2, EO did not affect ADG or ADFI, whereas pharmacological levels of Cu, Zn, and CTC increased (P &lt; 0.05) ADG with coinciding increases (P = 0.055, 0.006, and linear 0.079, respectively) in ADFI. Copper, Zn, and CTC did not affect G:F. EO decreased (P = 0.009) G:F. Diet treatments had minimal carryover effects on subsequent nursery pig growth performance. Overall from d 5 to 47, Cu increased (P = 0.018) ADG, Zn increased (P &lt; 0.05) ADG and ADFI, and EO tended to decrease (P = 0.086) G:F. In conclusion, increased dietary Cu, Zn, or CTC improved weanling pig performance while EO elicited no growth benefits. The benefits of added Zn from ZnO and CTC were additive and could be included together in diets to maximize growth performance of weaned pigs.
Dynamic integration of multisensory turn commands supports active reorienting during ongoing navigation
Authors: Currier Timothy A. , Nagel Katherine I. 
Published: March 2018

SummaryA longstanding goal of systems neuroscience is to quantitatively describe how the brain integrates cues from multiple modalities over time. Here we develop a closed-loop orienting paradigm inDrosophilato study the algorithms by which stimuli from different modalities are combined during ongoing navigation. We show that flies faced with an attractive visual and an aversive mechanosensory cue exhibit sequential responses, first turning away from the co-localized stimuli before turning back toward them. We also find that the presence of the aversive cue slows flies’ turns toward the attractive target, suggesting that conflicting unimodal turn commands are summed to produce multisensory turns of intermediate velocity. We then test a series of computational frameworks and find that integration is best described by a model in which multimodal stimuli are continuously and dynamically scaled, converted into turn commands, and then summed to produce ongoing orientation behavior.
Optimizing Disease Surveillance with Blockchain
Authors: Coelho Flávio Codeço 
Published: March 2018

AbstractDisease surveillance, especially for infectious diseases, is a complex and inefficient process. Here we propose an optimized, blockchain-based monitoring and reporting process which can achieve all the desired features of an ideal surveillance system while maintaining costs down and being transparent and robust. We describe the technical specifications of such a solution and discuss possibilities for its implementation. Finally, the impact of the adoption of distributed ledger technology for disease surveillance is discussed.
Zika Virus Outbreak, Barbados, 2015 – 2016
Authors: Ryan Sadie J. , Lippi Catherine A. , Carlson Colin J. , Stewart-Ibarra Anna M. , Borbor-Cordova Mercy J. , Romero Moory M. , Cox Shelly-Ann , Mahon Roché , Trotman Adrian , Rollock Leslie , Gittens-St. Hilaire Marquita , King Desmond , Daniel Stephen 
Published: March 2018

AbstractBarbados is a Caribbean island country of approximately 285,000 people, with a thriving tourism industry. In 2015, Zika spread rapidly throughout the Americas, and its proliferation through the Caribbean islands followed suit. Barbados reported its first confirmed autochthonous Zika transmission to the Pan American Health Organization (PAHO) in January 2016, a month before the global public health emergency was declared. Following detection of suspected Zika cases on Barbados in 2015, 926 individuals were described as suspected cases, and 147 lab confirmed cases were reported through December 2016, the end of the most recent epidemiological year. In this short report, we describe the epidemiological characteristics of 926 clinical case records which were originally suspected as cases of Zika, and which were subsequently sent for testing and confirmation; 147 were found positive for Zika, using RT-PCR methods, another 276 tested negative, and the remaining 503 were either pending results or still in the suspected category. Women were represented at about twice the rate of men in case records where sex was reported (71.9%), and confirmed cases (78.2%), and 19 of the confirmed positive cases were children under the age of 10.
Characterization of Diverse Homoserine Lactone Synthases inEscherichia coli
Authors: Daer René , Barrett Cassandra , Melendez Ernesto Luna , Wu Jiaqi , Tekel Stefan , Xu Jimmy , Dennison Brady , Muller Ryan , Haynes Karmella 
Published: March 2018

