bluuebunny/crossref_metadata_2025_split huggingface dataset:
Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age
Authors: Stearns Jennifer C , Davidson Carla J , McKeon Suzanne , Whelan Fiona J , Fontes Michelle E , Schryvers Anthony B , Bowdish Dawn M E , Kellner James D , Surette Michael G 
Published: January 2015

AbstractThe upper respiratory tract (URT) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. Young children are at high risk of respiratory illness, yet the composition of their URT microbiota is not well understood. Microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only report the relative abundance of bacterial populations. In the current study, we used both molecular profiling of the bacterial 16S rRNA gene and laboratory culture to examine the bacterial diversity from the oropharynx and nasopharynx of 51 healthy children with a median age of 1.1 years (range 1–4.5 years) along with 19 accompanying parents. The resulting profiles suggest that in young children the nasopharyngeal microbiota, much like the gastrointestinal tract microbiome, changes from an immature state, where it is colonized by a few dominant taxa, to a more diverse state as it matures to resemble the adult microbiota. Importantly, this difference in bacterial diversity between adults and children accompanies a change in bacterial load of three orders of magnitude. This indicates that the bacterial communities in the nasopharynx of young children have a fundamentally different structure from those in adults and suggests that maturation of this community occurs sometime during the first few years of life, a period that includes ages at which children are at the highest risk for respiratory disease.
Similarities and seasonal variations in bacterial communities from the blood of rodents and from their flea vectors
Authors: Cohen Carmit , Toh Evelyn , Munro Daniel , Dong Qunfeng , Hawlena Hadas 
Published: January 2015

Abstract
Vector-borne microbes are subject to the ecological constraints of two distinct microenvironments: that in the arthropod vector and that in the blood of its vertebrate host. Because the structure of bacterial communities in these two microenvironments may substantially affect the abundance of vector-borne microbes, it is important to understand the relationship between bacterial communities in both microenvironments and the determinants that shape them. We used pyrosequencing analyses to compare the structure of bacterial communities in Synosternus cleopatrae fleas and in the blood of their Gerbillus andersoni hosts. We also monitored the interindividual and seasonal variability in these bacterial communities by sampling the same individual wild rodents during the spring and again during the summer. We show that the bacterial communities in each sample type (blood, female flea or male flea) had a similar phylotype composition among host individuals, but exhibited seasonal variability that was not directly associated with host characteristics. The structure of bacterial communities in male fleas and in the blood of their rodent hosts was remarkably similar and was dominated by flea-borne Bartonella and Mycoplasma phylotypes. A lower abundance of flea-borne bacteria and the presence of Wolbachia phylotypes distinguished bacterial communities in female fleas from those in male fleas and in rodent blood. These results suggest that the overall abundance of a certain vector-borne microbe is more likely to be determined by the abundance of endosymbiotic bacteria in the vector, abundance of other vector-borne microbes co-occurring in the vector and in the host blood and by seasonal changes, than by host characteristics.
CCR7-dependent trafficking of RORγ+ ILCs creates a unique microenvironment within mucosal draining lymph nodes
Authors: Mackley Emma C. , Houston Stephanie , Marriott Clare L. , Halford Emily E. , Lucas Beth , Cerovic Vuk , Filbey Kara J. , Maizels Rick M. , Hepworth Matthew R. , Sonnenberg Gregory F. , Milling Simon , Withers David R. 
Published: January 2015

AbstractPresentation of peptide:MHCII by RORγ-expressing group 3 innate lymphoid cells (ILC3s), which are enriched within gut tissue, is required for control of CD4 T-cell responses to commensal bacteria. It is not known whether ILC populations migrate from their mucosal and peripheral sites to local draining secondary lymphoid tissues. Here we demonstrate that ILC3s reside within the interfollicular areas of mucosal draining lymph nodes, forming a distinct microenvironment not observed in peripheral lymph nodes. By photoconverting intestinal cells in Kaede mice we reveal constitutive trafficking of ILCs from the intestine to the draining mesenteric lymph nodes, which specifically for the LTi-like ILC3s was CCR7-dependent. Thus, ILC populations traffic to draining lymph nodes using different mechanisms.
On-chip detection of non-classical light by scalable integration of single-photon detectors
Authors: Najafi Faraz , Mower Jacob , Harris Nicholas C. , Bellei Francesco , Dane Andrew , Lee Catherine , Hu Xiaolong , Kharel Prashanta , Marsili Francesco , Assefa Solomon , Berggren Karl K. , Englund Dirk 
Published: January 2015

