bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the Survival Benchmark for Breast Cancer Patients with Systemic Relapse
Authors: Zeichner Simon B. , Ambros Tadeu , Zaravinos John , Montero Alberto J. , Mahtani Reshma L. , Ahn Eugene R. , Mani Aruna , Markward Nathan J. , Vogel Charles L. 
Published: April 2015

Background Our original paper, published in 1992, reported a median overall survival after first relapse in breast cancer of 26 months. The current retrospective review concentrates more specifically on patients with first systemic relapse, recognizing that subsets of patients with local recurrence are potentially curable. Methods Records of 5,168 patients from a largely breast-cancer-specific oncology practice were reviewed to identify breast cancer patients with their first relapse between 1996 and 2006 after primary treatment. There were 189 patients diagnosed with metastatic disease within 2 months of being seen by our therapeutic team and 101 patients diagnosed with metastatic disease greater than 2 months. The patients were divided in order to account for lead-time bias than could potentially confound the analysis of the latter 101 patients. Results Median survival for our primary study population of 189 patients was 33 months. As expected, the median survival from first systemic relapse (MSFSR) for the 101 patients excluded because of the potential for lead-time bias was better at 46 months. Factors influencing prognosis included estrogen receptor (ER) status, disease-free interval (DFI), and dominant site of metastasis. Compared with our original series, even with elimination of local-regional recurrences in our present series, the median survival from first relapse has improved by 7 months over the past two decades. Conclusion The new benchmark for MSFSR approaches 3 years.
Role of Hepatocyte Growth Factor in the Immunomodulation Potential of Amniotic Fluid Stem Cells
Authors: Maraldi Tullia , Beretti Francesca , Guida Marianna , Zavatti Manuela , De Pol Anto 
Published: April 2015

Abstract

Human amniotic fluid stem cells (hAFSCs) may be useful for regenerative medicine because of their potential to differentiate into all three germ layers and to modulate immune response with different types of secretion molecules. This last issue has not been completely elucidated. The aim of this study was to investigate the secretome profile of the hAFSC, focusing on the role of hepatocyte growth factor (HGF) in immunoregulation through short and long cocultures with human peripheral blood mononuclear cells. We found that HGF produced by hAFSCs exerts a cytoprotective role, inducing an increase in caspase-dependent apoptosis in human immune cells. This study provides evidence supporting the hypothesis that amniotic fluid is an ideal source of stem cells for expansion and banking properties for therapeutic use. hAFSCs not only are less immunogenic but also can secrete immunoregulatory factors that may be useful in autoimmune diseases or allogenic implants.

Significance
New information about the secretome pattern is reported in this paper. Human amniotic fluid stem cells (hAFSCs) possess immunomodulatory properties involving hepatocyte growth factor production. hAFSCs could be used in immunotherapies and might be able to avoid allogenic rejection.
The solar and Southern Oscillation components in the satellite altimetry data
Authors: Howard Daniel , Shaviv Nir J. , Svensmark Henrik 
Published: April 2015

AbstractWith satellite altimetry data accumulating over the past two decades, the mean sea level (MSL) can now be measured to unprecedented accuracy. We search for physical processes which can explain the sea level variations and find that at least 70% of the variance in the annually smoothed detrended altimetry data can be explained as the combined effect of both the solar forcing and the El Niño–Southern Oscillation (ENSO). The phase of the solar component can be used to derive the different steric and eustatic contributions. We find that the peak to peak radiative forcing associated with the solar cycle is 1.33 ± 0.34 W/m2, contributing a 4.4 ± 0.8 mm variation. The slow eustatic component (describing, for example, the cryosphere and large bodies of surface water) has a somewhat smaller peak to peak amplitude of 2.4 ± 0.6 mm. Its phase implies that warming the oceans increases the ocean water loss rate. Additional much smaller terms include a steric feedback term and a fast eustatic term. The ENSO contributes a peak to peak variation of 5.5 ± 0.8 mm, predominantly through a direct effect on the MSL and significantly less so indirectly through variations in the radiative forcing.
Experimental investigation of sediment resuspension beneath internal solitary waves of depression
Authors: Aghsaee Payam , Boegman Leon 
Published: April 2015

