bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical and Histopathological Prognostic Factors in Chondrosarcomas
Authors: Daugaard Søren , Myhre-Jensen Olaf , Schiødt Torben , Jurik Anne G. , Keller Johnny , Mouridsen Henning T. , Lund Bjarne 
Published: July 2002

Purpose. In an attempt to identify clinical and histopathological factors of prognostic
importance in chondrosarcomas, 115 cases of malignant and borderline chondromatous tumours were reviewed.Patients/methods. Histopathological features tested for prognostic information as well
as reproducibility included cellularity, nuclear pleomorphism, multinucleated cells, mitotic activity and grade.
Eleven patients had a biopsy only, and a short survival (median 2.0 years); these were excluded from further analysis.
The remaining 104 patients who had received intended curative treatment had a median survival of 14.7 years.Results. In univariate analysis, tumour size, extra‐compartmental growth, surgical margin and sex
were significantly correlated to recurrence‐free survival (RFS); sex was marginally significant while age, site and pathological
parameters were not significant. Overall survival (OAS) was likewise found to be independent of pathological features as well as site,
size and surgical margin; but age, sex and extra‐compartmental growth were statistically significant. However, when the
same parameters were entered into a stepwise Cox (multivariate) analysis, only surgical margin, cellularity and pleomorphism
were significantly related to RFS; margin, grade, pleomorphism and age to OAS. Overall inter‐observer agreement
on grade was relatively low: 0.54, with a Kappa value of 0.32. It was not better for the other histological parameters, with
the exception of the mitotic count. However, acceptable values were achieved when the material was divided into
low‐grade (grade I and below) vs high‐grade (grade II and III) lesions: overall agreement 0.79, Kappa 0.56.Discussion. Although the grading of chondrosarcomas is in need of improvement, its replacement by
semiquantitative evaluation of individual histopathological parameters as performed in this study offers no advantage.
Among the clinical parameters, only the adequacy of the surgical treatment and the patient′s age appear to be important.
Fine‐Needle Aspiration Cytology of Epithelioid Leiomyoblastoma
Authors: Thompson Karen Sue , Jensen Joanne , Reyes Cesar V. 
Published: July 2002

Purpose. Epithelioid leiomyoblastomas comprise the majority of gastric sarcomas
and are uncommon in other parts of the gastrointestinal tract. Diagnosis of this lesion
by fine‐needle aspiration cytology has been occasionally described in the literature.
Two additional cases are herein reported.Subjects . A 66‐year old male with an omental mass and a 47‐year old male with a
perihepatic tumor.Results and Discussion. Cytologic materials in both cases showed predominantly
round or epithelioid cells, along with polygonal to spindle cells, occuring singly and in
clusters, with oval to spindle‐shaped nuclei.The nuclei were monotonous, usually banal,
and centrally‐located with only focal suggestion of pleomorphism and rare mitosis.
Eosinophilic cytoplasm was noted in most of the cells, some demonstrating vacuolation.
Electron microscopy supported a primitive smooth cell derivation of the neoplastic cells.Conclusions. The cytomorphology of the tumors of the two cases reported here is not
adequately known. More cases need to be collected and studied.
Ewing′s Sarcoma of the Head and Neck: A Retrospective Analysis of 24 Cases
Authors: Allam Ayman , El-Husseiny Gamal , Khafaga Yasser , Kandil Alaa , Gray Alan , Ezzat Adnan , Schultz Henrik 
Published: July 2002

