bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying New Small Proteins in Escherichia coli
Authors: VanOrsdel Caitlin E. , Kelly John P. , Burke Brittany N. , Lein Christina D. , Oufiero Christopher E. , Sanchez Joseph F. , Wimmers Larry E. , Hearn David J. , Abuikhdair Fatimeh J. , Barnhart Kathryn R. , Duley Michelle L. , Ernst Sarah E. G. , Kenerson Briana A. , Serafin Aubrey J. , Hemm Matthew R. 
Published: April 2018

AbstractThe number of small proteins (SPs) encoded in the Escherichia coli genome is unknown, as current bioinformatics and biochemical techniques make short gene and small protein identification challenging. One method of small protein identification involves adding an epitope tag to the 3′ end of a short open reading frame (sORF) on the chromosome, with synthesis confirmed by immunoblot assays. In this study, this strategy was used to identify new E. coli small proteins, tagging 80 sORFs in the E. coli genome, and assayed for protein synthesis. The selected sORFs represent diverse sequence characteristics, including degrees of sORF conservation, predicted transmembrane domains, sORF direction with respect to flanking genes, ribosome binding site (RBS) prediction, and ribosome profiling results. Of 80 sORFs, 36 resulted in encoded synthesized proteins—a 45% success rate. Modeling of detected versus non‐detected small proteins analysis showed predictions based on RBS prediction, transcription data, and ribosome profiling had statistically‐significant correlation with protein synthesis; however, there was no correlation between current sORF annotation and protein synthesis. These results suggest substantial numbers of small proteins remain undiscovered in E. coli, and existing bioinformatics techniques must continue to improve to facilitate identification.
Support needs of couples with hereditary breast and ovarian cancer during reproductive decision making
Authors: Gietel‐Habets J.J.G. , de Die‐Smulders C.E.M. , Derks‐Smeets I.A.P. , Tibben A. , Tjan‐Heijnen V.C.G. , van Golde R. , Gomez‐Garcia E. , van Osch L.A.D.M. 
Published: April 2018

AbstractObjectiveReproductive decision making for couples with hereditary breast and ovarian cancer (HBOC) is complex and can result in decisional conflict or regret. This study investigated couples' support needs and aimed to identify vulnerable couples. Ultimately, we should strive to develop a clear standard of care guideline regarding reproductive decision support.MethodsMixed methods were used for data collection. A focus group study was conducted among 18 couples (N = 35) with HBOC who had made a reproductive decision after reproductive counselling. Subsequently, 129 similar couples (N = 258) were invited to complete a cross‐sectional survey based on the focus group study.ResultsClinical and practical aspects of reproductive counselling were positively evaluated in the focus group study, although couples indicated a need for additional support with emotional and social concerns in which their relationship, social environment, and the way they picture their desired family were key elements. The survey was completed by 86 participants. Making a reproductive choice was experienced as (very) difficult by 43%, and 69% showed a need for additional support during decision making. Younger participants and those who opted for a natural pregnancy experienced more difficulty with reproductive decision making, and partners showed a higher need for psychological support than carriers.ConclusionsCouples with HBOC who need to make a reproductive decision have specific needs for guidance and support, of which the desired content and methods can vary. It is therefore important to identify vulnerable couples and to attune counselling to couples' needs.
Fear of recurrence among older breast, ovarian, endometrial, and colorectal cancer survivors: Findings from the WHI LILAC study
Authors: Krok‐Schoen Jessica L. , Naughton Michelle J. , Bernardo Brittany M. , Young Gregory S. , Paskett Electra D. 
Published: April 2018

