bluuebunny/crossref_metadata_2025 huggingface dataset:
Discovering Psychological Principles by Mining Naturally Occurring Data Sets
Authors: Goldstone Robert L. , Lupyan Gary
Published: July 2016

The very expertise with which psychologists wield their tools for achieving laboratory control may have had the unwelcome effect of blinding psychologists to the possibilities of discovering principles of behavior without conducting experiments. When creatively interrogated, a diverse range of large, real‐world data sets provides powerful diagnostic tools for revealing principles of human judgment, perception, categorization, decision‐making, language use, inference, problem solving, and representation. Examples of these data sets include patterns of website links, dictionaries, logs of group interactions, collections of images and image tags, text corpora, history of financial transactions, trends in twitter tag usage and propagation, patents, consumer product sales, performance in high‐stakes sporting events, dialect maps, and scientific citations. The goal of this issue is to present some exemplary case studies of mining naturally existing data sets to reveal important principles and phenomena in cognitive science, and to discuss some of the underlying issues involved with conducting traditional experiments, analyses of naturally occurring data, computational modeling, and the synthesis of all three methods.
New BAR tools for mining expression data and exploring Cis‐elements in Arabidopsis thaliana
Authors: Austin Ryan S. , Hiu Shu , Waese Jamie , Ierullo Matthew , Pasha Asher , Wang Ting Ting , Fan Jim , Foong Curtis , Breit Robert , Desveaux Darrell , Moses Alan , Provart Nicholas J.
Published: July 2016

Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy‐to‐use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis‐elements in the promoters of sets of co‐expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio‐Analytic Resource at http://BAR.utoronto.ca.
Improvement of hemoglobin levels after a switch from intravenous to subcutaneous administration of immunoglobulin in chronic inflammatory demyelinating polyneuropathy and multifocal motor neuropathy
Authors: Markvardsen Lars Høj , Christiansen Ingelise , Jakobsen Johannes
Published: July 2016

BACKGROUND

Intravenous immunoglobulin (IVIG) is recommended treatment for chronic inflammatory demyelinating polyneuropathy (CIDP) and multifocal motor neuropathy (MMN). Recent studies have demonstrated that subcutaneous immunoglobulin (SCIG) is feasible, safe, and effective in both disorders. IVIG leads to transient hemolysis and, consequently, we hypothesized that frequent small doses of SCIG exerts less hemolytic activity than a few larger doses of IVIG.

STUDY DESIGN AND METHODS

In an open‐label study, 23 three patients treated with IVIG for CIDP or MMN were switched to SCIG at an equal dosage. IVIG was administered two to three times for 6 weeks. Two weeks after the last IVIG infusion at Week 8, SCIG was initiated with injections twice or thrice weekly until Week 20. Blood samples were drawn 2 weeks after IVIG at Weeks 2 and 8 and during SCIG at Weeks 14 and 20 determining hemoglobin (Hb) and hemolytic variables.

RESULTS

Seventeen patients completed the study. At enrollment, the Hb level was 138 ± 12 g/L, haptoglobin level was 1.4 ± 0.5 g/L, reticulocyte count was 58.7 × 109 ± 21.3 × 109/L, and bilirubin level was 6.6 ± 2.3 µmol/L. The average of the two blood samples drawn at comparable intervals during IVIG and SCIG showed that Hb increased from 135 ± 15 to 138 ± 15 g/L (p = 0.03). During IVIG the hemolytic variables showed signs of mild hemolysis that improved during SCIG, haptoglobin increasing from 1.2 ± 0.5 to 1.5 ± 0.6 g/L (p = 0.002), reticulocytes decreasing from 71.9 × 109 ± 35.8 × 109 to 54.5 × 109 ± 16.3 × 109/L (p = 0.02), and bilirubin decreasing from 7.3 ± 2.8 to 5.8 ± 1.8 µmol/L (p = 0.001).

CONCLUSION

A switch from IVIG to SCIG was associated with a slight increase of Hb levels and an improvement of laboratory variables related to hemolytic activity.
Combination of ciclopirox olamine and sphingosine‐1‐phosphate as granulation enhancer in diabetic wounds
Authors: Lim Natalie Sheng Jie , Sham Adeline , Chee Stella Min Ling , Chan Casey , Raghunath Michael
Published: July 2016