Introduction and purpose. Primary Ewing′s sarcoma arising from the
bones of the head and neck region is extremely rare representing only 1– 4% of all Ewing′s
sarcoma cases. Previous reports suggest a better prognosis for that particular anatomic site.
The purpose of this study was to analyze the clinico‐epidemiologic characteristics of that rare clinical presentation, as
well as its patterns of failure and prognosis following treatment.Materials and methods. This study included a retrospective review of the medical records
of patients with the diagnosis of Ewing′s sarcoma of the head and neck region treated at King
Faisal Specialist Hospital and Research Center between 1975 and 1996.Results. Out of a total number of 24 cases analyzed, there were 17 males and
7 females with a ratio of 2.4:1. The median age at diagnosis was 16.5 years. A painful swelling was
the most common clinical presentation.The maxilla was the most common site of presentation
(9/24 cases). There were 3/24 cases who presented with metastatic disease at diagnosis.The
majority of patients (16/24 cases) had a tumor size >10 cm. Most patients were treated with systemic
chemotherapy plus localized irradiation following an initial biopsy.With a mean follow
up of 3.4 years, the 5‐year actual overall survival (OS) for the whole group was 53%, while
the 5‐year actuarial disease‐free survival (DFS) was 30%. These figures were higher than those
repor ted from our institution for young patients (≤ 14 years treated for Ewing′ s sarcoma in other
anatomic locations (30% v 15%). The response to chemotherapy was the only prognostic factor
that affected both the OS and DFS.Conclusion. The prognosis of Ewing′s sarcoma of the head and neck
region is slightly better than that of other anatomic sites.The response to systemic chemotherapy
is one of the most important prognostic factors affecting both DFS and OS of Ewing′s sarcoma of
the head and neck. Multimodality therapy consisting of an initial biopsy, aggressive combination
chemotherapy and localized radiotherapy is the treatment of choice for Ewing′s sarcoma of
the head and neck region and may result in long‐term survival.
Interleukin 1β-converting Enzyme Related Proteases/Caspases Are Involved in TRAIL-induced Apoptosis of Myeloma and Leukemia Cells
Authors: Mariani Sara M. , Matiba Bernd , Armandola Elena A. , Krammer Peter H. 
Published: July 2002

The Fas/APO-1/CD95 ligand (CD95L) and the recently cloned TRAIL ligand belong to the TNFfamily and share the ability to induce apoptosis in sensitive target cells. Little information is available on the degree of functional redundancy between these two ligands in terms of target selectivity and intracellular signalling pathway(s). To address these issues, we have expressed and characterized recombinant mouse TRAIL. Specific detection with newly developed rabbit anti-TRAIL antibodies showed that the functional TRAIL molecule released into the supernatant of recombinant baculovirus-infected Sf9 cells is very similar to that associated with the membrane fraction of Sf9 cells. CD95L resistant myeloma cells were found to be sensitive to TRAIL, displaying apoptotic features similar to those of the CD95L- and TRAIL-sensitive T leukemia cells Jurkat. To assess if IL-1β-converting enzyme (ICE) and/or ICE-related proteases (IRPs) (caspases) are involved in TRAIL-induced apoptosis of both cell types, peptide inhibition experiments were performed. The irreversible IRP/caspase-inhibitor AcYVAD-cmk and the reversible IRP/caspase-inhibitor Ac-DEVD-CHO blocked the morphological changes, disorganization of plasma membrane phospholipids, DNA fragmentation, and loss of cell viability associated with TRAIL-induced apoptosis. In addition, cells undergoing TRAIL-mediated apoptosis displayed cleavage of poly(ADP)-ribose polymerase (PARP) that was completely blocked by Ac-DEVD-CHO.
These results indicate that TRAIL seems to complement the activity of the CD95 system as it allows cells, otherwise resistant, to undergo apoptosis triggered by specific extracellular ligands. Conversely, however, induction of apoptosis in sensitive cells by TRAIL involves IRPs/caspases in a fashion similar to CD95L. Thus, differential sensitivity to CD95L and TRAIL seems to map to the proximal signaling events associated with receptor triggering.
Direct and Regulated Interaction of Integrin αEβ7 with E-Cadherin
Authors: Higgins Jonathan M.G. , Mandlebrot Didier A. , Shaw Sunil K. , Russell Gary J. , Murphy Elizabeth A. , Chen Yih-Tai , Nelson W. James , Parker Christina M. , Brenner Michael B. 
Published: July 2002