AbstractObjectiveTo examine the prevalence of and factors associated with fear of recurrence (FCR) following treatment for breast, ovarian, endometrial, and colorectal cancer among older women.MethodsParticipants were enrolled in the Women's Health Initiative Life and Longevity After Cancer study. Descriptive statistics and multivariate logistic regression models were used to assess the association of demographic, clinical, and quality of life variables with survivors' FCR, dichotomized as <14 (low) or ≥14 (high) using the Cancer Worry Scale.ResultsOut of the 4259 participants, 3124 (73.3%) were diagnosed with breast cancer, 559 (13.1%) with colorectal cancer, 493 (11.6%) with endometrial cancer, and 83 (2%) with ovarian cancer. There were no significant differences in FCR by cancer type (P = .75), with a mean scale score of 10.8 ± 2.87 for all participants combined. Approximately 16% (n = 679) were in the high FCR group. Multivariable analyses indicated that being younger at diagnosis, reporting a symptom score of ≥8, receipt of chemotherapy, and lower self‐rated health were significantly associated with high FCR. Women who were widowed or never married were less likely to report high FCR.ConclusionsFear of recurrence was experienced by a small but important proportion of older, long‐term cancer survivors and is associated with multiple demographic and clinical variables. These results will better inform researchers and clinicians regarding the individuals who are at risk of FCR.
A comparison of extraction systems for plant water stable isotope analysis
Authors: Millar Cody , Pratt Dyan , Schneider David J. , McDonnell Jeffrey J. 
Published: April 2018

RationaleThe stable isotope ratios of water (δ2H and δ18O values) have been widely used to trace water in plants in a variety of physiological, ecohydrological, biogeochemical and hydrological studies. In such work, the analyte must first be extracted from samples, prior to isotopic analysis. While cryogenic vacuum distillation is currently the most widely used method reported in the literature, a variety of extraction‐collection‐analysis methods exist. A formal inter‐method comparison on plant tissues has yet to be carried out.MethodsWe performed an inter‐method comparison of six plant water extraction techniques: direct vapour equilibration, microwave extraction, two unique versions of cryogenic vacuum distillation, centrifugation, and high‐pressure mechanical squeezing. These methods were applied to four isotopically unique plant portions (head, stem, leaf, and root crown) of spring wheat (Triticum aestivumL.). Extracted plant water was analyzed via spectrometric (OA‐ICOS) and mass‐based (IRMS) analysis systems when possible. Spring wheat was grown under controlled conditions with irrigation inputs of a known isotopic composition.ResultsThe tested methods of extraction yielded markedly different isotopic signatures. Centrifugation, microwave extraction, direct vapour equilibration, and high‐pressure mechanical squeezing produced water more enriched in2H and18O content. Both cryogenic vacuum distillation systems and the high‐pressure mechanical squeezing method produced water more depleted in2H and18O content, depending upon the plant portion extracted. The various methods also produced differing concentrations of co‐extracted organic compounds, depending on the mode of extraction. Overall, the direct vapor equilibration method outperformed all other methods.ConclusionsDespite its popularity, cryogenic vacuum distillation was outperformed by the direct vapor equilibration method in terms of limited co‐extraction of volatile organic compounds, rapid sample throughput, and near instantaneous returned stable isotope results. More research is now needed with other plant species, especially woody plants, to see how far the findings from this study could be extended.
ADHM and the 4d quantum Hall effect
Authors: Barns-Graham Alec , Dorey Nick , Lohitsiri Nakarin , Tong David , Turner Carl 
Published: April 2018

AbstractYang-Mills instantons are solitonic particles ind= 4 + 1 dimensional gauge theories. We construct and analyse the quantum Hall states that arise when these particles are restricted to the lowest Landau level. We describe the ground state wavefunctions for both Abelian and non-Abelian quantum Hall states. Although our model is purely bosonic, we show that the excitations of this 4d quantum Hall state are governed by the Nekrasov partition function of a certain five dimensional supersymmetric gauge theory with Chern-Simons term. The partition function can also be interpreted as a variant of the Hilbert series of the instanton moduli space, counting holomorphic sections rather than holomorphic functions.It is known that the Hilbert series of the instanton moduli space can be rewritten using mirror symmetry of 3d gauge theories in terms of Coulomb branch variables. We generalise this approach to include the effect of a five dimensional Chern-Simons term. We demonstrate that the resulting Coulomb branch formula coincides with the corresponding Higgs branch Molien integral which, in turn, reproduces the standard formula for the Nekrasov partition function.
Topological defects in open string field theory
Authors: Kojita Toshiko , Maccaferri Carlo , Masuda Toru , Schnabl Martin 
Published: April 2018

AbstractWe show how conformal field theory topological defects can relate solutions of open string field theory for different boundary conditions. To this end we generalize the results of Graham and Watts to include the action of defects on boundary condition changing fields. Special care is devoted to the general case when nontrivial multiplicities arise upon defect action. Surprisingly the fusion algebra of defects is realized on open string fields only up to a (star algebra) isomorphism.
Meromorphic solutions of recurrence relations and DRA method for multicomponent master integrals
Authors: Lee Roman N. , Mingulov Kirill T. 
Published: April 2018

