bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ligand-Directed Surface Profiling of Human Cancer Cells with Combinatorial Peptide Libraries
Authors: Kolonin Mikhail G. , Bover Laura , Sun Jessica , Zurita Amado J. , Do Kim-Anh , Lahdenranta Johanna , Cardó-Vila Marina , Giordano Ricardo J. , Jaalouk Diana E. , Ozawa Michael G. , Moya Catherine A. , Souza Glauco R. , Staquicini Fernanda I. , Kunyiasu Akihiko , Scudiero Dominic A. , Holbeck Susan L. , Sausville Edward A. , Arap Wadih , Pasqualini Renata 
Published: January 2006

Abstract
A collection of 60 cell lines derived from human tumors (NCI-60) has been widely explored as a tool for anticancer drug discovery. Here, we profiled the cell surface of the NCI-60 by high-throughput screening of a phage-displayed random peptide library and classified the cell lines according to the binding selectivity of 26,031 recovered tripeptide motifs. By analyzing selected cell-homing peptide motifs and their NCI-60 recognition patterns, we established that some of these motifs (a) are similar to domains of human proteins known as ligands for tumor cell receptors and (b) segregate among the NCI-60 in a pattern correlating with expression profiles of the corresponding receptors. We biochemically validated some of the motifs as mimic peptides of native ligands for the epidermal growth factor receptor. Our results indicate that ligand-directed profiling of tumor cell lines can select functional peptides from combinatorial libraries based on the expression of tumor cell surface molecules, which in turn could be exploited as “druggable” receptors in specific types of cancer. (Cancer Res 2006; 66(1): 34-40)
The Interaction between Two Radiosensitizers: 5-Iododeoxyuridine and Caffeine
Authors: Seo Yuji , Yan Tao , Schupp Jane E. , Yamane Kazuhiko , Radivoyevitch Tomas , Kinsella Timothy J. 
Published: January 2006

Abstract
5-Iododeoxyuridine (IUdR) and caffeine are recognized as potential radiosensitizers with different mechanisms of interaction with ionizing radiation (IR). To assess the interaction of these two types of radiosensitizers, we compared treatment responses to these drugs alone and in combination with IR in two p53-proficient and p53-deficient pairs of human colon cancer cell lines (HCT116 versus HCT116 p53−/− and RKO versus RKO E6). Based on clonogenic survival, the three single agents (IR, IUdR, and caffeine) as well as IUdR or caffeine combined with IR are less or equally effective in p53-deficient human tumor cells compared with p53-proficient tumor cells. However, using both radiosensitizers, a significantly greater radiosensitization was found in p53-deficient human tumor cells. To better understand the interaction of these two radiosensitizers, additional studies on DNA repair and cell cycle regulation were done. We found that caffeine enhanced IUdR-DNA incorporation and IUdR-mediated radiosensitization by partially inhibiting repair (removal) of IUdR in DNA. The repair of IR-induced DNA double-strand breaks was also inhibited by caffeine. However, these effects of caffeine on IUdR-mediated radiosensitization were not found in p53-proficient cells. Cell cycle analyses also showed a greater abrogation of IR-induced S- and G2-phase arrests by caffeine in p53-deficient cells, particularly when combined with IUdR. Collectively, these data provide the mechanistic bases for combining these two radiosensitizers to enhance tumor cytotoxicity. This differential dual mode of radiosensitization by combining IUdR and caffeine-like drugs (e.g., UCN-01) in p53-deficient human tumors may lead to a greater therapeutic gain. (Cancer Res 2006; 66(1): 490-8)
BRCA1 Mutation Analysis of 41 Human Breast Cancer Cell Lines Reveals Three New Deleterious Mutants
Authors: Elstrodt Fons , Hollestelle Antoinette , Nagel Jord H.A. , Gorin Michael , Wasielewski Marijke , van den Ouweland Ans , Merajver Sofia D. , Ethier Stephen P. , Schutte Mieke 
Published: January 2006