AbstractInternal solitary waves (ISWs) of depression are common features of coastal environments and believed to resuspend sediments where they shoal. In this study, the sediment resupension process associated with ISWs propagating over a flat bed was investigated in the laboratory. The first‐ever profile measurements of the three‐dimensional instantaneous velocity field beneath the ISWs revealed that resuspension occurs during burst like vertical velocity events, which lift sediments into the water column, in the adverse pressure gradient region beneath the trailing part of the wave. Resuspension was not observed when the wave‐induced viscous bed stress was maximal directly beneath the ISW trough. Prediction of wave‐induced resuspension was, therefore, unsuccessful using a traditional viscous bed stress‐based Shields diagram. A parameterization for ISW‐induced resuspension is proposed as a function of the maximum instantaneous vertical velocity in the bursts
. Here we have replaced the viscous bed stress with
, where
is the instantaneous resuspending bed stress and
is the near‐bed fluid density. From these results, it is possible for field‐oceanographers to predict the occurrence of ISW‐induced resuspension from the bulk wave and stratifications characteristics in a two‐layer stratification. Further research is required to extend the parameterization to larger Reynolds numbers at field‐scale.
Beam attenuation, scattering and backscattering of marine particles in relation to particle size distribution and composition in Hudson Bay (Canada)
Authors: Xi Hongyan , Larouche Pierre , Michel Christine , Tang Shilin 
Published: April 2015

AbstractThis study investigated the relationships between the concentration of biogeochemical parameters and particulate beam attenuation (cp), scattering (bp), and backscattering (bbp) in Hudson Bay. Results showed that most of the variability resulted from the presence of a deep chlorophyll maximum. cp, bp, and bbp were all adequate proxies to estimate total suspended matter (TSM) but were mostly sensitive to particulate inorganic matter (PIM) in the surface layer, and particulate organic matter (POM) at the chlorophyll maximum depth. The backscattering ratio
varied in the range of 0.005–0.05 and was inversely related to the POM : TSM ratio. According to the Twardowski et al. (2001) model, the PSD slope ξ well represented
and bulk refractive index
in relation to particulate composition. For inorganic particulate dominated waters, both
and
had a larger range and a higher mean value than at organic particulate dominated waters. This knowledge on the optical properties related to the PSD and particulate composition provides valuable information for further investigation and broadens our understanding of ocean optics in high latitude waters leading to potential improvements of regional scale remote sensing algorithms.
Climatology of cloud water content associated with different cloud types observed by A‐Train satellites
Authors: Huang Lei , Jiang Jonathan H. , Wang Zhien , Su Hui , Deng Min , Massie Steven 
Published: April 2015

AbstractThis study investigates the climatology of vertical distributions of cloud liquid water content, ice water content, and cloud fraction (CFR) associated with eight different cloud types, by utilizing the combined CloudSat radar and Cloud‐Aerosol Lidar and Infrared Pathfinder Satellite Observations lidar measurements. The geographical and seasonal variations of these cloud properties for each cloud type are also analyzed. The cloud water content (CWC) of each cloud type is sorted by three parameters obtained from colocated satellite observations to investigate the relationships between large‐scale conditions and the vertical structure of clouds. Results show that different cloud types have different altitudes of CWC and CFR peaks, and the altitude of CFR peak does not always overlap with that of CWC peak. Each type of cloud shows a clear asymmetric pattern of spatial distribution between Northern Hemisphere (NH) and Southern Hemisphere (SH). Stratocumulus and stratus clouds make the greatest contribution to the liquid water path, while the ice water path is mostly contributed by deep convective cloud over the tropics and nimbostratus over the middle and high latitudes. Over both middle and high latitudes, clouds have larger seasonal variation in the NH than in the SH. Over ocean, large CWCs of deep convective cloud, cirrus, and altostratus are above 7 km, and are associated with high convective available potential energy (>2000 J/kg), warm sea surface temperature (>303 K), and relatively high precipitation (>1 mm/h). Over land, most of the middle and high clouds have similar CWC distributions compared to those over ocean, but altocumulus and low clouds are quite different from those over ocean.
Magnetic and geochemical characterization of Andosols developed on basalts in the Massif Central, France
Authors: Grison Hana , Petrovsky Eduard , Stejskalova Sarka , Kapicka Ales 
Published: April 2015

