bluuebunny/crossref_metadata_2025_split huggingface dataset:
Oncogenic KIT-containing exosomes increase gastrointestinal stromal tumor cell invasion
Authors: Atay Safinur , Banskota Samagya , Crow Jennifer , Sethi Geetika , Rink Lori , Godwin Andrew K. 
Published: December 2013

Significance
Elevated expression of matrix metalloproteinase 1 (MMP1) is associated with a poor prognosis in a wide variety of advancing tumors, and thus MMPs have emerged as attractive targets for therapeutic strategies of metastatic tumors. However, clinical trials using MMP inhibitors in cancer therapy have proved to be disappointing. These studies support the contention that the use of broad-spectrum inhibitors of MMPs is insufficient for clinical benefit, as new compensatory pathways such as continuous production of exosomes derived from the tumor will be unaffected and will enhance the MMP produced by stromal cells. Therefore, a better understanding of the mechanisms used by tumor-derived exosomes in the induction of MMPs would permit the development of successful clinical strategies for novel MMP inhibitors.
ParP prevents dissociation of CheA from chemotactic signaling arrays and tethers them to a polar anchor
Authors: Ringgaard Simon , Zepeda-Rivera Martha , Wu Xiaoji , Schirner Kathrin , Davis Brigid M. , Waldor Matthew K. 
Published: December 2013

Significance
Targeting of cellular components to a particular site in a cell is often a highly regulated process, even in cells as small as bacteria. Robust chemotactic signaling, which is used by motile bacteria to survey their environments and navigate in response to them, requires appropriate cellular distribution of a large chemosensory apparatus. Here, we report how polarly flagellated vibrios ensure polar localization of their chemotactic machinery by capturing signaling proteins at the pole. Polar localization is mediated by a tripartite protein interaction network in which one protein prevents disassociation of a key signaling component from chemotactic complexes and tethers the complexes to a polar anchor. Polar tethering and localization are prerequisites for proper chemotaxis.
Hemozoin-generated vapor nanobubbles for transdermal reagent- and needle-free detection of malaria
Authors: Lukianova-Hleb Ekaterina Y. , Campbell Kelly M. , Constantinou Pamela E. , Braam Janet , Olson John S. , Ware Russell E. , Sullivan David J. , Lapotko Dmitri O. 
Published: December 2013

Significance
We report a noninvasive rapid transdermal detection of malaria infection without drawing blood or using any reagents. Our method uses harmless laser pulses to generate and detect through the skin tiny vapor nanobubbles specifically in malaria parasites in a patient’s body. This method is distinct from all previous diagnostic approaches, which all rely upon using a needle to obtain blood, require reagents to detect the infection, and are time- and labor-consuming. This nanobubble transdermal detection adds a new dimension to malaria diagnostics and can in the future support the rapid, high-throughput, and high-sensitive diagnosis and screening by nonmedical personnel under field conditions, including the detection of early and asymptomatic disease.
Water access points and hydration pathways in CLC H
+
/Cl
−
transporters
Authors: Han Wei , Cheng Ricky C. , Maduke Merritt C. , Tajkhorshid Emad 
Published: December 2013

Significance
CLC transporters are biologically essential proteins that catalyze the transmembrane exchange of chloride for protons. The permeation pathway for chloride through the transporters has been well characterized. Here, we study the more elusive permeation pathway for protons. Through computational modeling, we show that water molecules can permeate deep inside the protein and form continuous wires. To test the hypothesis that these water wires mediate proton transport, we mutated residues predicted to impede water wire formation and experimentally evaluated the effects of the mutations. The results from our concerted computational and experimental approach strongly support the role of water in proton transport by CLCs and provide a valuable framework for investigating their overall transport mechanism.
Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy
Authors: Zhao Ziqing W. , Roy Rahul , Gebhardt J. Christof M. , Suter David M. , Chapman Alec R. , Xie X. Sunney 
Published: December 2013