AbstractPhotonic-integrated circuits have emerged as a scalable platform for complex quantum systems. A central goal is to integrate single-photon detectors to reduce optical losses, latency and wiring complexity associated with off-chip detectors. Superconducting nanowire single-photon detectors (SNSPDs) are particularly attractive because of high detection efficiency, sub-50-ps jitter and nanosecond-scale reset time. However, while single detectors have been incorporated into individual waveguides, the system detection efficiency of multiple SNSPDs in one photonic circuit—required for scalable quantum photonic circuits—has been limited to <0.2%. Here we introduce a micrometer-scale flip-chip process that enables scalable integration of SNSPDs on a range of photonic circuits. Ten low-jitter detectors are integrated on one circuit with 100% device yield. With an average system detection efficiency beyond 10%, and estimated on-chip detection efficiency of 14–52% for four detectors operated simultaneously, we demonstrate, to the best of our knowledge, the first on-chip photon correlation measurements of non-classical light.
Combining gene mutation with gene expression data improves outcome prediction in myelodysplastic syndromes
Authors: Gerstung Moritz , Pellagatti Andrea , Malcovati Luca , Giagounidis Aristoteles , Porta Matteo G Della , Jädersten Martin , Dolatshad Hamid , Verma Amit , Cross Nicholas C. P. , Vyas Paresh , Killick Sally , Hellström-Lindberg Eva , Cazzola Mario , Papaemmanuil Elli , Campbell Peter J. , Boultwood Jacqueline 
Published: January 2015

AbstractCancer is a genetic disease, but two patients rarely have identical genotypes. Similarly, patients differ in their clinicopathological parameters, but how genotypic and phenotypic heterogeneity are interconnected is not well understood. Here we build statistical models to disentangle the effect of 12 recurrently mutated genes and 4 cytogenetic alterations on gene expression, diagnostic clinical variables and outcome in 124 patients with myelodysplastic syndromes. Overall, one or more genetic lesions correlate with expression levels of ~20% of all genes, explaining 20–65% of observed expression variability. Differential expression patterns vary between mutations and reflect the underlying biology, such as aberrant polycomb repression for ASXL1 and EZH2 mutations or perturbed gene dosage for copy-number changes. In predicting survival, genomic, transcriptomic and diagnostic clinical variables all have utility, with the largest contribution from the transcriptome. Similar observations are made on the TCGA acute myeloid leukaemia cohort, confirming the general trends reported here.
Innate sensing of microbial products promotes wound-induced skin cancer
Authors: Hoste Esther , Arwert Esther N. , Lal Rohit , South Andrew P. , Salas-Alanis Julio C. , Murrell Dedee F. , Donati Giacomo , Watt Fiona M. 
Published: January 2015

AbstractThe association between tissue damage, chronic inflammation and cancer is well known. However, the underlying mechanisms are unclear. Here we characterize a mouse model in which constitutive epidermal extracellular-signal-regulated kinase-MAP-kinase signalling results in epidermal inflammation, and skin wounding induces tumours. We show that tumour incidence correlates with wound size and inflammatory infiltrate. Ablation of tumour necrosis factor receptor (TNFR)-1/-2, Myeloid Differentiation primary response gene 88 or Toll-like receptor (TLR)-5, the bacterial flagellin receptor, but not other innate immune sensors, in radiosensitive leukocytes protects against tumour formation. Antibiotic treatment inhibits, whereas injection of flagellin induces, tumours in a TLR-5-dependent manner. TLR-5 is also involved in chemical-induced skin carcinogenesis in wild-type mice. Leukocytic TLR-5 signalling mediates upregulation of the alarmin HMGB1 (High Mobility Group Box 1) in wound-induced papillomas. HMGB1 is elevated in tumours of patients with Recessive Dystrophic Epidermolysis Bullosa, a disease characterized by chronic skin damage. We conclude that in our experimental model the combination of bacteria, chronic inflammation and wounding cooperate to trigger skin cancer.
Tropomodulin3 is a novel Akt2 effector regulating insulin-stimulated GLUT4 exocytosis through cortical actin remodeling
Authors: Lim Chun-Yan , Bi Xuezhi , Wu Donghai , Kim Jae Bum , Gunning Peter W. , Hong Wanjin , Han Weiping 
Published: January 2015