Abstract
Germ line mutations of the BRCA1 gene confer a high risk of breast cancer and ovarian cancer to female mutation carriers. The BRCA1 protein is involved in the regulation of DNA repair. How specific tumor-associated mutations affect the molecular function of BRCA1, however, awaits further elucidation. Cell lines that harbor BRCA1 gene mutations are invaluable tools for such functional studies. Up to now, the HCC1937 cell line was the only human breast cancer cell line with an identified BRCA1 mutation. In this study, we identified three other BRCA1 mutants from among 41 human breast cancer cell lines by sequencing of the complete coding sequence of BRCA1. Cell line MDA-MB-436 had the 5396 + 1G&gt;A mutation in the splice donor site of exon 20. Cell line SUM149PT carried the 2288delT mutation and SUM1315MO2 carried the 185delAG mutation. All three mutations were accompanied by loss of the other BRCA1 allele. The 185delAG and 5396 + 1G&gt;A mutations are both classified as pathogenic mutations. In contrast with wild-type cell lines, none of the BRCA1 mutants expressed nuclear BRCA1 proteins as detected with Ab-1 and Ab-2 anti-BRCA1 monoclonal antibodies. These three new human BRCA1 mutant cell lines thus seem to be representative breast cancer models that could aid in further unraveling of the function of BRCA1. (Cancer Res 2006; 66(1): 41-5)
Dual-Color Imaging of Nuclear-Cytoplasmic Dynamics, Viability, and Proliferation of Cancer Cells in the Portal Vein Area
Authors: Tsuji Kazuhiko , Yamauchi Kensuke , Yang Meng , Jiang Ping , Bouvet Michael , Endo Hitoshi , Kanai Yoshikatsu , Yamashita Koji , Moossa Abdool R. , Hoffman Robert M. 
Published: January 2006

Abstract
We used dual-color in vivo cellular imaging to visualize trafficking, nuclear-cytoplasmic dynamics, and the viability of cancer cells after their injection into the portal vein of mice. For these studies, we used dual-color fluorescent cancer cells that express green fluorescent protein (GFP) linked to histone H2B in the nucleus and retroviral red fluorescent protein (RFP) in the cytoplasm. Human HCT-116-GFP-RFP colon cancer and mouse mammary tumor (MMT) cells were HCT-116-GFP-RFP in the portal vein of nude mice. The cells were observed intravitally in the liver at the single-cell level using the Olympus OV100 whole-mouse imaging system. Most HCT-116-GFP-RFP cells remained in sinusoids near peripheral portal veins. Only a small fraction of the cancer cells invaded the lobular area. Extensive clasmocytosis (destruction of the cytoplasm) of the HCT-116-GFP-RFP cells occurred within 6 hours. The number of apoptotic cells rapidly increased within the portal vein within 12 hours of injection. Apoptosis was readily visualized in the dual-color cells by their altered nuclear morphology. The data suggest rapid death of HCT-116-GFP-RFP cells in the portal vein. In contrast, dual-color MMT-GFP-RFP cells injected into the portal vein mostly survived in the liver of nude mice 24 hours after injection. Many surviving MMT-GFP-RFP cells showed invasive figures with cytoplasmic protrusions. The cells grew aggressively and formed colonies in the liver. However, when the host mice were pretreated with cyclophosphamide, the HCT-116-GFP-RFP cells also survived and formed colonies in the liver after portal vein injection. These results suggest that a cyclophosphamide-sensitive host cellular system attacked the HCT-116-GFP-RFP cells but could not effectively kill the MMT-GFP-RFP cells. (Cancer Res 2006; 66(1): 303-6)
IFN-β Is a Highly Potent Inhibitor of Gastroenteropancreatic Neuroendocrine Tumor Cell GrowthIn vitro
Authors: Vitale Giovanni , de Herder Wouter W. , van Koetsveld Peter M. , Waaijers Marlijn , Schoordijk Wenda , Croze Ed , Colao Annamaria , Lamberts Steven W.J. , Hofland Leo J. 
Published: January 2006