Granulation tissue formation requires a robust angiogenic response. As granulation tissue develops, collagen fibers are deposited and compacted. Forces generated in the wake of this process drive wound contraction to reduce the wound area. In diabetics, both angiogenesis and wound contraction are diminished leading to impaired wound healing. To emulate this pathology and to address it pharmacologically, we developed a wound healing model in the diabetic Zucker fatty rat and tested a topical proangiogenic strategy combining antifungal agent ciclopirox olamine (CPX) and lysophospholipid sphingosine‐1‐phosphate (S1P) to promote diabetic wound closure. In vitro, we demonstrated that CPX + S1P up‐regulates a crucial driver of angiogenesis, hypoxia‐inducible factor‐1, in endothelial cells. Injection of CPX + S1P into subcutaneously implanted sponges in experimental rats showed, in an additive manner, a fivefold increased endothelial infiltration and lectin‐perfused vessel length. We developed a splinted diabetic rodent model to achieve low wound contraction rates that are characteristic for the healing mode of diabetic ulcers in humans. We discovered specific dorsal sites that allowed for incremental full‐thickness excisional wound depths from 1 mm (superficial) to 3 mm (deep). This enabled us to bring down wound contraction from 51% in superficial wounds to 8% in deep wounds. While the effects of topical gel treatment of CPX + S1P were masked by the rodent‐characteristic dominant contraction in superficial wounds, they became clearly evident in deep diabetic wounds. Here, a fivefold increase of functional large vessels resulted in accelerated granulation tissue formulation, accompanied by a 40% increase of compacted thick collagen fibers. This was associated with substantially reduced matrix metalloproteinase‐3 and ‐13 expression. These findings translated into a fivefold increase in granulation‐driven contraction, promoting diabetic wound closure. With CPX and S1P analogues already in clinical use, their combination presents itself as an attractive proangiogenic treatment to be repurposed for diabetic wound healing.
Evaluation of validity of the new diabetic foot ulcer assessment scale in Indonesia
Authors: Arisandi Defa , Oe Makoto , Roselyne Yotsu Rie , Matsumoto Masaru , Ogai Kazuhiro , Nakagami Gojiro , Tamaki Takeshi , Suriadi  , Sanada Hiromi , Sugama Junko
Published: July 2016

We developed a new assessment tool for diabetic foot ulcers because no such tool specifically for diabetic foot ulcer exists. The diabetic foot ulcer assessment scale (DFUAS) has 11 domain items. The minimum and maximum scores on this scale are 0 and 98, respectively; higher scores indicate more severe wounds. The aim of this study was to evaluate the concurrent validity, construct validity and predictive validity of DFUAS in Indonesia. A prospective cohort study was conducted on patients with diabetic foot ulcer at Kitamura wound clinic in Indonesia. A total of 62 patients with 70 diabetic foot ulcers were assessed with DFUAS tool, Bates‐Jensen wound assessment tool (BWAT), and pressure ulcer scale for healing (PUSH). Concurrent validity was determined by correlation of the DFUAS total score with the external criterion (BWAT, PUSH, and wound surface area). A comparison between the total DFUAS score and chronic wound status was made to determine construct validity. We also analyzed 41 wounds that were followed for 4 weeks to evaluate predictive validity. The correlation coefficient total scores of the DFUAS against the BWAT, PUSH, and wound surface area were 0.92, 0.87, and 0.82, respectively. The comparison of the total DFUAS score with chronic wound status was p < 0.001. The predictive validity test indicated that a DFUAS cutoff score of 12 produced the best balance of sensitivity, specificity, positive predictive value, and negative predictive value (89%, 71%, 86%, and 77%, respectively). In conclusion, the newly developed DFUAS is a valid tool for assessing diabetic foot ulcers.
Adaptive Variable Structure Control for Mismatched Uncertain Systems
Authors: Dinh Bach Hoang , Huynh Van Van
Published: July 2016

This paper proposes an adaptive variable structure control (VSC) for a class of mismatched uncertain systems with unknown disturbances. First, a necessary and sufficient condition in terms of linear matrix inequalities is proposed to guarantee the system in sliding mode is asymptotically stable. Second, an adaptive output feedback variable structure controller is designed to force the system states reach the sliding surface and stay on it thereafter. Finally, the advantages and effectiveness of the proposed approaches are demonstrated via a numerical example.
Exploring different attributes of source information for speaker verification with limited test data
Authors: Das Rohan Kumar , Mahadeva Prasanna S. R.
Published: July 2016

This work explores mel power difference of spectrum in subband, residual mel frequency cepstral coefficient, and discrete cosine transform of the integrated linear prediction residual for speaker verification under limited test data conditions. These three source features are found to capture different attributes of source information, namely, periodicity, smoothed spectrum information, and shape of the glottal signal, respectively. On the NIST SRE 2003 database, the proposed combination of the three source features performs better [equal error rate (EER): 20.19%, decision cost function (DCF): 0.3759] than the mel frequency cepstral coefficient feature (EER: 22.31%, DCF: 0.4128) for 2 s duration of test segments.
Gulf of Mexico low-frequency ocean soundscape impacted by airguns
Authors: Wiggins Sean M. , Hall Jesse M. , Thayre Bruce J. , Hildebrand John A.
Published: July 2016

The ocean soundscape of the Gulf of Mexico (GOM) has not been well-studied, although it is an important habitat for marine mammals, including sperm and beaked whales, many dolphin species, and a potentially endangered baleen whale species. The GOM is also home to high levels of hydrocarbon exploration and extraction, heavily used commercial shipping ports, and significant fishery industry activity, all of which are known contributors to oceanic noise. From 2010–2013, the soundscape of three deep and two shallow water sites in the GOM were monitored over 10 – 1000 Hz. Average sound pressure spectrum levels were high, >90 dB re 1 μPa2/Hz at <40 Hz for the deep water sites and were associated with noise from seismic exploration airguns. More moderate sound pressure levels, <55 dB re 1 μPa2/Hz at >700 Hz, were present at a shallow water site in the northeastern Gulf, removed from the zone of industrial development and bathymetrically shielded from deep water anthropogenic sound sources. During passage of a high wind event (Hurricane Isaac, 2012), sound pressure levels above 200 Hz increased with wind speed, but at low frequencies (<100 Hz) sound pressure levels decreased owing to absence of noise from airguns.
Objective Assessment of Adherence to Global Recommendations on Physical Activity for Health in Relation to Spirometric Values in Nonsmoker Women Aged 60–75 Years
Authors: Nawrocka Agnieszka , Mynarski Władysław
Published: July 2016