AbstractAkt2 and its downstream effectors mediate insulin-stimulated GLUT4-storage vesicle (GSV) translocation and fusion with the plasma membrane (PM). Using mass spectrometry, we identify actin-capping protein Tropomodulin 3 (Tmod3) as an Akt2-interacting partner in 3T3-L1 adipocytes. We demonstrate that Tmod3 is phosphorylated at Ser71 on insulin-stimulated Akt2 activation, and Ser71 phosphorylation is required for insulin-stimulated GLUT4 PM insertion and glucose uptake. Phosphorylated Tmod3 regulates insulin-induced actin remodelling, an essential step for GSV fusion with the PM. Furthermore, the interaction of Tmod3 with its cognate tropomyosin partner, Tm5NM1 is necessary for GSV exocytosis and glucose uptake. Together these results establish Tmod3 as a novel Akt2 effector that mediates insulin-induced cortical actin remodelling and subsequent GLUT4 membrane insertion. Our findings suggest that defects in cytoskeletal remodelling may contribute to impaired GLUT4 exocytosis and glucose uptake.
Distinct p21 requirements for regulating normal and self-reactive T cells through IFN-γ production
Authors: Daszkiewicz Lidia , Vázquez-Mateo Cristina , Rackov Gorjana , Ballesteros-Tato André , Weber Kathrin , Madrigal-Avilés Adrián , Di Pilato Mauro , Fotedar Arun , Fotedar Rati , Flores Juana M. , Esteban Mariano , Martínez-A Carlos , Balomenos Dimitrios 
Published: January 2015

AbstractSelf/non-self discrimination characterizes immunity and allows responses against pathogens but not self-antigens. Understanding the principles that govern this process is essential for designing autoimmunity treatments. p21 is thought to attenuate autoreactivity by limiting T cell expansion. Here, we provide direct evidence for a p21 role in controlling autoimmune T cell autoreactivity without affecting normal T cell responses. We studied C57BL/6, C57BL/6/lpr and MRL/lpr mice overexpressing p21 in T cells and showed reduced autoreactivity and lymphadenopathy in C57BL/6/lpr and reduced mortality in MRL/lpr mice. p21 inhibited effector/memory CD4+ CD8+ and CD4−CD8−lpr T cell accumulation without altering defective lpr apoptosis. This was mediated by a previously non-described p21 function in limiting T cell overactivation and overproduction of IFN-γ, a key lupus cytokine. p21 did not affect normal T cell responses, revealing differential p21 requirements for autoreactive and normal T cell activity regulation. The underlying concept of these findings suggests potential treatments for lupus and autoimmune lymphoproliferative syndrome, without compromising normal immunity.
A unique mechanism of successful fertilization in a domestic bird
Authors: Sasanami Tomohiro , Izumi Shunsuke , Sakurai Naoki , Hirata Toshifumi , Mizushima Shusei , Matsuzaki Mei , Hiyama Gen , Yorinaga Eriko , Yoshimura Takashi , Ukena Kazuyoshi , Tsutsui Kazuyoshi 
Published: January 2015

AbstractFertilization is an indispensable step for formation of a zygote in sexual reproduction, leading to species survival. When mating occurs, sperm is transported to the female reproductive tracts via the seminal plasma (SP). SP is derived from male accessory sex glands and it plays pivotal roles for fertilization in animals. However, molecular mechanisms of SP or a fluid derived from male accessory sex glands for successful fertilization remain unclear. Here, we report that in male quail the cloacal gland (CG) produces prostaglandin F2α (PGF2α) that contributes to successful fertilization. PGF2α, as well as the secretion of CG (CGS), induced vaginal contractions and caused the opening of the entrance of the sperm storage tubules, the structures responsible for the long-term sperm storage and fertilization. The removal of CGS from the male before mating reduced the fertility, but the supplementation of CGS or PGF2α rescued the subfertility. We further showed that male CG contains glucose that is utilized as energy source for the intrinsic sperm mobility after transportation to female vagina. This mechanism, in concert with the excitatory effects of PGF2α enables successful fertilization in the domestic bird.
Wide‐range harmonic lock detector with real‐time delay measurement of delay‐locked loop
Authors: Kim Sangseob , Hyoung Chang‐Hee , Park Kyoung‐Hwan 
Published: January 2015