AbstractWe formulate a method to find the meromorphic solutions of higher-order recurrence relations in the form of the sum over poles with coefficients defined recursively. Several explicit examples of the application of this technique are given. The main advantage of the described approach is that the analytical properties of the solutions are very clear (the position of poles is explicit, the behavior at infinity can be easily determined). These are exactly the properties that are required for the application of the multiloop calculation method based on dimensional recurrence relations and analyticity (the DRA method).
Paleoearthquakes in the Uimon basin (Gorny Altai)
Authors: Deev E.V. , Zol’nikov I.D. , Turova I.V. , Rusanov G.G. , Ryapolova Yu.M. , Nevedrova N.N. , Kotler S.A. 
Published: April 2018

AbstractPaleoseismological studies confirm that the Uimon basin is thrust by its northern mountain border along the active South Terekta fault. The latest motion along the fault in the 7–8th centuries AD induced an earthquake with a magnitude of Mw = 7.4–7.7 and a shaking intensity of I = 9–11 on the MSK-64 scale. The same fault generated another event (M ≥ 7, I = 9–10), possibly, about 16 kyr ago, which triggered gravity sliding. The rockslide dammed the Uimon valley and produced a lake, where lacustrine deposition began about 14 ± 1 kyr ago, and a later M ≥ 7 (I = 9–10) earthquake at ~6 ka caused the dam collapse and the lake drainage. Traces of much older earthquakes that occurred within the Uimon basin are detectable from secondary deformation structures (seismites) in soft sediments deposited during the drainage of a Late Pleistocene ice-dammed lake between 100 and 90 ka and in ~77 ka alluvium. The magnitude and intensity of these paleoearthquakes were at least M ≥ 5.0–5.5 and I ≥ 6–7.
Magnetic measurements in electrical prospecting by resistivity methods
Authors: Mogilatov V.S. , Kozhevnikov N.O. , Zlobinsky A.V. 
Published: April 2018

Abstract
The electrical resistivity and induced polarization (IP) methods are widely used in geological mapping, prospecting and exploration of mineral deposits, engineering geology, hydrogeology, archaeology, and geotechnical and environmental applications. Historically, these methods have formed the basis of the electrical prospecting technique. In these methods, a DC or low-frequency AC electrical current is introduced into the earth through a grounded transmitter line. The measured quantity is the electric field. However, if the earth’s resistivity or chargeability changes horizontally, this change gives rise to an anomalous magnetic field, which is studied by the magnetometric resistivity (MMR) and magnetic induced polarization (MIP) methods, respectively. Along with advantages, some shortcomings are inherent in the MMR and MIP techniques. Apparently, the main drawback of these methods is that the magnetic fields of both the transmitter line wire and ground electrodes on the surface are several orders of magnitude greater than the anomalous magnetic field response. This introduces a significant “noise” to magnetic-resistivity data. We investigate the potential of using a circular electric dipole (CED) in magnetometric resistivity techniques. It has been found that the application of a CED, instead of a conventional transmitter line, dramatically enhances the signal-to-noise ratio.
Numerical and experimental transition results evaluation for a morphing wing and aileron system
Authors: Botez R.M. , Koreanschi A. , Gabor O.S. , Tondji Y. , Guezguez M. , Kammegne J.T. , Grigorie L.T. , Sandu D. , Mebarki Y. , Mamou M. , Amoroso F. , Pecora R. , Lecce L. , Amendola G. , Dimino I. , Concilio A. 
Published: April 2018

ABSTRACTA new wing-tip concept with morphing upper surface and interchangeable conventional and morphing ailerons was designed, manufactured, bench and wind-tunnel tested. The development of this wing-tip model was performed in the frame of an international CRIAQ project, and the purpose was to demonstrate the wing upper surface and aileron morphing capabilities in improving the wing-tip aerodynamic performances. During numerical optimisation with ‘in-house’ genetic algorithm software, and during wind-tunnel experimental tests, it was demonstrated that the air-flow laminarity over the wing skin was promoted, and the laminar flow was extended with up to 9% of the chord. Drag coefficient reduction of up to 9% was obtained when the morphing aileron was introduced.
Observation versus experimentation in natural-history teaching in Portuguese secondary schools: educational laws from 1836 to 1933
Authors: GOMES INÊS 
Published: April 2018