Significance
We developed an optical imaging technique that combines reflected light-sheet illumination with superresolution microscopy, allowing us to image inside mammalian nuclei at subdiffraction-limit resolution and to count biomolecules with single-copy accuracy. Applying this technique to probe the spatial organization of RNA polymerase II-mediated transcription, we found that the majority of the transcription foci consist of only one RNAP II molecule, contrary to previous proposals. By quantifying the global extent of clustering across RNAP II molecules in the nucleus, we provide clear and convincing answers to the controversy surrounding the prevalent existence of “transcription factories.” Moreover, our work presents imaging and analysis tools for the quantitative characterization of nuclear structures, which could be generally applied to probe many other mammalian systems.
Catfish Sampling Techniques: Where We Are Now and Where We Should Go
Authors: Bodine Kristopher A , Shoup Daniel E , Olive Jason , Ford Zachary L , Krogman Rebecca , Stubbs Tyler J 
Published: December 2013

ABSTRACT
We review the peer-reviewed literature regarding sampling of the three most commonly managed ictalurids: Channel Catfish, Blue Catfish, and Flathead Catfish. For each species, we summarize what is known about data quality (accuracy and precision) and sampling efficiency of the most commonly used gears for surveying these species. We identify research needs and provide information to guide gear selection based on different sampling objectives. To rank gear-specific sampling efficiency (catch/h and catch/person-h), we report median catch rates and the interpolated 25th and 75th percentiles of published means. We also describe the accuracy of relative abundance and size-related metrics for each gear. For Channel Catfish, tandem baited hoop nets provide the most efficient (11–24 fish/net/tandem set, 20–60 fish/person-h) and accurate samples. Low-frequency electrofishing provides the most efficient samples of Blue Catfish (23–373 fish/h, 2.1–11.3 fish/person-h) and Flathead Catfish (19–62 fish/h, 2.1–2.5 fish/person-h) and the most accurate samples of Blue Catfish. No accuracy studies exist for Flathead Catfish. Other gears examined for each species may also be useful for some sampling objectives; however, most are inefficient or lack accuracy.
RESUMEN
en este trabajo se hace una revisión de la literatura sobre el muestreo de los tres ictalúridos más comunmente explotados: el bagre de canal, el bagre azul y el bagre piltontle. Para cada especie, se resume lo que se sabe sobre la calidad de los datos (exactitud y precisión) y la eficiencia de muestreo de las artes (equipo) más frecuentemente utilizadas para muestrear estas especies. Se identifican necesidades de investigación y se brinda información que puede servir de guía para la selección de artes de pesca de acuerdo a los objetivos de muestreo. Con la finalidad de calificar la eficiencia específica del equipo de muestreo (captura-h y captura/persona-h) se reporta tanto la mediana de las tasas de captura como una extrapolación de los percentiles 25 y 75 de las medias reportadas en la literatura. También se describe la exactitud de las medidas de abundancia relativa y las relacionadas a la talla para cada arte. Para el bagre de canal, el tándem de redes de aros con carnada produjo las muestras más eficientes (11–24 peces/red/tándem, 20–60 peces/persona-h) y exactas. La electro-pesca de baja frecuencia fue el arte más eficiente para el bagre azul (23–373 peces-h, 2.1–11.3 peces/persona-h) y el bagre piltontle (19–62 peces-h, 2.1–2.5 peces/persona-h) y produjo las muestras más exactas en el caso del bagre azul. No existen estudios de exactitud para el bagre piltontle. Para cada especie se examinaron otras artes que pudieran ser útiles para ciertos objetivos de pesca; no obstante, la mayoría son ineficientes o carecen de exactitud.
The EU shark finning ban at the beginning of the new millennium: the legal framework
Authors: Passantino Annamaria 
Published: December 2013

Abstract
The strong international market for shark fins, but the often relatively low value of shark meat and the practical constraints for preserving it on board, have led to the practice whereby fins are removed from any shark caught by a fishing vessel and retained on board while the remainder of the shark is discarded at sea. This practice, known as “shark finning”, has raised increasing concerns, at both the international and European levels, due to the killing of large quantities of sharks, with devastating and unsustainable effects on shark populations. Despite the importance of shark fisheries for EC fleets, to date shark fisheries are not subject to a comprehensive management framework at the European level. A number of measures aiming directly or indirectly at the conservation and management of sharks have been adopted over time. Considering that, the range of existing measures must be strengthened to ensure the rebuilding of many depleted stocks fished by the EU fleet both in and outside EU waters. At the EC level a new regulation has recently been implemented. This paper carries out an overview of the legal framework for the finning bans in the EU to improve current knowledge about this topic and to aid in focusing future research.
The puzzle of the CNO abundances of α Cygni variables resolved by the Ledoux criterion
Authors: Georgy Cyril , Saio Hideyuki , Meynet Georges 
Published: December 2013