A new robust harmonic lock detector (HLD) suitable for a wide‐range delay‐locked loop (DLL) is presented. This detector is composed of some delay indicators measuring the total delay of the DLL in real time, and it can detect the harmonic lock for a wide frequency range close to 1–20 times higher than the minimum frequency. Owing to its seamless operation without any initialising process using external reset control, it can ensure reliable lock detection despite some unusual conditions, such as frequency change, electrical surge input or power‐ground fluctuation. The proposed HLD and the DLL were designed in 0.13 µm CMOS technology, and the simulation results showed the exact harmonic lock detection and reliable DLL locking properties over the whole frequency range from 25 to 500 MHz of the input clock.
Emerging vector-borne diseases and the potential to prevent them spreading.
Authors: Sánchez-Vizcaíno J. M. , Martínez-Avilés M. , Sánchez-Matamoros A. , Rodríguez-Prieto V. 
Published: January 2015

Abstract
Europe has experienced an increasing number of emerging vector-borne diseases and the recrudescence or re-emergence of others. Global warming offers suitable conditions for arthropod proliferation, some of which can be competent vectors of such diseases. With the increased risk of introduction of potentially infected animals because of shortened travelling times to any part of the world, vector-borne diseases are likely to emerge if the conditions for competent vector proliferation and suitable hosts are found at the destination. Vector-borne diseases are generally complex to deal with, so cooperation and collaboration of the different sectors implied, and with neighbouring countries, are fundamental to coordinate control and prevention actions. Among these, surveillance to detect these infections early is crucial, since susceptible hosts are frequently asymptomatic or mildly symptomatic. However, when conditions are suitable, the impact of these diseases can be very severe. The combination of epidemiological and diagnostic tools to identify locations, time and populations where an outbreak is expected to occur, and how to detect it as soon as possible, are fundamental for an effective surveillance. Another area of cooperation is the preparedness, through vaccine banks, against the different known strains, profound knowledge of immunity to vector-borne pathogens, and the development of diagnostic tests that can differentiate vaccinated from infected individuals. In this paper we review bluetongue, African horse sickness, West Nile fever and Rift Valley fever, and we focus on Europe's experience in tackling the emergence of these pathogens.
THE AKARI 2.5–5.0 μm SPECTRAL ATLAS OF TYPE-1 ACTIVE
GALACTIC NUCLEI: BLACK HOLE MASS ESTIMATOR, LINE RATIO, AND HOT DUST
TEMPERATURE
Authors: Kim Dohyeong , Im Myungshin , Kim Ji Hoon , Jun Hyunsung David , Woo Jong-Hak , Lee Hyung Mok , Lee Myung Gyoon , Nakagawa Takao , Matsuhara Hideo , Wada Takehiko , Oyabu Shinki , Takagi Toshinobu , Ohyama Youichi , Lee Seong-Kook 
Published: January 2015

ABSTRACT
We present 2.5–5.0 μm spectra of 83 nearby
(0.002 < z < 0.48) and bright (K <
14 mag) type-1 active galactic nuclei (AGNs) taken with the Infrared Camera on
board AKARI. The 2.5–5.0 μm spectral region contains emission
lines such as Brβ (2.63 μm), Brα (4.05 μm), and polycyclic aromatic hydrocarbons
(3.3 μm), which can be used for studying the black hole (BH) masses and star
formation activity in the host galaxies of AGNs. The spectral region also
suffers less dust extinction than in the ultra violet (UV) or optical
wavelengths, which may provide an unobscured view of dusty AGNs. Our sample is
selected from bright quasar surveys of Palomar-Green and SNUQSO, and AGNs with
reverberation-mapped BH masses from Peterson et al. Using 11 AGNs with reliable
detection of Brackett lines, we derive the Brackett-line-based BH mass
estimators. We also find that the observed Brackett line ratios can be explained
with the commonly adopted physical conditions of the broad line region.
Moreover, we fit the hot and warm dust components of the dust torus by adding
photometric data of SDSS, 2MASS, WISE, and ISO
to the AKARI spectra, finding hot and warm dust temperatures of
∼1100 K and ∼220 K, respectively, rather than the commonly cited hot dust
temperature of 1500 K.
LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors
Authors: Druet Tom , Georges Michel 
Published: January 2015