AbstractThe idea that a public and secular institution was needed to prepare citizens for higher education proliferated throughout Europe during the nineteenth century. However, because of local political, economic and social contexts the underlying model of what is now meant by secondary education has developed differently in each country. This essay provides a historical account of the development of secondary education in Portugal, in what concerns the study of nature (zoology, botany, geology and mineralogy) inliceus, during the nineteenth and early twentieth centuries. In particular, the importance given to specimens and collections will be emphasized. The emergence of laboratory-based teaching never replaced traditional approaches centred on observation of specimens. By focusing on the Portuguese case, this article aims ultimately to contribute to a broader understanding of the secondary-educational model implemented throughout Europe in the nineteenth century.
Stability of the wakes of cylinders with triangular cross-sections
Authors: Ng Zhi Y. , Vo Tony , Sheard Gregory J. 
Published: April 2018

The stability of the wakes of cylinders with triangular cross-sections at incidence is investigated using Floquet stability analysis to elucidate the effects of cylinder inclination on the dominant flow instability. The upper limit of the Reynolds numbers (scaled by the height projected by the cylinder in this study) at which the wake of the two-dimensional base flow is time periodic is$Re\approx 140$for most cylinder inclinations, exceeding which the flow becomes aperiodic, restricting the range of Reynolds numbers permitted for the stability analysis. Two different instability modes are predicted to manifest as the first-occurring mode at various cylinder inclinations – a regular mode possessing perturbation structures consistent with mode A dominates the wakes of cylinders at inclinations$\unicode[STIX]{x1D6FC}\lesssim 34.6^{\circ }$and$\unicode[STIX]{x1D6FC}\gtrsim 55.4^{\circ }$, with a subharmonic mode consistent with mode C emerging as the primary mode in the wakes of the cylinder at the intermediate range of inclinations. For all inclinations, the mode B branch is not detected within the range of Reynolds numbers examined. The peak instability growth rates corresponding to mode A for all cylinder inclinations describe a linear variation with$(Re-Re_{A})/Re_{A}$, where$Re_{A}$is the mode A transition Reynolds number, while those corresponding to mode C vary only approximately linearly. The generalized trend most pertinently shows mode C to develop more rapidly than mode A at inclinations which permit it. Examination of the near wake of the two-dimensional time-periodic base flow demonstrates the dependence of the development and intensity of mode C on imbalances in the flow solution over each shedding period, directly implying that the two-dimensional base flow solutions deviate from the half-period-flip map as the cylinder inclination is increased. The degree of asymmetry of the two-dimensional base flow relative to the ideal half-period-flip map is quantified using several measures. The results show distinctly different trends in these asymmetry measures between inclinations where modes A or C are dominant, agreeing with results from the stability analysis. The nature of the predicted instability modes at transition are also investigated by applying the Stuart–Landau equation, showing the transitions to be supercritical for all cylinder inclinations, with mode C being consistently more strongly supercritical than mode A.
Fat-soluble vitamins A and E and health disparities in a cohort of pregnant women at delivery
Authors: Hanson Corrine , Schumacher Marina Verdi , Lyden Elizabeth , Su Dejun , Furtado Jeremy , Cammack Rex , Bereitschaft Bradley , Van Ormer Matthew , Needelman Howard , McGinn Elizabeth , Rilett Katherine , Cave Caleb , Johnson Rebecca , Weishaar Kara , Anderson-Berry Ann 
Published: April 2018