Abstract
Recent stellar evolution computations show that the blue supergiant (BSG) stars could come from two distinct populations: a first group arising from massive stars that just left the main sequence and are crossing the Hertzsprung–Russell diagram (HRD) towards the red supergiant (RSG) branch, and a second group coming from stars that have lost considerable amount of mass during the RSG stage and are crossing the HRD for a second time towards the blue region. Due to very different luminosity-to-mass ratio, only stars from the second group are expected to have excited pulsations observable at the surface. In a previous work, we have shown that our models were able to reproduce the pulsational properties of BSGs. However, these models failed to reproduce the surface chemical composition of stars evolving back from an RSG phase. In this Letter, we show how the use of the Ledoux criterion instead of the Schwarzschild one for convection allows us to significantly improve the agreement with the observed chemical composition, while keeping the agreement with the pulsation periods. This gives some support to the Ledoux criterion.
Modelling baryon acoustic oscillations with perturbation theory and stochastic halo biasing
Authors: Kitaura Francisco-Shu , Yepes Gustavo , Prada Francisco 
Published: December 2013

Abstract
In this work we investigate the generation of mock halo catalogues based on perturbation theory and non-linear stochastic biasing with the novel patchy code. In particular, we use Augmented Lagrangian Perturbation Theory (ALPT) to generate a dark matter density field on a mesh starting from Gaussian fluctuations and to compute the peculiar velocity field. ALPT is based on a combination of second order LPT (2LPT) on large scales and the spherical collapse model on smaller scales. We account for the systematic deviation of perturbative approaches from N-body simulations together with halo biasing adopting an exponential bias model. We then account for stochastic biasing by defining three regimes: a low-, an intermediate- and a high-density regime, using a Poisson distribution in the intermediate regime and the negative binomial distribution – including an additional parameter – to model over-dispersion in the high-density regime. Since we focus in this study on massive haloes, we suppress the generation of haloes in the low-density regime. The various non-linear and stochastic biasing parameters, and density thresholds, are calibrated with the large BigMultiDark N-body simulation to match the power spectrum of the corresponding halo population. Our model effectively includes only five parameters, as they are additionally constrained by the halo number density. Our mock catalogues show power spectra, in both real- and redshift-space, which are compatible with N-body simulations within about 2 per cent up to k ∼ 1 h Mpc−1 at z = 0.577 for a sample of haloes with the typical Baryon Oscillation Spectroscopic Survey (BOSS) CMASS (constant stellar mass galaxy sample) galaxy number density. The corresponding correlation functions are compatible down to a few Mpc. We also find that neglecting over-dispersion in high-density regions produces power spectra with deviations of 10 per cent at k ∼ 0.4 h Mpc−1. These results indicate the need to account for an accurate statistical description of the galaxy clustering for precise studies of large-scale surveys.
Genomic Resources Notes accepted 1 October 2013 – 30 November 2013
Authors:   Genomic Resources Development Consortium, Keller Stephen R. , Nelson David M. , Pylant Cortney , Santos Scott R. , Trott Regina 
Published: December 2013

AbstractThis article documents the public availability of (i) genomic sequence data and 43 microsatellite loci for the bat species, Lasiurus borealis and Lasiurus cinereus, and (ii) complete mitochondrial and partial nuclear genomes for two jack species, Caranx ignobilis, Caranx melampygus.
Stillbirth and infant death among generations of Pakistani immigrant descent: a population‐based study
Authors: Sørbye Ingvil K. , Stoltenberg Camilla , Sundby Johanne , Daltveit Anne K. , Vangen Siri 
Published: December 2013

