bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is Adenocarcinoma of the Gastric Cardia a Distinct Entity Independent of Subcardial Carcinoma?
Authors: Ichikura Takashi , Ogawa Toshiya , Kawabata Toshinobu , Chochi Kentaro , Sugasawa Hidekazu , Mochizuki Hidetaka 
Published: February 2003

AbstractCardia carcinoma has been defined diversely. The purpose of this study was to determine whether cardia carcinoma should be categorized as a distinct entity independent of subcardial carcinoma. We retrospectively analyzed 65 patients undergoing resection for adenocarcinoma involving the esophagogastric junction (EGJ) with the tumor center within 5 cm of the EGJ. Adenocarcinomas of the EGJ were classified into Type I, Type II, and Type III according to Siewert’s criteria. There was only one Type I adenocarcinoma, and it was associated with Barrett’s esophagus. No tumors had their center between 1 cm and 2 cm proximal to the EGJ. Clinicopathologic features and prognosis were compared among patients with Type II adenocarcinomas (n = 31), patients with Type III adenocarcinomas (n = 33), and patients with adenocarcinomas in the upper third of the stomach not invading the EGJ (n = 153). Siewert’s Type II adenocarcinoma was associated with a higher male/female ratio and with higher incidences of well‐demarcated appearance and differentiated histology than carcinoma of the upper third of the stomach without esophageal invasion. Lymph nodes along the greater curvature and parapyloric nodes were rarely involved in Type II tumors. Within the pT2 category, patients with Siewert’s Type II tumors showed a higher incidence of lymph node metastasis and a significantly lower survival rate than did patients with tumors of the upper third of the stomach without esophageal invasion. In conclusion, cardia carcinoma, appropriately defined as adenocarcinoma with its epicenter between 1 cm proximal and 2 cm distal to the EGJ, should be categorized as a distinct entity.
Chloromethane:tetrahydrofolate methyl transfer by two proteins from Methylobacterium chloromethanicum strain CM4
Authors: Studer Alex , Stupperich Erhard , Vuilleumier Stéphane , Leisinger Thomas 
Published: February 2003

The cmuA and cmuB genes are required for growth of Methylobacterium chloromethanicum strain CM4 with chloromethane as the sole carbon source. While CmuB was previously shown to possess methylcobalamin:tetrahydrofolate methyltransferase activity, sequence analysis indicated that CmuA represented a novel and so far unique two‐domain methyltransferase/corrinoid‐binding protein involved in methyl transfer from chloromethane to a corrin moiety. CmuA was purified from wild‐type M. chloromethanicum strain CM4 and characterized as a monomeric, cobalt‐containing and zinc‐containing enzyme of molecular mass 67 kDa with a bound vitamin B12 cofactor. In combination, CmuA and CmuB proteins catalyze the in vitro transfer of the methyl group of chloromethane to tetrahydrofolate, thus affording a direct link between chloromethane dehalogenation and core C1 metabolism of Methylobacterium. Chloromethane dehalogenase activity in vitro is limited by CmuB, as formation of methyltetrahydrofolate from chloromethane displays apparent Michaelis–Menten kinetics with respect to methylated CmuA, with an apparent Km of 0.27 µm and a Vmax of 0.45 U·mg−1. This contrasts with sequence‐related systems for methyl transfer from methanogens, which involve methyltransferase and corrinoid protein components in well‐defined stoichiometric ratios.
Age‐dependent decrease in adenosine A1 receptor binding sites in the rat brain
Authors: Cunha Rodrigo A. , Constantino M. Dolores , Fonseca Ema , Ribeiro J. A. 
Published: February 2003