AbstractQuorum sensing networks have been identified in over one hundred bacterial species to date. A subset of these networks regulate group behaviors, such as bioluminescence, virulence, and biofilm formation, by sending and receiving small molecules called homoserine lactones (HSLs). Bioengineers have incorporated quorum sensing pathways into genetic circuits to connect logical operations. However, the development of higher-order genetic circuitry is inhibited by crosstalk, in which one quorum sensing network responds to HSLs produced by a different network. Here, we report the construction and characterization of a library of ten synthases including some that are expected to produce HSLs that are incompatible with the Lux pathway, and therefore show no crosstalk. We demonstrated their function in a common lab chassis,Escherichia coliBL21, and in two contexts, liquid and solid agar cultures, using decoupled Sender and Receiver pathways. We observed weak or strong stimulation of a Lux Receiver by longer-chain or shorter-chain HSL-generating Senders, respectively. We also considered the under-investigated risk of unintentional release of incompletely deactivated HSLs in biological waste. We found that HSL-enriched media treated with bleach is still bioactive, while autoclaving deactivates LuxR induction. This work represents the most extensive comparison of quorum sensing synthases to date and greatly expands the bacterial signaling toolkit while recommending practices for disposal based on empirical, quantitative evidence.
Dynamic Kinetochore Size Regulation Promotes Microtubule Capture and Chromosome Biorientation in Mitosis
Authors: Sacristan Carlos , Ahmad Misbha , Keller Jenny , Fermie Job , Groenewold Vincent , Tromer Eelco , Fish Alexander , Melero Roberto , Carazo José María , Klumperman Judith , Musacchio Andrea , Perrakis Anastassis , Kops Geert JPL 
Published: March 2018

ABSTRACTFaithful chromosome segregation depends on the ability of sister kinetochores to attach to spindle microtubules. An outer layer of the kinetochore known as the fibrous corona transiently expands in early mitosis and disassembles upon microtubule capture. Neither the functional importance nor the mechanistic basis for this are known. Here we show that the dynein adaptor Spindly and the RZZ kinetochore complex drive fibrous corona formation in a dynein-independent manner. C-terminal farnesylation and MPS1 kinase activity cause conformational changes of Spindly that promote oligomerization of RZZ:Spindly complexes into a corona-like meshwork in cells and in vitro. Concurrent with corona expansion, Spindly potentiates corona shedding by recruiting dynein via three conserved short linear motifs. Expanded, non-sheddable fibrous coronas engage in extensive, long-lived lateral microtubule interactions that persist to metaphase and result in fused sister kinetochores, formation of merotelic attachments and chromosome segregation errors in anaphase. Thus, dynamic kinetochore size regulation in mitosis is coordinated by a single, Spindly-based mechanism that promotes initial microtubule capture and subsequent correct maturation of attachments.
Transcription-driven Chromatin Repression of Intragenic Promoters
Authors: Nielsen Mathias , Ard Ryan , Leng Xueyuan , Ivanov Maxim , Kindgren Peter , Pelechano Vicente , Marquardt Sebastian 
Published: March 2018

SummaryProgression of RNA polymerase II (RNAPII) transcription relies on the appropriately positioned activities of elongation factors. The resulting profile of factors and chromatin signatures along transcription units provides a “positional information system” for transcribing RNAPII. Here, we investigate a chromatin-based mechanism that suppresses intragenic initiation of RNAPII transcription. We demonstrate that RNAPII transcription across gene promoters represses their function in plants. This repression is characterized by reduced promoter-specific molecular signatures and increased molecular signatures associated with RNAPII elongation. The FACT histone chaperone complex is required for this repression mechanism. Genome-wide mapping of Transcription Start Sites (TSSs) reveals thousands of discrete intragenic TSS positions in FACT mutants. Histone 3 lysine 4 mono-methylation poises exonic sites to initiate RNAPII transcription in FACT mutants. Uncovering the mechanism for intragenic TSS repression through the act of RNAPII elongation has important implications for understanding pervasive RNAPII transcription and the regulation of transcript isoform diversity.
Experimental loss of generalist plants reveals alterations in plant-pollinator interactions and a constrained flexibility of foraging
Authors: Biella Paolo , Akter Asma , Ollerton Jeff , Tarrant Sam , Janeček Štěpán , Jersáková Jana , Klečka Jan 
Published: March 2018