The purpose of this study was to determine the strength of the relationship between forced expiratory spirometric tests and physical activity levels in older women divided into two groups based on whether they met or did not meet guidelines for weekly physical activity according to the Global Recommendations on Physical Activity for Health (WHO, 2011). Research included 61 healthy, nonsmoker female seniors (Mage = 66 years, SDage = 4.4 years). Weekly physical activity was assessed using an ActiGraph GT3X triaxial accelerometer. To evaluate pulmonary function, forced spirometry tests were performed. The women who met criteria of physical activity for health achieved significantly higher values for forced vital capacity (FVC), t(59) = –1.58, p < .001, and forced expiratory volume in 1 s (FEV1), t(59) = –3.33, p = .002. Meeting criteria of Global Recommendations on Physical Activity for Health is associated with better FVC and FEV1 parameters in healthy older women.
Determining Criteria to Predict Repeatability of Performance in Older Adults: Using Coefficients of Variation for Strength and Functional Measures
Authors: Raj Isaac Selva , Bird Stephen R. , Westfold Ben A. , Shield Anthony J.
Published: July 2016

Reliable measures of muscle strength and functional capacity in older adults are essential. The aim of this study was to determine whether coefficients of variation (CVs) of individuals obtained at the first session can infer repeatability of performance in a subsequent session. Forty-eight healthy older adults (mean age 68.6 ± 6.1 years; age range 60–80 years) completed two assessment sessions, and on each occasion undertook: dynamometry for isometric and isokinetic quadriceps strength, 6 meter fast walk (6MFWT), timed up and go (TUG), stair climb and descent, and vertical jump. Significant linear relationships were observed between CVs in session 1 and the percentage difference between sessions 1 and 2 for torque at 60, 120, 240 and 360°/s, 6MFWT, TUG, stair climb, and stair descent. The results of this study could be used to establish criteria for determining an acceptably reliable performance in strength and functional tests.
Long-term dynamics of adaptive evolution in a globally important phytoplankton species to ocean acidification
Authors: Schlüter Lothar , Lohbeck Kai T. , Gröger Joachim P. , Riebesell Ulf , Reusch Thorsten B. H.
Published: July 2016

Phytoplankton may evolve complex plasticity that can affect biogeochemically important traits such as calcification.
Interface-driven topological Hall effect in SrRuO
3
-SrIrO
3
bilayer
Authors: Matsuno Jobu , Ogawa Naoki , Yasuda Kenji , Kagawa Fumitaka , Koshibae Wataru , Nagaosa Naoto , Tokura Yoshinori , Kawasaki Masashi
Published: July 2016

Electronic transport measurements reveal the formation of swirling spin textures, skyrmions, at high-quality oxide interface.
Innate immune memory and homeostasis may be conferred through crosstalk between the TLR3 and TLR7 pathways
Authors: Liu Bing , Liu Qian , Yang Lei , Palaniappan Sucheendra K. , Bahar Ivet , Thiagarajan P. S. , Ding Jeak Ling
Published: July 2016

Mathematical modeling uncovers how macrophages use the JAK-STAT pathway to fine-tune their responses to different Toll-like receptor stimuli.
Signaling proteins in the spotlight
Authors: Gough Nancy R.
Published: July 2016

The mechanisms that regulate biomolecular function, interaction, and dynamics are an exciting area of signaling research.
Papers of note in
Science
Authors: Gough Nancy R. , VanHook Annalisa M.
Published: July 2016

This week’s articles highlight engineering T cells to treat autoimmunity and computational approaches to understanding complex networks.
Block a phosphatase to shut down kinase signaling
Authors: Ferrarelli Leslie K.
Published: July 2016

An allosteric inhibitor of SHP2 opens new avenues for treating cancers with aberrant kinase signaling.
Detectable Tenofovir Levels in Breast-Feeding Infants of Mothers Exposed to Topical Tenofovir
Authors: Noguchi Lisa M. , Montgomery Elizabeth T. , Biggio Joseph R. , Hendrix Craig W. , Bogen Debra L. , Hillier Sharon L. , Dai James Y. , Piper Jeanna M. , Marzinke Mark A. , Dezzutti Charlene S. , Isaacs S. Karen , Schwartz Jill L. , Watts D. Heather , Beigi Richard H.
Published: July 2016

Lactation studies are necessary evaluations of medications for reproductive-age women. We evaluated pharmacokinetics (PK), pharmacodynamics, safety, and adherence profiles associated with 7 days of 1% tenofovir (TFV) vaginal gel use during lactation. Tenofovir levels (maternal/infant serum, milk) and anti-HIV activity (milk), adverse events (AEs), and adherence were measured for 17 HIV-1-seronegative breast-feeding mother-infant pairs. Tenofovir use was well-tolerated and detected at low levels in maternal serum, milk, and infant serum but demonstrated no anti-HIV activity in milk.
In Vitro
and
In Vivo
Synergy of the Oxadiazole Class of Antibacterials with β-Lactams
Authors: Janardhanan Jeshina , Meisel Jayda E. , Ding Derong , Schroeder Valerie A. , Wolter William R. , Mobashery Shahriar , Chang Mayland
Published: July 2016