Unsaturated free fatty acids and adenosine operate two neuromodulatory systems with opposite effects on neuronal function. Here, we tested if fatty acids controlled inhibitory adenosine A1 receptors. Arachidonate (AA, 10 µm) decreased the Bmax of an A1 receptor agonist, (R)‐[3H]phenylisopropyladenosine (PIA; from 812 to 267 fmol·mg−1 protein), and antagonist, [3H]1,3‐dipropyl‐8‐cyclopentylxanthine (DPCPX; from 994 to 311 fmol·mg−1 protein) and decreased the Kd of [3H]PIA (from 1.20 to 0.57 nm) binding to brain membranes of young adult rats (2 months old), these effects being mimicked by other cis but not trans unsaturated or saturated fatty acids. AA (10 µm) increased the potency of the A1 receptor agonist, 2‐chloroadenosine to inhibit hippocampal synaptic transmission in young adult rats (EC50 decreased from 337 to 237 nm), which may constitute a safety feedback mechanism to control AA‐induced neurotoxicity. Upon aging, there were increased free fatty acid levels and a concomitant decreased density of A1 receptors. This was more marked in hippocampal nerve terminals of aged rats (24 months old) and may be the determinant factor contributing to the lower potency of 2‐choloroadenosine in aged rats (EC50 = 955 nm), in spite of the decreased Kd of PIA binding upon aging. The effects of AA on A1 receptor binding were attenuated upon aging, AA being devoid of effects in aged rats. Accordingly, AA (10 µm) failed to modify the potency of 2‐choloroadenosine in aged rats (EC50 = 997 nm). However, albumin, which quenches free fatty acids, increased A1 receptor density by 65% and 2‐chloroadenosine potency (EC50 = 703 nm) in aged rats, suggesting that the increased fatty acids levels in aged rats may contribute to the decreased potency of A1 receptor agonists in aged rats. Also, the observed saturation of the control by AA of A1 receptors may contribute to the decreased adaptability of neuromodulation to different firing conditions in aged rats.
The uniform phase space representation of product state distributions of elementary chemical reactions
Authors: Faist Michael B. 
Published: February 2003

The uniform phase space (UPS) representation of translational or internal degrees of freedom of the products of a chemical reaction is presented. Procedures are developed to deal with cases in which the final state distribution is discrete or approximately continuous; extensions cover multidimensional distributions. Explicit realistic models are used to demonstrate these situations.
In the UPS representation, the statistical or phase space distribution over product states is constant, yielding equal volumes of phase space for equal intervals along the coordinate in the UPS representation. As a consequence, an actual distribution over product states, cast into the UPS representation, becomes a direct measure of its deviance from a statistical distribution. The information content (in the information theoretic sense) is invariant under transformation to this representation, and its value can be readily approximated by a simple histogrammic procedure. Calculations for realistic model problems illustrate the superiority of the UPS representation of the energy disposal in elementary chemical reactions.
The effect of vibrational excitation on the reaction of O(3P) with H2 and the distribution of vibrational energy in the product OH
Authors: Light Glenn C. 
Published: February 2003

The overall rate constant and the product branching rate constants have been measured for the first time for the reaction where k2=k2a+k2b. The measurements were made in a flow tube apparatus at T=302±2 °K at a total pressure of 3 Torr. O(3P) was produced by the titration of active nitrogen with NO. H2(v=1) was produced by a heated tungsten filament and its concentration was determined from vuv absorption measurements in the Lyman band system of H2. Absolute concentrations of OH(v=0) and OH(v=1) were deduced from laser induced fluorescence in OH in a calibrated fluorescence system. The rates and uncertainties are k2= (1.0+0.9−0.6) ×10−14 cc/molecule-sec, k2a= (1.0+0.4−0.6) ×10−14 cc/molecule-sec, k2b?4.7×10−15 cc/molecule-sec.
The reported value for k2 represents an increase owing to vibrational excitation in hydrogen by a factor of ?2.6×103 over the fully ground state reaction rate constant. Measurements of the fully ground state reaction rate constant and recent theoretical treatments of the O+H2 reaction are discussed in relation to these results.
The gas phase reactions of CN and NO
Authors: Lam L. , Dugan C. H. , Sadowski C. M. 
Published: February 2003

Absolute rate constants have been measured for the reactions between CN (v) and NO. Flash photolysis of cyanogen was used to generate CN (v), while laser induced fluorescence was used to monitor this radical. The depletion of CN (v) was considered in terms of the following scheme:
The following values were obtained for the rate constants: CN(v=0), k1=1.2±0.6×10−13 cm3 molecule−1⋅s−1; k3=7.7±1.4×10−31 cm6 molecule−2⋅s−1; CN(v=1), (k1+k2) =2.6±0.5×10−13 cm3 molecule−1⋅s−1; k3=3.0±1.1×10−31 cm6 molecule−2⋅S−1.
Simple molecular orbital treatment of diatomic force constants
Authors: Zerner Michael C. , Parr Robert G. 
Published: February 2003