AbstractIdentification of Andosols is primarily based upon the content of their colloidal constituents—clay and metal‐humus complexes—and on the determining of andic properties. This needs time and cost‐consuming geochemical analyses. Our primary aim of this study is to describe the magnetic and geochemical properties of soils rich in iron oxides derived from strongly magnetic volcanic basement (in this case Andosols). Secondary aim is to explore links between magnetic and chemical parameters of andic soils with respect to genesis factors: parent material age, precipitation, and thickness of the soil profile. Six pedons of andic properties, developed on basaltic lavas, were analyzed down to parent rock by a set of magnetic and geochemical methods. Magnetic data of soil and rock samples reflect the type, concentration, and particle‐size distribution of ferrimagnetic minerals. Geochemical data include soil reaction (pH in H2O), cation exchange capacity, organic carbon, and different forms of extractable iron and aluminum content. Our results suggest the following: (1) magnetic measurements of low‐field mass‐specific magnetic susceptibility can be a reliable indicator for estimating andic properties, and in combination with thermomagnetic curves may be suitable for discriminating between alu‐andic and sil‐andic subtypes. (2) In the studied Andosols, strong relationships were found between (a) magnetic grain‐size parameters, precipitation, and exchangeable bases; (b) concentration of ferrimagnetic particles and degree of crystallization of free iron; and (c) parameters reflecting changes in magneto‐mineralogy and soil genesis (parent material age + soil depth).
Selenocysteine
Authors: Rother Michael 
Published: April 2015

Abstract

The trace element selenium is present in the form of selenocysteine in selected proteins of organisms from all three domains of life. Most of the selenoproteins (i.e. proteins containing selenocysteine) investigated thus far are oxidoreductases with selenocysteine present in the active site and playing a crucial role in – or creating the required environment for – catalysis. Selenocysteine incorporation is DNA encoded, determined by the UGA codon, and occurs via a unique mechanism representing an expansion of the genetic code. Despite the conceptual conservation of the principal mechanism of selenocysteine synthesis and incorporation in all lines of descent, the bacterial system differs from the archaeal/eukaryal system. Detailed biochemical and structural knowledge of selenoprotein synthesis has allowed rewiring bacterial translation for targeted selenocysteine insertion.

Key Concepts

Selenium is an essential trace element for many organisms including humans.

The most important form of biologically active selenium is the amino acid selenocysteine.

Selenocysteine is co‐translationally inserted into growing polypeptides.

Selenocysteine insertion proceeds via a unique mechanism recoding UGA.

The mechanism of selenocysteine insertion differs in Bacteria, Archaea, and Eukarya.
Plant Virus Transmission by Insects
Authors: Fereres Alberto , Raccah Benjamin 
Published: April 2015

Abstract

Most plant viruses depend on insect vectors for their survival, transmission and spread. They transmit plant viruses by two principal modes, circulative (circulating through the insect's haemocoel, CV) and non‐circulative (carried on the cuticle lining of mouthparts or foregut, NC). Transmissibility and specificity between NC viruses and their vectors depends on the coat protein (CP) of the virus in addition to virus‐encoded helper proteins. Circulative viruses cross the gut, circulate in the haemocoel and cross the salivary glands to render the insect infective. Circulative luteoviruses depend on small CP and the read‐through protein (RTD) for transmission. Electrical penetration graphs have provided evidence on insect feeding behaviour and virus transmission. Recently, studies have shown that viruses can modify vector behaviour in a way that transmission is enhanced. Cultural, physical and novel biotechnological tools can provide virus control by interfering with vector landing and the retention of viruses in their vectors.