The oxadiazole antibacterials target the bacterial cell wall and are bactericidal. We investigated the synergism of ND-421 with the commonly used β-lactams and non-β-lactam antibiotics by the checkerboard method and by time-kill assays. ND-421 synergizes well with β-lactam antibiotics, and it also exhibits a long postantibiotic effect (4.7 h). We also evaluated the
in vivo
efficacy of ND-421 in a murine neutropenic thigh infection model alone and in combination with oxacillin. ND-421 has
in vivo
efficacy by itself in a clinically relevant infection model (1.49 log
10
bacterial reduction for ND-321 versus 0.36 log
10
for linezolid with NRS119) and acts synergistically with β-lactam antibiotics
in vitro
and
in vivo
, and the combination of ND-421 with oxacillin is efficacious in a mouse neutropenic thigh methicillin-resistant
Staphylococcus aureus
(MRSA) infection model (1.60 log
10
bacterial reduction). The activity of oxacillin was potentiated in the presence of ND-421, as the strain would have been resistant to oxacillin otherwise.
Interaction of Avibactam with Class B Metallo-β-Lactamases
Authors: Abboud Martine I. , Damblon Christian , Brem Jürgen , Smargiasso Nicolas , Mercuri Paola , Gilbert Bernard , Rydzik Anna M. , Claridge Timothy D. W. , Schofield Christopher J. , Frère Jean-Marie
Published: July 2016

β-Lactamases are the most important mechanisms of resistance to the β-lactam antibacterials. There are two mechanistic classes of β-lactamases: the serine β-lactamases (SBLs) and the zinc-dependent metallo-β-lactamases (MBLs). Avibactam, the first clinically useful non-β-lactam β-lactamase inhibitor, is a broad-spectrum SBL inhibitor, which is used in combination with a cephalosporin antibiotic (ceftazidime). There are multiple reports on the interaction of avibactam with SBLs but few such studies with MBLs. We report biochemical and biophysical studies on the binding and reactivity of avibactam with representatives from all 3 MBL subfamilies (B1, B2, and B3). Avibactam has only limited or no activity versus MBL-mediated resistance in pathogens. Avibactam does not inhibit MBLs and binds only weakly to most of the MBLs tested; in some cases, avibactam undergoes slow hydrolysis of one of its urea N-CO bonds followed by loss of CO
2
, in a process different from that observed with the SBLs studied. The results suggest that while the evolution of MBLs that more efficiently catalyze avibactam hydrolysis should be anticipated, pursuing the development of dual-action SBL and MBL inhibitors based on the diazabicyclooctane core of avibactam may be productive.
Organic Cation Transporter 2 Overexpression May Confer an Increased Risk of Gentamicin-Induced Nephrotoxicity
Authors: Gai Zhibo , Visentin Michele , Hiller Christian , Krajnc Evelin , Li Tongzhou , Zhen Junhui , Kullak-Ublick Gerd A.
Published: July 2016

Nephrotoxicity is a relevant limitation of gentamicin, and obese patients have an increased risk for gentamicin-induced kidney injury. This damage is thought to depend on the accumulation of the drug in the renal cortex. Obese rats showed substantially higher levels of gentamicin in the kidney than did lean animals. This study characterized the role of organic cation transporters (OCTs) in gentamicin transport and elucidated their possible contribution in the increased renal accumulation of gentamicin in obesity. The mRNA and protein expression levels of the organic cation transporters Oct2 (Slc22a2) and Oct3 (Slc22a3) were increased in kidney samples from obese mice fed a high-fat diet. Similarly, OCT2 (∼2-fold) and OCT3 (∼3-fold) showed increased protein expression in the kidneys of obese patients compared with those of nonobese individuals. Using HEK293 cells overexpressing the different OCTs, human OCT2 was found to transport [
3
H]gentamicin with unique sigmoidal kinetics typical of homotropic positive cooperativity (autoactivation). In mouse primary proximal tubular cells, [
3
H]gentamicin uptake was reduced by approximately 40% when the cells were coincubated with the OCT2 substrate metformin. The basolateral localization of OCT2 suggests that gentamicin can enter proximal tubular cells from the blood side, probably as part of a slow tubular secretion process that may influence intracellular drug concentrations and exposure time. Increased expression of OCT2 may explain the higher accumulation of gentamicin, thereby conferring an increased risk of renal toxicity in obese patients.
Basic Reproduction Number and Transmission Dynamics of Common Serogroups of Enterohemorrhagic Escherichia coli
Authors: Chen Shi , Sanderson Michael W. , Lee Chihoon , Cernicchiaro Natalia , Renter David G. , Lanzas Cristina
Published: July 2016

Understanding the transmission dynamics of pathogens is essential to determine the epidemiology, ecology, and ways of controlling enterohemorrhagic
Escherichia coli
(EHEC) in animals and their environments. Our objective was to estimate the epidemiological fitness of common EHEC strains in cattle populations. For that purpose, we developed a Markov chain model to characterize the dynamics of 7 serogroups of enterohemorrhagic
Escherichia coli
(O26, O45, O103, O111, O121, O145, and O157) in cattle production environments based on a set of cross-sectional data on infection prevalence in 2 years in two U.S. states. The basic reproduction number (
R
0
) was estimated using a Bayesian framework for each serogroup based on two criteria (using serogroup alone [the O-group data] and using O serogroup, Shiga toxin gene[s], and intimin [
eae
] gene together [the EHEC data]). In addition, correlations between external covariates (e.g., location, ambient temperature, dietary, and probiotic usage) and prevalence/
R
0
were quantified.
R
0
estimates varied substantially among different EHEC serogroups, with EHEC O157 having an
R
0
of >1 (∼1.5) and all six other EHEC serogroups having an
R
0
of less than 1. Using the O-group data substantially increased
R
0
estimates for the O26, O45, and O103 serogroups (
R
0
> 1) but not for the others. Different covariates had distinct influences on different serogroups: the coefficients for each covariate were different among serogroups. Our modeling and analysis of this system can be readily expanded to other pathogen systems in order to estimate the pathogen and external factors that influence spread of infectious agents.