AbstractIFN-α controls hormone secretion and symptoms in human gastroenteropancreatic neuroendocrine tumors (GEP-NET) but it rarely induces a measurable tumor size reduction. The effect of other type I IFNs, e.g., IFN-β, has not been evaluated. We compared the antitumor effects of IFN-α and IFN-β in BON cells, a functioning human GEP-NET cell line. As determined by quantitative reverse transcription-PCR analysis and immunocytochemistry, BON cells expressed the active type I IFN receptor mRNA and protein (IFNAR-1 and IFNAR-2c subunits). After 3 and 6 days of treatment, IFN-β significantly inhibited BON cell growth in a time- and dose-dependent manner. IC50 and maximal inhibitory effect on day 6 were 8 IU/mL and 98%, respectively. In contrast, the effect of IFN-α resulted significantly in a less potent effect (IC50: 44 IU/mL, maximal inhibition: 26%). IFN-α induced only cell cycle arrest, with an accumulation of the cells in S phase. IFN-β, apart from a more potent delay in S-G2-M phase transit of the cell cycle, also induced a strong stimulation of apoptosis, evaluated by flow cytometry (Annexin V and 7-AAD) and measurement of the DNA fragmentation. Besides, only IFN-β severely suppressed chromogranin A levels in the medium from BON cells after 6 days of treatment. In conclusion, IFN-β is much more potent, compared with IFN-α, in its inhibitory effect on GEP-NET cell proliferation in vitro through the induction of apoptosis and cell cycle arrest. Further studies are required to establish whether IFN-β has comparable potent tumor growth inhibitory effects in vivo. (Cancer Res 2006; 66(1): 554-62)
"Ten Times More Difficult to Treat": Female Bodies in Medical Texts from Early Imperial China
Authors: Wilms Sabine 
Published: January 2006

AbstractThis paper examines the interpretation of female bodies by male medical authors in post-Han China, investigating medical theories and practices as reflected in the applied medical literature of "prescriptions for women." Between the Han and Song periods, this paper argues, the negative association of the female body with the vague category of pathologies "below the girdle," referring most notably to conditions of vaginal discharge, was replaced with a more positive focus on menstruation, which symbolized regular and predictable cycles of generativity and free flow. As male physicians came to recognize the female body as gendered and accepted the need for a specialized treatment of women, menstruation became the window through which they gained access to the hidden processes inside the female body. By "balancing/regulating the menses," they learned to treat and prevent such dreaded chronic conditions as infertility, susceptibility to cold, or general emaciation and weakness, all which were seen as related to the female reproductive processes. Thus, the practice of menstrual regulation ultimately served to ensure female fertility and the continuation of the family line.
Medicine for Women in Early China: A Preliminary Survey
Authors: Yates Robin 
Published: January 2006

AbstractThis study reviews aspects of the history of medicine for women from approximately the third century BCE to the tenth century CE. It focuses on therapies during the months of pregnancy and childbirth as recorded in newly discovered texts, on the developing pharmacopeia, and on ritual procedures. It argues that acupuncture was used only rarely on pregnant women and that many cultural and religious beliefs and practices, including those drawn from the Buddhist, Daoist, and popular traditions, influenced procedures undertaken in preparation for and during the birth process.
Nonlinear Atmospheric Adjustment to Thermal Forcing
Authors: Fanelli Paul F. , Bannon Peter R. 
Published: January 2006

Abstract
A nonlinear, numerical model of a compressible atmosphere is used to simulate the hydrostatic and geostrophic adjustment to a localized prescribed heating applied over five minutes with a size characteristic of an isolated, deep, cumulus cloud. This thermal forcing generates both buoyancy waves and a horizontally propagating Lamb wave packet as well as a steady state rich in potential vorticity. The adjustments in three model atmospheres (an isothermal, a constant lapse rate, and one with a stratosphere) are studied.
The Lamb wave packet and the two lowest-order buoyancy waves are relatively unaffected by nonlinearities but the higher-order modes and the steady state are. The heating generates a vertically stacked dipole of potential vorticity with a cyclonic perturbation below an anticyclonic perturbation. In contrast to the linear results, the nonlinear dipole is severely distorted by vertical and horizontal advections. In addition, the Lamb wave packet contains some weak positive perturbation potential vorticity.
The energetics is examined using traditional and Eulerian available energetics. Traditional energetics consists of kinetic, internal, and potential energies. It is shown that the Lamb wave packet contains more total traditional energy than that input to the atmosphere by the heating. The traditional energy in the packet resides primarily in the form of internal energy and only secondarily in the form of potential energy. The passage of the Lamb wave packet produces an atmosphere that, overall, is cooler, less dense, and with less total traditional energy than the initial atmosphere. Eulerian available energetics consists of kinetic, available potential, and available elastic energies. The heating generates both available elastic and potential energy that is then converted into kinetic energy. Most of the available elastic energy projects onto the Lamb packet, while almost all of the available potential energy is associated with the buoyancy waves and the steady state.
The effects of varying the spatial and temporal scale of the heating, while keeping the net heating the same, are examined. As the duration of the heating decreases, the amount of energy projected onto the waves increases. Increasing the size of the heating decreases the amount of energy projected onto the waves.
The adjustment is kinetically more vigorous in the nonisothermal atmospheres because of the reduction in the base-state static stability. The presence of a stratosphere produces large anomalies at and above the tropopause that are linked to the vertical motions of the buoyancy wave field.
An Equation for Moist Entropy in a Precipitating and Icy Atmosphere
Authors: Zeng Xiping , Tao Wei-Kuo , Simpson Joanne 
Published: January 2006