Key Concepts

Most plant viruses rely on insect vectors for survival, transmission and spread.

Aphids and whiteflies are by far the most important insects transmitting plant viruses.

Some plant viruses are associated to the cuticle of the insect mouthparts (non‐circulative), whereas others are retained in the salivary glands after they circulate through the insect's body (circulative).

Some non‐circulative viruses are retained in the common duct of the aphid's maxillary stylets and are inoculated by salivation during brief superficial intracellular probes.

Circulative viruses are inoculated during salivation stylet activities in phloem sieve elements.

Recent findings in the nature of insect proteins involved in the retention of virus or virus‐encoded helper proteins will help to develop new molecules to interfere with the transmission process.
NMR
Spectroscopy for Monitoring Functional Dynamics in Solution
Authors: Sivanandam VN , Millet Oscar 
Published: April 2015

Abstract

Protein functional dynamics are defined as the atomic thermal fluctuations or the segmental motions that are essential for the function of a biomolecule. NMR is a very versatile technique that is well suited for obtaining quantitative information from these processes at atomic resolution and in multiple timescales. This article focuses on recent NMR developments to study functional dynamics, making special incidence in the experiments aimed for the characterisation of chemical–conformational exchange in the microsecond to millisecond timescale. In a second section, the novel‐solution NMR techniques that combine chemical exchange with saturation transfer experiments are addressed to finish with an overview on the dynamic information that can be extracted from residual dipolar couplings.

Key Concepts

NMR is well suited to study biomolecular dynamics at multiple timescales.

Many enzymatic reactions occur in the microsecond to millisecond timescale.

Relaxation dispersion experiments can extract quantitative information about the exchange process.

CEST and DEST experiments provide useful information on conformations that are invisible in the NMR spectrum.

Residual dipolar couplings contain information about spin dynamics that can be extracted and quantified.
The Status of Women in the Life Sciences
Authors: Peters Jan W , Lane Nancy J 
Published: April 2015

AbstractWomen in the life sciences seem to attract less concern and attention than women in physics, IT or engineering. Perhaps because women in the life sciences at undergraduate and, more recently, postgraduate level have equalled or exceeded men for the past 30 or so years. The poor representation of women at professorial level in biology – still only 15% in the United Kingdom – shows an appalling waste of potential talent, often referred to as the ‘leaky pipeline’. Given the significant attention paid to the under‐representation of women across STEM (science, technology, engineering and maths) subjects globally by national academies, employers and governments over the past 15 years, it is disappointing to observe such poor progress.More attention needs to be paid to the career planning and professional preparation of young women, so that more will be able to progress to senior positions and decision‐making roles. Educational institutions and employers need to evolve in the form of inclusive leadership, structural changes and good management policies and practices. Also, shifts from a purely male orientation of science and changes in cultural stances need to be implemented, including addressing unconscious bias by both women and men towards women and the recognition of the importance of diversity and inclusion.Key ConceptsWomen leave the life sciences at every step of the career ladder in greater proportions than men. This is termed the ‘leaky pipeline’.Unconscious bias and discrimination against women, preventing their career advancement, results in fewer women in senior positions.Much of scientific research is undertaken with little thought about whether there is a gender context; for example, omitting women from studies and trials.There is a lack of career planning, personal development and preparation for leadership for women in the life sciences.Creating a level playing field for women in life science requires the effective implementation of policies around recruitment, promotion and workplace cultures.
K
eilin,
D
avid
Authors: Prebble John N 
Published: April 2015