AbstractObjectiveTo examine the risk of stillbirth and infant death among offspring of Pakistani‐born and Norwegian‐born women of Pakistani immigrant descent.DesignPopulation‐based study linking the Medical Birth Registry of Norway to immigration data from Statistics Norway.SettingNorway.PopulationBirths to women of Pakistani immigrant descent classified as Pakistani‐born (n = 8814) or Norwegian‐born (n = 1801), and to the host population of Norwegian descent (n = 712 430) from 1995 to 2010.MethodsThe relative risk of stillbirth and infant death by country of descent and birth was estimated by odds ratios with 95% confidence intervals (95% CI) using logistic regression.Main outcome measuresStillbirth and infant death.ResultsRisk of stillbirth was highest in the Pakistani‐born group (7.4/1000, 95% CI 5.7–9.4) followed by the Norwegian‐born group (5.0/1000, 95% CI 1.7–8.3) and finally the host population (3.5/1000, 95% CI 3.3–3.6). Relative to the host population, risk of stillbirth was higher in both Pakistani‐born (odds ratios 2.8, 95% CI 2.2–3.6) and Norwegian‐born (odds ratios 2.2, 95% CI 1.1–4.2) groups, after adjustment for year of birth, age, parity and residence. For infant death, absolute risks were 6.9/1000 (95% CI 5.2–8.8), 5.6/1000 (95% CI 2.7–10.2), and 2.9/1000 (95% CI 2.7–3.0), with adjusted odds ratios of 2.8 (95% CI 2.1–3.7) and 2.4 (95% CI 1.3–4.6), respectively.ConclusionsAn elevated risk of stillbirth and infant death persists across generations of Pakistani immigrant descent living in Norway. While translating into few excess deaths, the elevated risks should be taken into account by obstetric and pediatric care providers.
Host plant‐related variation in thermal tolerance of Eldana saccharina
Authors: Kleynhans Elsje , Conlong Des E. , Terblanche John S. 
Published: December 2013

AbstractUnderstanding tolerance of thermal extremes by pest insects is essential for developing integrated management strategies, as tolerance traits can provide insights into constraints on activity and survival. A major question in thermal biology is whether thermal limits vary systematically with microclimate variation, or whether other biotic or abiotic factors can influence these limits in a predictable manner. Here, we report the results of experiments determining thermal limits to activity and survival at extreme temperatures in the stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae), collected from either Saccharum spp. hybrids (sugarcane) (Poaceae) or Cyperus papyrus L. (Cyperaceae) and then reared under standard conditions in the laboratory for 1–2 generations. Chill‐coma temperature (CTmin), critical thermal maximum (CTmax), lower lethal temperatures (LLT), and freezing temperature between E. saccharina collected from the two host plants were compared. CTmin and CTmax of E. saccharina moths collected from sugarcane were significantly lower than those from C. papyrus (CTmin = 2.8 ± 0.4 vs. 3.9 ± 0.4 °C; CTmax = 44.6 ± 0.1 vs. 44.9 ± 0.2 °C). By contrast, LLT of moths and freezing temperatures of pupae did not vary with host plant [LLT for 50% (LT50) of the moth population, when collected from sugarcane: −3.2 ± 0.5 °C, from C. papyrus: −3.9 ± 0.8 °C]. Freezing temperatures of pupae collected from C. papyrus were −18.0 ± 1.0 °C and of those from sugarcane −17.5 ± 1.8 °C. The E. saccharina which experienced the lowest minimum temperature (in C. papyrus) did not have the lowest CTmin, although the highest estimate of CTmax was found in E. saccharina collected from C. papyrus and this was also the microsite which reported the highest maximum temperatures. These results therefore suggest that host plant may strongly mediate lower critical thermal limits, but not necessarily LLT or freezing temperatures. These results have significant implications for ongoing pest management and thermal biology of these and other insects.
Predictive immunogenicity of Refacto®AF
Authors: Delignat S. , Repessé Y. , Gilardin L. , Dimitrov J. D. , Lone Y.C. , Kaveri S. V. , Lacroix‐Desmazes S. 
Published: December 2013