AbstractThe objective of the present study was to evaluate intakes and serum levels of vitamin A, vitamin E, and related compounds in a cohort of maternal–infant pairs in the Midwestern USA in relation to measures of health disparities. Concentrations of carotenoids and tocopherols in maternal serum were measured using HPLC and measures of socio-economic status, including food security and food desert residence, were obtained in 180 mothers upon admission to a Midwestern Academic Medical Center labour and delivery unit. The Kruskal–Wallis and independent-samplesttests were used to compare measures between groups; logistic regression models were used to adjust for relevant confounders.P < 0·05 was considered statistically significant. The odds of vitamin A insufficiency/deficiency were 2·17 times higher for non-whites when compared with whites (95 % CI 1·16, 4·05;P = 0·01) after adjustment for relevant confounders. Similarly, the odds of being vitamin E deficient were 3·52 times higher for non-whites (95 % CI 1·51, 8·10;P = 0·003). Those with public health insurance had lower serum lutein concentrations compared with those with private health insurance (P = 0·05), and living in a food desert was associated with lower serum concentrations of β-carotene (P = 0·02), after adjustment for confounders. Subjects with low/marginal food security had higher serum levels of lutein and β-cryptoxanthin compared with those with high food security (P = 0·004 and 0·02 for lutein and β-cryptoxanthin). Diet quality may be a public health concern in economically disadvantaged populations of industrialised societies leading to nutritional disadvantages as well.
Vitamin D deficiency and insufficiency among US adults: prevalence, predictors and clinical implications
Authors: Liu Xuefeng , Baylin Ana , Levy Phillip D. 
Published: April 2018

AbstractVitamin D deficiency (VDD) and insufficiency (VDI) are increasing at a global level, and they are associated with increased risk of various diseases. However, little information is available on the prevalence and predictors of VDD and VDI in a representative population of US adults. Serum 25-hydroxyvitamin D (25(OH)D) measurements were collected from 26 010 adults aged ≥18 years from the National Health and Nutrition Examination Survey (NHANES) 2001–2010. Using thresholds recommended by the Endocrine Society, VDD was defined as 25(OH)D<50 nmol/l and VDI as 50≤25(OH)D<75 nmol/l. Weighted multinomial log-binomial regression was conducted to estimate prevalence ratios of VDD and VDI. The prevalences of VDD and VDI in 2001–2010 were 28·9 and 41·4 %, respectively. Adults who were black, less educated, poor, obese, current smokers, physically inactive and infrequent milk consumers had a higher prevalence of VDD. After adjustment for other potential predictors, obese adults showed 3·09 times higher prevalence of VDD and 1·80 times higher prevalence of VDI than non-obese adults. Physically inactive adults had 2·00 and 1·36 times higher prevalence of VDD and VDI than active peers. Compared with frequent consumers, rare consumers of milk had 2·44 and 1·25 times higher prevalence of VDD and VDI, respectively. Current alcohol drinkers had 38 % lower prevalence of VDD than non-drinkers. Awareness of the high prevalence of VDD and VDI among US adults and related predictors could inform behavioural and dietary strategies for preventing VDD and monitoring VDI, especially in old, black, obese and inactive individuals who report rare consumption of milk.
Petrogenesis of the Harsin–Sahneh serpentinized peridotites along the Zagros suture zone, western Iran: new evidence for mantle metasomatism due to oceanic slab flux
Authors: NOURI FATEMEH , ASAHARA YOSHIHIRO , AZIZI HOSSEIN , TSUBOI MOTOHIRO 
Published: April 2018

AbstractThe Harsin–Sahneh serpentinized peridotites are widely exposed along the Zagros suture zone in the western region of Iran and are considered to represent remnants of Neo-Tethys oceanic lithosphere at the junction of the Arabian and Iran Plates. These rocks are characterized by low contents of SiO2 (38.8–43.5 wt%), Al2O3 (0.1–3.8 wt%), CaO (0.2–8.2 wt%) and TiO2 (< 1 wt%) and high MgO contents (31.1–46.0 wt%). Their enrichments of large ion lithophile elements and light rare earth elements, with high 87Sr/86Sr(i) values (0.7036–0.7109) and relatively high variations in their εNd(t) (–7.5 to +7.8) values, indicate that the Harsin–Sahneh peridotites were metasomatized by flux released from the oceanic subducting slab in an active margin. The chemical compositions and isotopic ratios of these rocks suggest that they were formed as residue of mid-oceanic ridge basalt in the lithosphere that was then subsequently re-melted and metasomatized in a supra-subduction zone system. The occurrence of both mid-oceanic ridge and supra-subduction zone-type peridotites suggests that the heterogeneity of the upper mantle may have occurred due to the different ratios of partial melting and melt–rock reaction processes in different tectonic settings within the Neo-Tethys realm. The Harsin–Sahneh peridotites provide a good explanation of multistage melt extraction as well as melt–rock and metasomatic reactions in the mantle sequence of the Zagros ophiolite complex.