IMPORTANCE
In this paper we describe a Bayesian modeling framework to estimate basic reproduction numbers of multiple serotypes of Shiga toxin-producing
Escherichia coli
according to a cross-sectional study. We then coupled a compartmental model to reconstruct the infection dynamics of these serotypes and quantify their risk in the population. We incorporated different sensitivity levels of detecting different serotypes and evaluated their potential influence on the estimation of basic reproduction numbers.
Vitamin D Deficiency Does Not Result in a Breach of Host Defense in Murine Models of Pneumonia
Authors: Niederstrasser Julia , Herr Christian , Wolf Lisa , Lehr Claus M. , Beisswenger Christoph , Bals Robert
Published: July 2016

Vitamin D (VitD) has a role in the regulation of calcium and phosphate metabolism and in addition impacts the activity of the immune system. VitD deficiency might be linked to increased susceptibility to respiratory tract infection. The aim of the present study was to characterize the impact of VitD deficiency on the susceptibility to bacterial infection in murine models. C57BL/6N mice were fed a diet with or without VitD for 10 weeks. The VitD-deficient or -sufficient mice were infected with
Pseudomonas aeruginosa
or
Streptococcus pneumoniae
. The colonization and inflammatory response in the lung were analyzed at defined time points. The serum 25-hydroxy-VitD concentration was significantly lower in mice on the VitD-deficient diet. In infection experiments with
Pseudomonas aeruginosa
or
Streptococcus pneumoniae
, no differences could be observed in the numbers of viable bacteria or in differential cell counts in the bronchoalveolar lavage fluids. Measurements of inflammatory cytokines (KC and interleukin-1β [IL-1β]) did not show significant differences between the groups. In conclusion, VitD-deficient animals did not show significantly increased susceptibility to infection or an altered course of infection. The immune systems of humans and mice likely respond differently to VitD. Murine models are likely not appropriate for drawing conclusions on the role of VitD in human pulmonary host defense.
Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation
Authors: Ouellette Scot P. , Rueden Kelsey J. , Rucks Elizabeth A.
Published: July 2016

In evolving to an obligate intracellular niche,
Chlamydia
has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However,
Chlamydia
can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-γ), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from
Chlamydia
. Thus, how
Chlamydia
, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that
C. pneumoniae
responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from
C. pneumoniae
genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous
C. pneumoniae
microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis.
Small RNAs Repress Expression of Polysaccharide Utilization Loci of Gut Bacteroides Species
Authors: Comstock Laurie E.
Published: July 2016

Bacteroides
species can metabolize numerous plant polysaccharides and host glycans present in the mammalian gut. The regulatory systems governing the induction of particular polysaccharide utilization loci when the cognate glycan is present are known, but how expression is repressed when a higher-priority glycan is present is largely unknown. In this issue of the
Journal of Bacteriology
, Cao et al. (J. Bacteriol. 198:2410–2418, 2016,
http://dx.doi.org/10.1128/JB.00381-16
) reveal a conserved mechanism in
Bacteroides
whereby antisense small RNAs (sRNA) repress expression of genes involved in utilization of host glycans.
ASM Journals Eliminate Impact Factor Information from Journal Websites
Authors: Casadevall Arturo , Bertuzzi Stefano , Buchmeier Michael J. , Davis Roger J. , Drake Harold , Fang Ferric C. , Gilbert Jack , Goldman Barbara M. , Imperiale Michael J. , Matsumura Philip , McAdam Alexander J. , Pasetti Marcela F. , Sandri-Goldin Rozanne M. , Silhavy Thomas , Rice Louis , Young Jo-Anne H. , Shenk Thomas
Published: July 2016

Many scientists attempt to publish their work in a journal with the highest possible journal impact factor (IF). Despite widespread condemnation of the use of journal IFs to assess the significance of published work, these numbers continue to be widely misused in publication, hiring, funding, and promotion decisions (1, 2).
Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales
Authors: Kirkpatrick John B. , Walsh Emily A. , D’Hondt Steven
Published: July 2016