AbstractThis paper addresses an equation for moist entropy in the framework of cloud-resolving models. After rewriting the energy equation with moist entropy in the place of temperature, an equation for moist entropy is obtained. The equation expresses the internal and external sources of moist entropy explicitly, providing a basis for the use of moist entropy as a prognostic variable in long-term cloud-resolving modeling. In addition, a precise formula for the surface flux of moist entropy from the underlying surface into the air above is derived.The equation for moist entropy is used to express the Neelin–Held model for the diagnosis of large-scale vertical velocity. After applying the model to a tropical oceanic atmosphere with mean annual soundings, the paper shows the sensitivity of large-scale vertical circulations to the radiative cooling rate and the surface flux of moist entropy, which demonstrates the necessity for a precise equation for moist entropy in the analysis and modeling of large-scale tropical circulations.
The 29 June 2000 Supercell Observed during STEPS. Part I: Kinematics and Microphysics
Authors: Tessendorf Sarah A. , Miller L. Jay , Wiens Kyle C. , Rutledge Steven A. 
Published: January 2006

Abstract
This is a two-part study that addresses the kinematic, microphysical, and electrical aspects of a severe storm that occurred in western Kansas on 29 June 2000 observed during the Severe Thunderstorm Electrification and Precipitation Study (STEPS) field campaign. In this first part, polarimetric and Doppler radar data are used along with a simple particle growth model to examine the evolution of the kinematic and microphysical properties of the storm from its earliest developing phase through its mature and dissipating phases. During its severe stage, the storm exhibited frequent positive cloud-to-ground lightning strikes, very large (∼5 cm) hail, and a tornado.
Doppler-derived winds, radar reflectivity, and hydrometeor classifications from the polarimetric data over a nearly 4-h period are presented. It is shown that updraft velocity and vertical vorticity had to reach magnitudes of at least 10 m s−1 and 10−2 s−1 and occupy major portions of the storm before it could produce most of the observed severe storm characteristics. Furthermore, the establishment of cyclonic horizontal flow around the right flank of the updraft core was essential for hail production. Most of the largest hail grew from near millimeter-sized particles that originated in the mid- to upper-level stagnation region that resulted from obstacle-like flow of environmental air around the divergent outflow from the upper part of the updraft. These recycling embryonic particles descended around the right flank of the updraft core and reentered the updraft, intermingling with other smaller particles that had grown from cloud base along the main low-level updraft stream.
Large-Scale Waves in the Mesosphere and Lower Thermosphere Observed by SABER
Authors: Garcia Rolando R. , Lieberman Ruth , Russell James M. , Mlynczak Martin G. 
Published: January 2006

Abstract
Observations made by the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on board NASA’s Thermosphere–Ionosphere–Mesosphere Energetics and Dynamics (TIMED) satellite have been processed using Salby’s fast Fourier synoptic mapping (FFSM) algorithm. The mapped data provide a first synoptic look at the mean structure and traveling waves of the mesosphere and lower thermosphere (MLT) since the launch of the TIMED satellite in December 2001. The results show the presence of various wave modes in the MLT, which reach largest amplitude above the mesopause and include Kelvin and Rossby–gravity waves, eastward-propagating diurnal oscillations (“non-sun-synchronous tides”), and a set of quasi-normal modes associated with the so-called 2-day wave. The latter exhibits marked seasonal variability, attaining large amplitudes during the solstices and all but disappearing at the equinoxes. SABER data also show a strong quasi-stationary Rossby wave signal throughout the middle atmosphere of the winter hemisphere; the signal extends into the Tropics and even into the summer hemisphere in the MLT, suggesting ducting by westerly background zonal winds. At certain times of the year, the 5-day Rossby normal mode and the 4-day wave associated with instability of the polar night jet are also prominent in SABER data.
An Energy-Balance Analysis of Deep Convective Self-Aggregation above Uniform SST
Authors: Bretherton Christopher S. , Blossey Peter N. , Khairoutdinov Marat 
Published: January 2006