Abstract
Summary: Many applications in genetics require haplotype reconstruction. We present a phasing program designed for large half-sibs families (as observed in plant and animals) that is robust to genotyping and map errors. We demonstrate that it is more efficient than previous versions and other programs, particularly in the presence of genotyping errors.
Availability and implementation: The software LINKPHASE3 is included in the PHASEBOOK package and can be freely downloaded from www.giga.ulg.ac.be/jcms/prod_381171/software. The package is written in FORTRAN and contains source codes. A manual is provided with the package.
Contact: tom.druet@ulg.ac.be
Supplementary information: Supplementary data are available at Bioinformatics online.
Combining tree-based and dynamical systems for the inference of gene regulatory networks
Authors: Huynh-Thu Vân Anh , Sanguinetti Guido 
Published: January 2015

Abstract
Motivation: Reconstructing the topology of gene regulatory networks (GRNs) from time series of gene expression data remains an important open problem in computational systems biology. Existing GRN inference algorithms face one of two limitations: model-free methods are scalable but suffer from a lack of interpretability and cannot in general be used for out of sample predictions. On the other hand, model-based methods focus on identifying a dynamical model of the system. These are clearly interpretable and can be used for predictions; however, they rely on strong assumptions and are typically very demanding computationally.
Results: Here, we propose a new hybrid approach for GRN inference, called Jump3, exploiting time series of expression data. Jump3 is based on a formal on/off model of gene expression but uses a non-parametric procedure based on decision trees (called ‘jump trees’) to reconstruct the GRN topology, allowing the inference of networks of hundreds of genes. We show the good performance of Jump3 on in silico and synthetic networks and applied the approach to identify regulatory interactions activated in the presence of interferon gamma.
Availability and implementation: Our MATLAB implementation of Jump3 is available at http://homepages.inf.ed.ac.uk/vhuynht/software.html.
Contact: vhuynht@inf.ed.ac.uk or G.Sanguinetti@ed.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification
Authors: Borozan Ivan , Watt Stuart , Ferretti Vincent 
Published: January 2015

Abstract
Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the complementary nature of alignment-based and alignment-free similarity measures with the aim to improve the accuracy with which DNA and protein sequences are characterized.
Results: Our model classifies sequences using a combined sequence similarity score calculated by adaptively weighting the contribution of different sequence similarity measures. Weights are determined independently for each sequence in the test set and reflect the discriminatory ability of individual similarity measures in the training set. Because the similarity between some sequences is determined more accurately with one type of measure rather than another, our classifier allows different sets of weights to be associated with different sequences. Using five different similarity measures, we show that our model significantly improves the classification accuracy over the current composition- and alignment-based models, when predicting the taxonomic lineage for both short viral sequence fragments and complete viral sequences. We also show that our model can be used effectively for the classification of reads from a real metagenome dataset as well as protein sequences.
Availability and implementation: All the datasets and the code used in this study are freely available at https://collaborators.oicr.on.ca/vferretti/borozan_csss/csss.html.
Contact: ivan.borozan@gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Using isoelectric point to determine the pH for initial protein crystallization trials
Authors: Kirkwood Jobie , Hargreaves David , O’Keefe Simon , Wilson Julie 
Published: January 2015

Abstract
Motivation: The identification of suitable conditions for crystallization is a rate-limiting step in protein structure determination. The pH of an experiment is an important parameter and has the potential to be used in data-mining studies to help reduce the number of crystallization trials required. However, the pH is usually recorded as that of the buffer solution, which can be highly inaccurate.
Results: Here, we show that a better estimate of the true pH can be predicted by considering not only the buffer pH but also any other chemicals in the crystallization solution. We use these more accurate pH values to investigate the disputed relationship between the pI of a protein and the pH at which it crystallizes.
Availability and implementation: Data used to generate models are available as Supplementary Material.
Contact: julie.wilson@york.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.