From the molecular orbital theory for diatomic molecules, the virial theorem, and the Heisenberg equation of motion, expressions are derived for off-diagonal matrix elements of the one-electron Hamiltonian for a limited basis set of atomic orbitals that display exact zero differential diatomic overlap. The resulting expressions are combined to yield analytic equations for the force constants ke and higher derivatives of the diatomic potential energy surface. These expressions depend only on the density matrix of a single calculation near enough to the equilibrium geometry. Under the approximation that all nonvanishing Coulomb interactions are given by classical electrostatics, a simple formula for the force constant is obtained which has mean square error of 3% for a number of first- and second-row diatomic molecules. If reasonable approximations are made for the density matrix and the equilibrium separation Re is estimated by a ’’tangent sphere’’ model, the following simple equations are obtained: keR3e=η/2(1+nAζB+nBζA) (two atoms with an s,p basis), keR3e=η/2[1+nbζa +1/2ζb(na+ζa)] (hydrides), keR3e=η/2[1+1/2(nAζB+nbζA)] (hydrogen molecule).
Here, η is the number of bonds, n the principal quantum number, and ζ the orbital exponent of the valence electrons as, for example, given by Slater’s rules. These equations yield predictions generally within ±10% of the experimental values.
Unr Is Required In Vivo for Efficient Initiation of Translation from the Internal Ribosome Entry Sites of both Rhinovirus and Poliovirus
Authors: Boussadia Oréda , Niepmann Michael , Créancier Laurent , Prats Anne-Catherine , Dautry François , Jacquemin-Sablon Hélène 
Published: February 2003

ABSTRACT

Translation of picornavirus RNAs is mediated by internal ribosomal entry site (IRES) elements and requires both standard eukaryotic translation initiation factors (eIFs) and IRES-specific cellular
trans
-acting factors (ITAFs). Unr, a cytoplasmic RNA-binding protein that contains five cold-shock domains and is encoded by the gene upstream of N-
ras
, stimulates translation directed by the human rhinovirus (HRV) IRES in vitro. To examine the role of Unr in translation of picornavirus RNAs in vivo, we derived murine embryonic stem (ES) cells in which either one (−/+) or both (−/−) copies of the
unr
gene were disrupted by homologous recombination. The activity of picornaviral IRES elements was analyzed in
unr
+/+
,
unr
+/−
, and
unr
−/−
cell lines. Translation directed by the HRV IRES was severely impaired in
unr
−/−
cells, as was that directed by the poliovirus IRES, revealing a requirement for Unr not previously observed in vitro. Transient expression of Unr in
unr
−/−
cells efficiently restored the HRV and poliovirus IRES activities. In contrast, the IRES elements of encephalomyocarditis virus and foot-and-mouth-disease virus are not Unr dependent. Thus, Unr is a specific regulator of HRV and poliovirus translation in vivo and may represent a cell-specific determinant limiting replication of these viruses.
The STAT2 Activation Process Is a Crucial Target of Sendai Virus C Protein for the Blockade of Alpha Interferon Signaling
Authors: Gotoh Bin , Takeuchi Kenji , Komatsu Takayuki , Yokoo Junko 
Published: February 2003

ABSTRACTSendai virus (SeV) C protein functions as an interferon (IFN) antagonist and renders cells unresponsive to both alpha/beta IFN (IFN-α/β) and IFN-γ. We have recently found the physical association of the C protein with signal transducer and activator of transcription 1 (STAT1) in infected cells. However, involvement of the C-STAT1 interaction in the blockade of IFN signaling has remained unclear. We generated here a series of C mutant proteins that retained or lost the STAT1-binding capacity and examined their effects on IFN-α signaling. All of the C mutant proteins with no STAT1-binding capacity lost the ability to inhibit the IFN-α response. In contrast, the C mutant proteins retaining the STAT1-binding capacity suppressed IFN-α-stimulated tyrosine phosphorylation of both STAT2 and STAT1 to various degrees. Remarkably, their anti-IFN-α capacities correlated well with the inhibitory effect on phosphorylation of STAT2 rather than STAT1. In infected cells, the levels of tyrosine-phosphorylated (pY) STAT2 were below the detection level irrespective of duration of IFN-α stimulation, whereas the levels of pY-STAT1 strikingly increased after long-term IFN-α stimulation. These results suggest that the STAT2 activation process is a crucial target for the blockade of IFN-α signaling. An in vitro binding assay with extracts from (STAT1-deficient) U3A and (STAT1-expressing) U3A-ST1 cells suggested the requirement of STAT1 for the C-STAT2 interaction. Furthermore, expression of STAT1 enhanced the inhibitory effect of the C protein on STAT2 activation in U3A cells. The C protein thus appears to participate in the inhibitory process for STAT2 activation through the STAT1 interaction.
Autographa californica
Nucleopolyhedrovirus
orf69
Encodes an RNA Cap (Nucleoside-2′-
O
)-Methyltransferase
Authors: Wu Xiaofeng , Guarino Linda A. 
Published: February 2003