AbstractSpecies extinctions undermine ecosystem functioning but species do not disappear at random. Ecosystem dynamics are ruled by a subset of dominant species, but it is not clear how losing several of these key species would affect plant-pollinator interactions. We tested how the experimental loss of the most highly visited generalist plants would affect flower visitor abundances (visitation) and pollinator effectiveness (quantity of pollen-tubes within pistils) in several sites. Significant changes in the plant-pollinator communities were detected. Firstly, visitation decreased after removing 1-2 most visited plants, suggesting that these species mostly facilitate other plants by keeping high flower visitor abundances in the sites. Nevertheless, we recorded within-site variations of these trends, especially among sampled transects and among plant species, suggesting that complex facilitation-competition interactions occur among plants, but that these vary among transects within the same sites. Pollinator effectiveness fluctuated but not in a clear linear way and was not directly linked to changes of flower visitation. This suggests that fluctuations of pollinator effectiveness might be due to destabilization of the pollinators by the removal of key resources. In addition, we detected a constrained flexibility of the foraging of flower visitors because they did not switch among flower shapes and they favoured specific plant traits such as high sugar content, small inflorescences and taller plants. Indeed, these constraints would eventually limit utilisation of new resources after perturbations, possibly undermining the stability of the system. In conclusion, our work demonstrates that the loss of dominant, highly generalist plants alters plant-pollinator interactions with implications for pollination and insect foraging. Therefore, in order to preserve ecosystems, generalist plants should not get lost, because they sustain the complex pattern of interactions between plants and flower visitors.
A genome-wide scan for correlated mutations detects macromolecular and chromatin interactions in Arabidopsis thaliana
Authors: Perlaza-Jiménez Laura , Walther Dirk 
Published: March 2018

AbstractThe concept of exploiting correlated mutations has been introduced and applied successfully to identify interactions within and between biological macromolecules. Its rationale lies in the preservation of physical interactions via compensatory mutations. With the massive increase of available sequence information, approaches based on correlated mutations have regained considerable attention.We analyzed a set of 10,707,430 single nucleotide polymorphisms detected in 1,135 accessions of the plant Arabidopsis thaliana. To measure their covariance and to reveal the global genome-wide sequence correlation structure of the Arabidopsis genome, the adjusted mutual information has been estimated for each possible pair of polymorphic sites. We developed a series of filtering steps to account for genetic linkage and lineage relations between Arabidopsis accessions, as well as transitive covariance as possible confounding factors. We show that upon appropriate filtering, correlated mutations prove indeed informative with regard to molecular interactions, and furthermore, appear to reflect on chromosomal interactions.Our study demonstrates that the concept of correlated mutations can also be applied successfully to within-species sequence variation and establishes a promising approach to help unravel the complex molecular interactions in A. thaliana and other species with broad sequence information.
Dendritic NMDA receptors in parvalbumin neurons enable strong and stable neuronal assemblies
Authors: Cornford Jonathan , Mercier Marion S , Leite Marco , Magloire Vincent , Häusser Michael , Kullmann Dimitri M 
Published: March 2018

AbstractParvalbumin-expressing (PV+) GABAergic interneurons mediate feedforward and feedback inhibition and have a key role in gamma oscillations and information processing. The importance of fast synaptic recruitment, action potential initiation and repolarization, and rapid synchronous GABA release by PV+ cells is well established. In contrast, the functional significance of PV+ cell NMDA receptors (NMDARs), which generate relatively slow postsynaptic currents, is unclear. Underlining their importance, several studies implicate PV+ cell NMDAR disruption in impaired network function and circuit pathologies. Here, we show that dendritic NMDARs underlie supralinear integration of feedback excitation from local pyramidal neurons onto mouse CA1 PV+ cells. Furthermore, by incorporating NMDARs at feedback connections onto PV+ cells in spiking networks, we show that these receptors enable cooperative recruitment of PV+ interneurons, strengthening and stabilising principal cell assemblies. Failure of this phenomenon provides a parsimonious explanation for cognitive and sensory gating deficits in pathologies with impaired PV+ NMDAR signalling.
Quantifying how constraints limit the diversity of viable routes to adaptation
Authors: Yeaman Sam , Gerstein Aleeza C. , Hodgins Kathryn A. , Whitlock Michael C. 
Published: March 2018

AbstractConvergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.
SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
Authors: Nagy Gabor , Igaev Maxim , Hoffmann Søren V. , Jones Nykola C. , Grubmüller Helmut 
Published: March 2018

AbstractCircular dichroism spectroscopy is a highly sensitive, but low-resolution technique to study the structure of proteins. Combined with molecular modelling or other complementary techniques, CD spectroscopy can provide essential information at higher resolution. To this end, we introduce a new computational method to calculate the electronic circular dichroism spectra of proteins from a structural model or ensemble using the average secondary structure composition and a pre-calculated set of basis spectra. We compared the predictive power of our method to existing algorithms – namely DichroCalc and PDB2CD – and found that it predicts CD spectra more accurately, with a 50% smaller average deviation from the measured CD spectra. Our results indicate that the derived basis sets are robust to experimental errors in the reference spectra and to the choice of the secondary structure classification algorithm. For over 80% of the globular reference proteins, our basis sets accurately predict the experimental spectrum solely from their secondary structure composition. For the remaining 20%, correcting for intensity normalization considerably improves the prediction power. Additionally, we show that the predictions for short peptides and intrinsically disordered proteins strongly benefit from accounting for side-chain contributions and structural flexibility.Table Of Content Graphics:
Telomere-loop dynamics in chromosome end protection
Authors: Van Ly David , Jie Low Ronnie Ren , Frölich Sonja , Bartolec Tara K. , Kafer Georgia R. , Pickett Hilda A. , Gaus Katharina , Cesare Anthony J. 
Published: March 2018

SUMMARYWe used super-resolution microscopy to investigate the role of macromolecular telomere structure in chromosome end protection. In murine and human cells with reduced TRF2, we find that ATM-activation at chromosome ends occurs with a structural change from t-loops to linearized chromosome ends through t-loop unfolding. Comparably, we find Aurora B kinase regulates telomere linearity concurrent with ATM activation at telomeres during mitotic arrest. Using a separation of function allele, we find that the TRFH domain of TRF2 regulates t-loop formation while suppressing ATM activity. Notably, we demonstrate that telomere linearity and ATM activation occur separately from telomere fusion via non-homologous end-joining (NHEJ). Further, we show that linear DDR-positive telomeres can remain resistant to fusion, even during an extended G1-arrest when NHEJ is most active. Collectively, these results suggest t-loops act as conformational switches that regulate ATM activation at chromosome ends independent of mechanisms to suppress chromosome end fusion.
Broad-scale mercury bioaccumulation patterns in two freshwater sport fishes: testing the role of growth dilution in a warming climate
Authors: Thomas Shyam M. , Melles Stephanie J. , Bhavsar Satyendra P. 
Published: March 2018

AbstractSport fishes at the apex of aquatic food webs are indicators of mercury in the environment. However bioaccumulation of mercury in fish is a complex process that varies in space and time. Both large-scale climatic and environmental, as well as biological factors are drivers of these space-time variations. In this study, we avail a long-running monitoring program from Ontario, Canada to better understand spatiotemporal variations in fish mercury bioaccumulation. Focussing on two common large-bodied fishes (Walleye and Northern Pike), the data were first stratified by latitudinal zone (north, mid, and south) and eight temporal periods (between 1975 & 2015). A series of linear mixed-effects models (LMEMs) with latitudinal zone, time period, and their interactions as random effects were used to capture the spatial, temporal, and spatiotemporal variations in mercury bioaccumulation. The random slopes from the best-fitting LMEM were used to define bioaccumulation index and capture trends in space and time. Given the generally warming climate trend over the past 45 years, the role of growth dilution in modulating the bioaccumulation trends was also evaluated. The full model comprising of space, time and space-time interactions was the best-fit with interaction effects explaining most of the variation. Spatiotemporal trends showed overall similar patterns for both species. Growth dilution in conjunction with estimated rates of warming for different latitudinal zones failed to explain the spatiotemporal trends. Temporal trends showed contrasting bioaccumulation patterns-increasing in Northern Pike and decreasing in Walleye, suggesting temperature-driven growth dilution is more likely in latter. However, a space-for-time substitution revealed only a weak presence of growth dilution in Walleye, and it was not attributable to temperature differences. Overall, our study summarizes broad-scale variations in fish mercury and explores the role of growth dilution in shaping the observed patterns.