DNA in marine sediment contains both fossil sequences and sequences from organisms that live in the sediment. The demarcation between these two pools and their respective rates of turnover are generally unknown. We address these issues by comparing the total extractable DNA pool to the fraction of sequenced chloroplast DNA (cpDNA) in sediment from two sites in the Bering Sea. We assume that cpDNA is a tracer of non-reproducing fossil DNA. Given >150,000 sequence reads per sample, cpDNA is easily detectable in the shallowest samples but decays with depth, suggesting that sequencing-based richness assessments of communities in deep subseafloor sediment are relatively unaffected by fossil DNA. The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age. This can be explained by biological activity decreasing with sediment age and/or by preferential long-term survival of only the most thoroughly protected DNA. The association of cpDNA reads with published records of siliceous microfossils, including diatom spores, at the same sites suggests that microfossils may help to preserve DNA. This DNA may be useful for studies of paleoenvironmental conditions and biological evolution on time scales that approach or exceed 1 m.y.
Paradigm shift in determining Neoproterozoic atmospheric oxygen
Authors: Blamey Nigel J.F. , Brand Uwe , Parnell John , Spear Natalie , Lécuyer Christophe , Benison Kathleen , Meng Fanwei , Ni Pei
Published: July 2016

We present a new and innovative way of determining the oxygen level of Earth’s past atmosphere by directly measuring inclusion gases trapped in halite. After intensive screening using multiple depositional, textural/fabric, and geochemical parameters, we determined that tectonically undisturbed cumulate, chevron, and cornet halite inclusions may retain atmospheric gas during crystallization from shallow saline, lagoonal, and/or saltpan brine. These are the first measurements of inclusion gas for the Neoproterozoic obtained from 815 ± 15–m.y.–old Browne Formation chevron halite of the Officer Basin, southwest Australia. The 31 gas measurements afford us a direct glimpse of the composition of the mid- to late Neoproterozoic atmosphere and register an average oxygen content of 10.9%. The measured pO2 puts oxygenation of Earth’s paleoatmosphere ∼100–200 m.y. ahead of current models and proxy studies. It also puts oxygenation of the Neoproterozoic atmosphere in agreement with time of diversification of eukaryotes and in advance of the emergence of marine animal life.
Empirical constraints on shock features in monazite using shocked zircon inclusions
Authors: Erickson Timmons M. , Cavosie Aaron J. , Pearce Mark A. , Timms Nicholas E. , Reddy Steven M.
Published: July 2016

Shock deformation microstructures in monazite have been systematically characterized for the first time in grains from the Vredefort impact structure in South Africa. Electron backscatter diffraction mapping has identified 12 unique orientations of monazite deformation twins, including 7 orientations that have not previously been described in experiments or nature. Other shock features include planar deformation bands and strain-free neoblasts, which have been shown to date deformation. Shock-twinned zircon inclusions within the deformed monazite require pressures of 20 GPa, thus providing critical empirical constraints on formation conditions, confirming a hypervelocity impact origin of the monazite microstructures. The Vredefort monazite grains described here represent the first case of using shocked mineral inclusions to empirically calibrate shock microstructures formed in the host mineral. These results conclusively establish monazite as a recorder of shock deformation, and highlight its use in identifying and dating impact structures.
The answers are blowin’ in the wind: Ultra-distal ashfall zircons, indicators of Cretaceous super-eruptions in eastern Gondwana
Authors: Barham M. , Kirkland C.L. , Reynolds S. , O’Leary M.J. , Evans N.J. , Allen H. , Haines P.W. , Hocking R.M. , McDonald B.J. , Belousova E. , Goodall J.
Published: July 2016

An Early Cretaceous siliceous large igneous province (SLIP) that developed on the eastern margin of Gondwana produced some of the most voluminous siliceous volcaniclastic deposits known globally. We report U-Pb ages and trace-element and Hf-isotopic signatures of detrital zircons from the Madura Shelf (onshore Bight Basin), Western Australia. These zircons include a geochemically distinct 106 Ma component with age and Hf characteristics that match SLIP volcanics some 2300 km distant in eastern Australia. This young subpopulation shows limited grain abrasion, which contrasts with older detrital components that are stratigraphically persistent. Regional detrital zircon provenance demonstrates that sediment routing systems were disconnected in the eastern and western Bight Basin, negating terrestrial transport mechanisms as a possible vector of the zircons from the SLIP to their recovered position. Palynology indicates that the 106 Ma zircons are syn-depositional, and we interpret them as being significantly transported in an eruption plume. Given the grain size and distance from source, such distal zircon emplacement suggests previously undocumented 106 Ma super-eruptions. The 106 Ma zircons likely reflect Southern Hemisphere winter eruptions when tropospheric polar easterly winds would have been favored across southeastern Australia.
Vigorous deep-sea currents cause global anomaly in sediment accumulation in the Southern Ocean
Authors: Dutkiewicz Adriana , Müller R. Dietmar , Hogg Andrew McC. , Spence Paul
Published: July 2016

The vigorous current systems in the Southern Ocean play a key role in regulating the Earth’s oceans and climate, with the record of long-term environmental change mostly contained in deep-sea sediments. However, the well-established occurrence of widespread regional disconformities in the abyssal plains of the Southern Ocean attests to extensive erosion of deep-sea sediments during the Quaternary. We show that a wide belt of rapid sedimentation rates (>5.5 cm/k.y.) along the Southeast Indian Ridge (SEIR) is a global anomaly and occurs in a region of low surface productivity bounded by two major disconformity fields associated with the Kerguelen Plateau to the east and the Macquarie Ridge to the west. Our high-resolution numerical ocean circulation model shows that the disconformity fields occur in regions of intense bottom-current activity where current speeds reach 0.2 m/s and are favorable for generating intense nepheloid layers. These layers are transported toward and along the SEIR to regions where bottom-current velocities drop to <0.03 m/s and fine particles settle out of suspension, consistent with focusing factors significantly greater than 1. We suggest that the anomalous accumulation of sediment along an 8000-km-long segment of the SEIR represents a giant succession of contourite drifts that is a major extension of the much smaller contourite east of Kerguelen Plateau and has occurred since 3–5 Ma based on the age of the oldest crust underlying the deposit. These inferred contourite drifts provide exceptionally valuable drilling targets for high-resolution climatic investigations of the Southern Ocean.
Exploring the impact of early life factors on inequalities in risk of overweight in UK children: findings from the UK Millennium Cohort Study
Authors: Massion Samuel , Wickham Sophie , Pearce Anna , Barr Ben , Law Catherine , Taylor-Robinson David
Published: July 2016