Abstract
David Keilin (1887–1963) was born in Moscow and grew up in Poland. At an early age, he moved via Liège to Paris where he acquired a reputation as a parasitologist. In 1914, he moved to Cambridge where he remained for the rest of his life and became the Director of the Molteno Institute. Here, he rediscovered the cytochromes, previously observed by MacMunn whose work was ignored, and went on to describe the respiratory chain. For a while his work brought him into conflict with Otto Warburg over the latter's respiratory enzyme, which Keilin eventually showed was the same as his cytochrome oxidase.
M
asatoshi
N
ei
Authors: Pievani Telmo 
Published: April 2015

Abstract

Evolutionary biology must recognise Masatoshi Nei's merit for three outstanding contributions: (1) an advancement in the scientific status of the discipline, which has been made by ‘molecular evolutionary biology’ more quantitative through a set of statistical methods for studying genetic diversity, changes in DNA, neutral evolution and molecular phylogenies; (2) the application of Nei's evolutionary genetic distance to the phylogenetic tree of human populations, supporting the out of Africa model of global dispersal, and (3) the overall recognition of the central role of mutations in evolution and the idea that the changes in DNA are not just ‘raw material’ for the natural selection but the main sources of innovation. Nei's alternative theory of evolution, intended as a process driven by mutation, seems biased by a narrow focus on molecular determination and tends to underestimate the large
corpus
of interdisciplinary evidence supporting the causal role of selective processes in evolution.
Protein Folding and Chaperones
Authors: Sinnige Tessa , Karagöz G Elif , Rüdiger Stefan GD 
Published: April 2015

Abstract

Proteins fold via specific pathways to achieve their native structure. Protein structures are, however, inherently unstable, hence folding and unfolding are in equilibrium. Protein instability is a major concern inside the cell. Specialised proteins called molecular chaperones are, therefore, required to assist proteins in folding and to prevent aggregation of folding intermediates. Many different classes of chaperones are conserved throughout all kingdoms of life, many of which are known as heat shock proteins. Chaperones typically recognise hydrophobic patches, but the exact functions and mechanisms of action of the various chaperone classes are very different. The main chaperone classes Hsp70, Hsp90, Hsp100 and chaperonins all depend on ATPase cycles, whose activities are fine‐tuned by co‐chaperones. The molecular understanding of the mechanism of both chaperones and protein folding are key problems in present‐day life sciences and molecular medicine.

Key Concepts

Proteins fold via pathways.

Protein structures are labile.

Protein folding
in vivo
is assisted by molecular chaperones.

Assisted protein folding requires ATP energy.

Molecular chaperones are evolutionary conserved.

Chaperone activity is controlled by co‐chaperones and co‐factors.

Chaperone families differ in structure and function.
Tuberculosis: Immunity
Authors: Orme Ian M 
Published: April 2015

Abstract

For centuries, tuberculosis has been recognised as one of the most dangerous diseases on the planet, and in the twenty‐first century, this situation has not changed. In fact, both in the context of prevention by vaccination and treatment by chemotherapy, it has proven very difficult to halt the continued global epidemic of this deadly disease – a situation further compounded by the concomitant HIV epidemic. The immune response to tuberculosis involves both innate and acquired immune responses. Should an infection established an integrated response involving antigen‐specific T lymphocytes and macrophages ensues (‘TH1 response’) that involves the formation of a cellular barrier (‘granuloma’) that is controlled by cytokines and chemokines. As the infection becomes contained, the effector immune response contracts and is gradually replaced by T cells capable of an accelerated memory response to further exposure.

Key Concepts

Immunity to tuberculosis is cell mediated.

The central even involves the interaction between antigen‐specific T cells and infected macrophages.

The response is complex and involves multiple soluble mediators including cytokines and chemokines.

The primary containment device involves the formation of a structure called the granuloma.

Contraction of effector immunity is followed by the emergence of still poorly understood memory immunity.