ABSTRACT

The AcNPV
orf69
gene encodes a protein that contains an
S
-adenosylmethionine (AdoMet)-dependent methyltransferase signature motif. More significantly, ORF69 shows high conservation at residues diagnostic for (nucleoside 2′-
O
)-methyltransferase activity. To analyze the function of this protein, which was renamed MTase1, it was overexpressed in
Escherichia coli
and purified to homogeneity. Photo cross-linking experiments showed that MTase1 bound AdoMet, and functional assays demonstrated cap 0-dependent methyltransferase activity. In vivo expression assays in insect cells showed that MTase1 was synthesized during the late phase of infection and that its expression was dependent on viral DNA replication. Primer extension analysis identified a late promoter motif, ATAAG, at the transcription start site. A mutant virus was constructed by inserting the
lacZ
gene into the coding region of
mtase1
. Immunoblot analysis confirmed that MTase1 was not synthesized in these cells, and single-step growth curves revealed that the rate of virus replication in tissue culture was not affected by the absence of MTase1.
Interactions between the Transmembrane Segments of the Alphavirus E1 and E2 Proteins Play a Role in Virus Budding and Fusion
Authors: Sjöberg Mathilda , Garoff Henrik 
Published: February 2003

ABSTRACT

The alphavirus envelope is built by heterodimers of the membrane proteins E1 and E2. The complex is formed as a p62E1 precursor in the endoplasmic reticulum. During transit to the plasma membrane (PM), it is cleaved into mature E1-E2 heterodimers, which are oligomerized into trimeric complexes, so-called spikes that bind both to each other and, at the PM, also to nucleocapsid (NC) structures under the membrane. These interactions drive the budding of new virus particles from the cell surface. The virus enters new cells by a low-pH-induced membrane fusion event where both inter- and intraheterodimer interactions are reorganized to establish a fusion-active membrane protein complex. There are no intact heterodimers left after fusion activation; instead, an E1 homotrimer remains in the cellular (or viral) membrane. We analyzed whether these transitions depend on interactions in the transmembrane (TM) region of the heterodimer. We observed a pattern of conserved glycines in the TM region of E1 and made two mutants where either the glycines only (SFV/E1
4L
) or the whole segment around the glycines (SFV/E1
11L
) was replaced by leucines. We found that both mutations decreased the stability of the heterodimer and increased the formation of the E1 homotrimer at a suboptimal fusion pH, while the fusion activity was decreased. This suggested that TM interactions play a role in virus assembly and entry and that anomalous or uncoordinated protein reorganizations take place in the mutants. In addition, the SFV/E1
11L
mutant was completely deficient in budding, which may reflect an inability to form multivalent NC interactions at the PM.
The Human Cytomegalovirus UL82 Gene Product (pp71) Accelerates Progression through the G
1
Phase of the Cell Cycle
Authors: Kalejta Robert F. , Shenk Thomas 
Published: February 2003

ABSTRACT

As viruses are reliant upon their host cell to serve as proper environments for their replication, many have evolved mechanisms to alter intracellular conditions to suit their own needs. For example, human cytomegalovirus induces quiescent cells to enter the cell cycle and then arrests them in late G
1
, before they enter the S phase, a cell cycle compartment that is presumably favorable for viral replication. Here we show that the protein product of the human cytomegalovirus UL82 gene, pp71, can accelerate the movement of cells through the G
1
phase of the cell cycle. This activity would help infected cells reach the late G
1
arrest point sooner and thus may stimulate the infectious cycle. pp71 also induces DNA synthesis in quiescent cells, but a pp71 mutant protein that is unable to induce quiescent cells to enter the cell cycle still retains the ability to accelerate the G
1
phase. Thus, the mechanism through which pp71 accelerates G
1
cell cycle progression appears to be distinct from the one that it employs to induce quiescent cells to exit G
0
and subsequently enter the S phase.
A Virus-Virus Interaction Circumvents the Virus Receptor Requirement for Infection by Pathogenic Retroviruses
Authors: Wensel David L. , Li Weihua , Cunningham James M. 
Published: February 2003