Background

Overweight and obesity in childhood are socially patterned, with higher prevalence in more disadvantaged populations, but it is unclear to what extent early life factors attenuate the social inequalities found in childhood overweight/obesity.

Methods

We estimated relative risks (RRs) for being overweight (combining with obesity) at age 11 in 11 764 children from the UK Millennium Cohort Study (MCS) according to socio-economic circumstances (SEC). Early life risk factors were explored to assess if they attenuated associations between SECs and overweight.

Results

28.84% of children were overweight at 11 years. Children of mothers with no academic qualifications were more likely to be overweight (RR 1.72, 95% CI 1.48 to 2.01) compared to children of mothers with degrees and higher degrees. Controlling for prenatal, perinatal, and early life characteristics (particularly maternal pre-pregnancy overweight and maternal smoking during pregnancy) reduced the RR for overweight to 1.44, 95% CI 1.23 to 1.69 in the group with the lowest academic qualifications compared to the highest.

Conclusions

We observed a clear social gradient in overweight 11-year-old children using a representative UK sample. Moreover, we identified specific early life risk factors, including maternal smoking during pregnancy and maternal pre-pregnancy overweight, that partially account for the social inequalities found in childhood overweight. Policies to support mothers to maintain a healthy weight, breastfeed and abstain from smoking during pregnancy are important to improve maternal and child health outcomes, and our study provides some evidence that they may also help to address the continuing rise in inequalities in childhood overweight.
Neonatal thyroid-stimulating hormone concentration and psychomotor development at preschool age
Authors: Trumpff Caroline , De Schepper Jean , Vanderfaeillie Johan , Vercruysse Nathalie , Van Oyen Herman , Moreno-Reyes Rodrigo , Tafforeau Jean , Vandevijvere Stefanie
Published: July 2016

Objective

Thyroid hormones are essential for normal brain development. The aim of this study is to assess if high concentration of thyroid stimulating hormone (TSH) that is below the clinical threshold (5–15 mIU/L) at neonatal screening is linked to psychomotor development impairments in the offspring at preschool age.

Design

A total of 284 Belgian preschool children 4–6 years old and their mothers were included in the study. The children were randomly selected from the total list of neonates screened in 2008, 2009 and 2010 by the Brussels newborn screening centre. The sampling was stratified by gender and TSH range (0.45–15 mIU/L). Infants with congenital hypothyroidism (>15 mIU/L), low birth weight and/or prematurity were excluded. Psychomotor development was assessed using the Charlop-Atwell scale of motor coordination. The iodine status of children was determined using median urinary iodine concentration. Socioeconomic, parental and child potential confounding factors were measured through a self-administered questionnaire.

Results

TSH level was not significantly associated with total motor score (average change in z-score per unit increase in TSH is 0.02 (−0.03, 0.07), p=0.351), objective motor score (p=0.794) and subjective motor score (p=0.124). No significant associations were found using multivariate regression model to control confounding factors.

Conclusions

Mild thyroid dysfunction in the newborn—reflected by an elevation of TSH that is below the clinical threshold (5–15 mIU/L)—was not associated with impaired psychomotor development at preschool age.
Psychological maladjustment and quality of life in adolescents with constipation
Authors: Ranasinghe Nishadi , Devanarayana Niranga Manjuri , Benninga Marc Alexander , van Dijk Marieke , Rajindrajith Shaman
Published: July 2016

Objectives

To assess psychological maladjustment in adolescents with functional constipation.

Study design

We conducted a cross-sectional survey in five schools. Adolescents aged between 13 and 18 years were included in the study. Validated questionnaires were used to collect bowel habits and demographic data, health-related quality of life (HRQoL) and psychological maladjustment. Rome III criteria were used to diagnose constipation.

Results

1697 adolescents were recruited (boys 779 (45.9%), mean age 15.06 years and SD 1.6 years). Prevalence of constipation was 6.7%, of whom 52 were boys (45.6%) and 62 were girls (54.4%). 38 adolescents (33.3%) with constipation and 230 controls (14.5%) had significant psychological maladjustment. Among seven different personality dimensions used to assess psychological maladjustment, children with constipation had significantly more deficits than controls in hostility and aggression (14.2 vs 12.6 in controls (mean difference 1.54, 95% CI (0.89 to 2.19) p<0.001), negative self-esteem (12.0 vs 10.5 in controls, mean difference 1.54 95% CI (0.96 to 2.06) p<0.001), negative self-adequacy (11.9 vs 9.8 controls, mean difference 2.07 95% CI (1.46 to 2.67) p<0.001), emotional unresponsiveness (12.9 vs 11.5 controls, mean difference 1.44 95% CI (0.84 to 2.04) p<0.001), emotional instability (17.1 vs 15.6, mean difference 1.53 95% CI (0.86 to 2.2) p<0.001) and negative world view (12.1 vs 10.2 controls, mean difference 1.91 95% CI (1.24 to 2.59) p<0.001). The total HRQoL of adolescents with constipation was lower than controls (70.6 vs 79.0 mean difference 9.48 95% CI (1.4 to 6.7) p<0.05).