Abstract
The spatial organization of deep moist convection in radiative–convective equilibrium over a constant sea surface temperature is studied. A 100-day simulation is performed with a three-dimensional cloud-resolving model over a (576 km)2 domain with no ambient rotation and no mean wind. The convection self-aggregates within 10 days into quasi-stationary mesoscale patches of dry, subsiding and moist, rainy air columns. The patches ultimately merge into a single intensely convecting moist patch surrounded by a broad region of very dry subsiding air.
The self-aggregation is analyzed as an instability of a horizontally homogeneous convecting atmosphere driven by convection–water vapor–radiation feedbacks that systematically dry the drier air columns and moisten the moister air columns. Column-integrated heat, water, and moist static energy budgets over (72 km)2 horizontal blocks show that this instability is primarily initiated by the reduced radiative cooling of air columns in which there is extensive anvil cirrus, augmented by enhanced surface latent and sensible heat fluxes under convectively active regions due to storm-induced gustiness. Mesoscale circulations intensify the later stages of self-aggregation by fluxing moist static energy from the dry to the moist regions. A simple mathematical model of the initial phase of self-aggregation is proposed based on the simulations.
In accordance with this model, the self-aggregation can be suppressed by horizontally homogenizing the radiative cooling or surface fluxes. Lower-tropospheric wind shear leads to slightly slower and less pronounced self-aggregation into bands aligned along the shear vector. Self-aggregation is sensitive to the ice microphysical parameterization, which affects the location and extent of cirrus clouds and their radiative forcing. Self-aggregation is also sensitive to ambient Coriolis parameter f, and can induce spontaneous tropical cyclogenesis for large f. Inclusion of an interactive mixed-layer ocean slows but does not prevent self-aggregation.
Constraints on Wave Drag Parameterization Schemes for Simulating the Quasi-Biennial Oscillation. Part I: Gravity Wave Forcing
Authors: Campbell Lucy J. , Shepherd Theodore G. 
Published: January 2006

Abstract
Parameterization schemes for the drag due to atmospheric gravity waves are discussed and compared in the context of a simple one-dimensional model of the quasi-biennial oscillation (QBO). A number of fundamental issues are examined in detail, with the goal of providing a better understanding of the mechanism by which gravity wave drag can produce an equatorial zonal wind oscillation. The gravity wave–driven QBOs are compared with those obtained from a parameterization of equatorial planetary waves. In all gravity wave cases, it is seen that the inclusion of vertical diffusion is crucial for the descent of the shear zones and the development of the QBO. An important difference between the schemes for the two types of waves is that in the case of equatorial planetary waves, vertical diffusion is needed only at the lowest levels, while for the gravity wave drag schemes it must be included at all levels. The question of whether there is downward propagation of influence in the simulated QBOs is addressed. In the gravity wave drag schemes, the evolution of the wind at a given level depends on the wind above, as well as on the wind below. This is in contrast to the parameterization for the equatorial planetary waves in which there is downward propagation of phase only. The stability of a zero-wind initial state is examined, and it is determined that a small perturbation to such a state will amplify with time to the extent that a zonal wind oscillation is permitted.
Geographical Dependence of Upper-Level Blocking Formation Associated with Intraseasonal Amplification of the Siberian High
Authors: Takaya Koutarou , Nakamura Hisashi 
Published: January 2006

Abstract
Intraseasonal amplification events of the surface Siberian high in winter are generally associated with blocking ridge formation in the upper troposphere. Composite analysis applied to the 20 strongest intraseasonal events of upper-level anticyclonic anomalies at every grid point over Siberia reveals that the blocking formation differs fundamentally between the east and west of the climatological upper-level trough over the Far East. To the west, what can be called “wave-train (Atlantic-origin)” type is common, where a blocking ridge develops from anomalies as a component of a quasi-stationary Rossby wave train propagating across the Eurasian continent under modest feedback forcing from transient eddies. To the east of the trough, what can be called “Pacific-origin” type dominates, where a blocking ridge forms in association with westward development of anticyclonic anomalies from the North Pacific under stronger feedback forcing from the Pacific storm track. Regardless of a particular type of blocking formation in the upper troposphere, a cold air outbreak tends to occur once anomalously cold air reaches the northeastern slope of the Tibetan Plateau.