ABSTRACT

During ongoing C-type retrovirus infection, the probability of leukemia caused by insertional gene activation is markedly increased by the emergence of recombinant retroviruses that repeatedly infect host cells. The murine mink cell focus-inducing (MCF) viruses with this property have acquired characteristic changes in the N-terminal domain of their envelope glycoprotein that specify binding to a different receptor than the parental ecotropic virus. In this report, we show that MCF virus infection occurs through binding to this receptor (termed Syg1) and, remarkably, by a second mechanism that does not utilize the Syg1 receptor. By the latter route, the N-terminal domain of the ecotropic virus glycoprotein expressed on the cell surface in a complex with its receptor activates the fusion mechanism of the MCF virus in
trans
. The rate of MCF virus spread through a population of permissive human cells was increased by establishment of
trans
activation, indicating that Syg1 receptor-dependent and -independent pathways function in parallel. Also,
trans
activation shortened the interval between initial infection and onset of cell-cell fusion associated with repeated infection of the same cell. Our findings indicate that pathogenic retrovirus infection may be initiated by virus binding to cell receptors or to the virus envelope glycoprotein of other viruses expressed on the cell surface. Also, they support a broader principle: that cooperative virus-virus interactions, as well as virus-host interactions, shape the composition and properties of the retrovirus quasispecies.
Human Immunodeficiency Virus Type 1 Infection and Replication in Normal Human Oral Keratinocytes
Authors: Liu Xuan , Zha Junli , Chen Hongying , Nishitani Junko , Camargo Paulo , Cole Steve W. , Zack Jerome A. 
Published: February 2003

ABSTRACT
Recent epidemiologic studies show increasing human immunodeficiency virus type 1 (HIV-1) transmission through oral-genital contact. This paper examines the possibility that normal human oral keratinocytes (NHOKs) might be directly infected by HIV or might convey infectious HIV virions to adjacent leukocytes. PCR analysis of proviral DNA constructs showed that NHOKs can be infected by CXCR4-tropic (NL4-3 and ELI) and dualtropic (89.6) strains of HIV-1 to generate a weak but productive infection. CCR5-tropic strain Ba-L sustained minimal viral replication. Antibody inhibition studies showed that infection by CXCR4-tropic viral strains is mediated by the galactosylceramide receptor and the CXCR4 chemokine coreceptor. Coculture studies showed that infectious HIV-1 virions can also be conveyed from NHOKs to activated peripheral blood lymphocytes, suggesting a potential role of oral epithelial cells in the transmission of HIV infection.
Cellular Mobile Genetic Elements in the Regulatory Region of the Pneumotropic Mouse Polyomavirus Genome: Structure and Function in Viral Gene Expression and DNA Replication
Authors: Zhang Shouting , Magnusson Göran 
Published: February 2003

ABSTRACT

DNA from the murine pneumotropic virus was extracted from virus in lung tissue of infected mice, and the regulatory region of the genome was amplified by PCR. The regulatory region of individual plasmid cloned DNA molecules appeared to have heterogeneous enhancer segments, whereas the protein-coding part of the genome had a uniform length. Nucleotide sequence analysis revealed that the majority of the DNA molecules had a structure differing from the standard type. A 220-bp insertion at nucleotide position 142 with a concomitant deletion of nucleotides 143 to 148 was prominent. There were two variants of the 220-bp insertion, differing at two nucleotide positions at one of the termini. Other DNA molecules had complete or partial deletions of these structures and surrounding sequences in the viral enhancer. However, the end of the insertion at nucleotide 142 was frequently preserved. The viral early and late promoter activity of the variant regulatory regions was tested in a luciferase reporter assay by using transfected NIH 3T3 cells. In relation to the standard-type DNA, all variants, including a G272T mutant, had much stronger late promoters. In contrast, the early promoter activity was influenced in a positive or negative direction by individual mutations. Also, the activity of the viral origin of DNA replication was affected by the sequence variation of the regulatory region, although the effects were smaller than for the late promoter. Analysis by Southern blotting and quantification using dot blots showed that approximately 10
3
copies of material related to the 220-bp insert in murine pneumotropic virus DNA was present in mouse and human DNA but not in
Escherichia coli
DNA. Moreover, analysis by PCR indicated that there were multiple copies in the mouse genome of sequences that were identical or closely related to the 220-bp viral DNA segment. These data together with the nucleotide sequence analysis suggest that the 220-bp insertion is related to a transposable element of a novel type.