Conclusion

A significant proportion of children with constipation are suffering from psychological maladjustment.
In vivo early retinal structural alterations following laser photocoagulation using three-dimensional spectral domain optical coherence tomography
Authors: Saxena Sandeep , Mishra Nibha , Ruia Surabhi , Akduman Levent
Published: July 2016

To study the retinal structural alterations and surface topography of retinal pigment epithelium (RPE) immediately following laser photocoagulation up to day 7. Cross-sectional retinal imaging and RPE segmentation maps on spectral domain optical coherence tomography were obtained immediately at hour 1, day 1, day 4 and day 7 following 532 nm neodymium:YAG laser photocoagulation in a 56-year-old male patient for branch retinal vein occlusion. Immediately postlaser, loss of reflectivity of all the retinal layers was observed. At hour 1, hyper-reflectivity of outer retinal layers was observed with increase in hyporeflective spaces by day 1. Immediately postlaser, pitting of the RPE was observed on surface topography which regressed at day 1. On day 4, smooth RPE surface topography was observed with the occurrence of small elevated areas on day 7. The present report provides an insight into the in vivo changes in the retinal structure and RPE surface topography after laser photocoagulation.
Birth brachial plexus palsy: a race against time
Authors: Patra Sambeet , Narayana Kurup Jayakrishnan K , Acharya Ashwath M , Bhat Anil K
Published: July 2016

A 5-year-old child presented to us with weakness of the left upper limb since birth. With the given history of obstetric trauma and limb examination, a diagnosis of birth brachial plexus palsy was made. Brachial plexus exploration along with microsurgery was performed at the same time which included extrinsic neurolysis of the roots and trunks and nerve transfer for better shoulder external rotation and elbow flexion. Both the movements were severely restricted previously due to co-contractures with the shoulder internal rotators and triceps. The problem of birth brachial plexus palsy is proving to be a global health burden both in developed countries and in developing countries such as India. The lack of awareness among the general public and primary healthcare providers and inadequate orthopaedic and neurosurgeons trained to treat the condition have worsened the prognosis. This case lays stress on the delayed complications in birth brachial palsy and its effective management.
Barraquer-Simons syndrome: a unique patient's perspective on diagnosis, disease progression and recontouring treatment
Authors: Heidemann Lene Nyhøj , Thomsen Jørn Bo , Sørensen Jens Ahm
Published: July 2016

This case report describes a female patient diagnosed with Barraquer-Simons syndrome, a rare form of acquired partial lipodystrophy characterised by symmetrical loss of adipose tissue from face, neck, upper extremities and the trunk with onset in early childhood. Initial symptoms were seen at the age of 8 years. Our patient did not show signs of renal impairment and this may be associated with the syndrome. Treatment of lipoatrophy in these patients is limited to cosmetic restoration, and autologous fat grafting has shown sustained positive effects with no or very little loss of volume at follow-ups. Furthermore, the treatment has resulted in considerable improvements in her quality of life and daily functioning. She has not experienced any adverse effects. Accurate and early diagnosis is important, and clinicians should consider early intervention for these patients. Autologous fat grafting is recommended as a safe procedure.
Is coffee consumption associated with a lower risk of hyperuricaemia or gout? A systematic review and meta-analysis
Authors: Zhang Yi , Yang Tuo , Zeng Chao , Wei Jie , Li Hui , Xiong Yi-lin , Yang Ye , Ding Xiang , Lei Guanghua
Published: July 2016

Objectives

To examine the associations of coffee consumption with the serum uric acid (SUA) level, hyperuricaemia (HU) and gout.

Design

Systematic review and meta-analysis.

Data sources and study eligibility criteria

A comprehensive literature search up to April 2015, using PubMed and EMBASE databases, was conducted to identify the observational researches that examined the associations of coffee consumption with the SUA level, HU and gout. The standard mean difference (SMD), OR, relative risk (RR) and their corresponding 95% CIs for the highest and the lowest categories of coffee intake were determined.

Results

A total of 11 observational studies (6 cross-sectional, 3 cohort and 2 case–control studies) were included in this systematic review and meta-analysis. The combined SMD suggested that there was no significant difference between the highest and the lowest coffee intake categories in terms of the SUA level (SMD=−0.09, 95% CI −0.23 to 0.05; p=0.21). Meanwhile, the overall multivariable adjusted OR for HU showed no significant difference between the highest and the lowest coffee intake categories (OR=0.84, 95% CI 0.65 to 1.09; p=0.20). However, the overall multivariable adjusted RR for gout showed a significant inverse association between coffee consumption and the incidence of gout (RR=0.43, 95% CI 0.31 to 0.59, p<0.001).

Conclusions

Current evidences are insufficient to validate the association between coffee consumption and a lower risk of HU. Owing to the limited number of studies, the available data show that coffee consumption may be associated with a lower risk of incident gout. Further well-designed prospective researches and randomised controlled trials are therefore needed to elaborate on these issues.