SummaryThe administration of therapeutic factor VIII (FVIII) to treat or prevent haemorrhages in haemophilia A patients results, in up to 30% of the cases, in the development of inhibitory anti‐FVIII antibodies. Much debate has taken place on the relevance of the nature of the FVIII product as a risk factor for inhibitor development. Thus, the plasma‐derived vs. recombinant origin, the second vs. third generation of the product, or the presence of the B domain have been controversially evoked. A few years ago, Refacto® AF, a third‐generation recombinant B domain‐deleted FVIII was marketed. The aim of this study was to compare the immunogenicity of Refacto® AF to that of two recombinant full‐length FVIII products: Helixate® and Advate®. For the three recombinant FVIII products, we compared the binding to the mannose‐sensitive endocytic receptor CD206, the dose‐dependent endocytosis by immature monocyte‐derived dendritic cells (DCs), the activation by FVIII‐loaded DCs of a FVIII‐specific HLA‐DRB1*0101‐restricted mouse T‐cell hybridoma and the induction of inhibitory anti‐FVIII IgG in FVIII‐deficient mice. At elevated FVIII concentrations, Refacto® AF was less endocytosed than full‐length recombinant products. At lower concentrations, however, Refacto® AF was endocytosed by DCs and activated T cells as well as Helixate® and Advate®. The levels of inhibitory anti‐FVIII IgG induced by Refacto® AF in FVIII‐deficient mice were lower or equal to that induced by Helixate® and Advate® respectively. The predicted immunogenicity of Refacto® AF is identical to or lower than that of the two recombinant full‐length FVIII products available on the French market.
Pigmentation of axillary sentinel nodes from extensive skin tattoo mimics metastatic melanoma: case report
Authors: Manganoni Ausilia Maria , Sereni Elena , Pata Giacomo , Ungari Marco , Pavoni Laura , Farisoglio Camillo , Calzavara‐Pinton Pier Giacomo , Farfaglia Roberto 
Published: December 2013

AbstractBackgroundThe relationship between the occurrence of skin diseases and skin tattoos remains unclear. Dermatologic disorders have been reported to occur in about 2% of cases. In addition, tattoo pigment can migrate to the regional lymph nodes through the lymphatic vessels and subsequently mimic metastatic disease from melanoma.MethodsA 23‐year‐old Caucasian man presented with a pigmented lesion on the left scapular region, which had slowly enlarged over time. The patient exhibited an extensive tattoo on the left upper arm, left shoulder, and part of the upper back. His medical history was unremarkable. The pigmented lesion was excised. Histology confirmed malignant melanoma. Ultrasound examination of the abdomen, neck, and inguinal and axillary lymph nodes and a total body computed tomography scan showed no sign of disease. A re‐excision with 2‐cm margins and sentinel lymph node biopsy (SLNB) were performed. Two grossly enlarged, black sentinel lymph nodes (SLNs) highly suggestive of melanoma metastases were removed.ResultsNo evidence of melanoma metastasis was found in any of the sampled tissues. Large amounts of pigment were present within the subcapsular space and sinusoid areas of the two clinically suspicious lymph nodes. Immunohistochemical analysis was negative.ConclusionsSentinel lymph node biopsy is widely performed in cutaneous melanoma. Histologic confirmation of any enlarged, pigmented SLN is essential prior to radical surgery, especially when pigmented SLNs are found near a tattoo. Tattoo pigments may deposit in the regional lymph nodes and may clinically mimic metastatic disease. A history of tattooing should be considered in all melanoma patients eligible for SLNB. In a finding of darkly pigmented nodes during SLNB, radical lymphadenectomy should be withheld until immunohistologic confirmation of metastasis in the SLN is obtained.
Impact of amorphous and crystalline lactose on milk chocolate properties
Authors: Bolenz Siegfried , Römisch Josefine , Wenker Thorsten 
Published: December 2013

SummaryChocolate mass of low viscosity is preferred for most applications. Milk powder influences processing behaviour, flow properties and taste of milk chocolate. The project aimed to investigate influences of skim milk powders containing amorphous or crystalline lactose on flow properties after producing samples by roller milling and conching or alternatively by ball milling. For the first case, it was found that mass consistency before roller milling is strongly influenced by lactose type; producers must specify it and adapt initial mass fat content. Little impact on final products was found after processing milk powders at equilibrium moisture. If predried powders are used for reducing conching time, crystalline lactose leads to chocolate with slightly lower viscosity. At ball mill processing, crystalline lactose resulted in significantly lower viscosity, for example 15% at 40 s−1; thus, for this process, it can be recommended to use special milk powders high in crystalline lactose content.