The cadherins are a family of homophilic adhesion molecules that play a vital role in the formation of cellular junctions and in tissue morphogenesis. Members of the integrin family are also involved in cell to cell adhesion, but bind heterophilically to immunoglobulin superfamily molecules such as intracellular adhesion molecule (ICAM)–1, vascular cell adhesion molecule (VCAM)–1, or mucosal addressin cell adhesion molecule (MadCAM)–1. Recently, an interaction between epithelial (E-) cadherin and the mucosal lymphocyte integrin, αEβ7, has been proposed. Here, we demonstrate that a human E-cadherin–Fc fusion protein binds directly to soluble recombinant αEβ7, and to αEβ7 solubilized from intraepithelial T lymphocytes. Furthermore, intraepithelial lymphocytes or transfected JY′ cells expressing the αEβ7 integrin adhere strongly to purified E-cadherin–Fc coated on plastic, and the adhesion can be inhibited by antibodies to αEβ7 or E-cadherin.
The binding of αEβ7 integrin to cadherins is selective since cell adhesion to P-cadherin–Fc through αEβ7 requires &gt;100-fold more fusion protein than to E-cadherin–Fc. Although the structure of the αE-chain is unique among integrins, the avidity of αEβ7 for E-cadherin can be regulated by divalent cations or phorbol myristate acetate. Cross-linking of the T cell receptor complex on intraepithelial lymphocytes increases the avidity of αEβ7 for E-cadherin, and may provide a mechanism for the adherence and activation of lymphocytes within the epithelium in the presence of specific foreign antigen. Thus, despite its dissimilarity to known integrin ligands, the specific molecular interaction demonstrated here indicates that E-cadherin is a direct counter receptor for the αEβ7 integrin.
Endothelial Cell “Memory” of Inflammatory Stimulation: Human Venular Endothelial Cells Store Interleukin 8 in Weibel-Palade Bodies
Authors: Wolff Barbara , Burns Alan R. , Middleton James , Rot Antal 
Published: July 2002

The expression and secretion of interleukin (IL)-8, the prototype member of the C-X-C subfamily of chemokines, can be induced by diverse inflammatory stimuli in many cells, including endothelial cells (EC). Upon de novo synthesis, IL-8 localizes intracellularly in the Golgi apparatus, from where it is secreted. In addition to this constitutive secretory pathway, we describe a depot storage and separate regulated secretory pathway of IL-8 in EC.
The prolonged stimulation of primary human EC with inflammatory mediators resulted in the accumulation of IL-8 in Weibel-Palade bodies, where it colocalized with von Willebrand factor. IL-8 was retained in these storage organelles for several days after the removal of the stimulus and could be released by EC secretagogues such as phorbol myristate acetate, the calcium ionophore A23187, and histamine. These findings suggest that storage of IL-8 in Weibel-Palade bodies may serve as the EC “memory” of a preceding inflammatory insult, which then enables the cells to secrete IL-8 immediately without de novo protein synthesis.
Packing measure of the sample paths of fractional Brownian motion
Authors: Xiao Yimin 
Published: July 2002

Let

X
(
t
)
(
t
∈

R

)

X(t) (t \in \mathbf {R})

be a fractional Brownian motion of index

α
\alpha

in

R

d

.

\mathbf {R}^d.

If

1
>
α
d

1 > \alpha d

, then there exists a positive finite constant

K
K

such that with probability 1,
\[

ϕ
−
p
(
X
(
[
0
,
t
]
)
)
=
K
t

for any

t
>
0

,

\phi -p(X([0,t])) = Kt\quad \text {for any $t > 0$},

\]
where

ϕ
(
s
)
=

s

1
α

/

(
log
⁡
log
⁡

1
s

)

1

2
α

\phi (s) = s^{\frac 1 { \alpha }}/ (\log \log \frac 1 s)^{\frac 1 {2 \alpha }}

and

ϕ
\phi

-

p
(
X
(
[
0
,
t
]
)
)

p (X([0,t]))

is the

ϕ
\phi

-packing measure of

X
(
[
0
,
t
]
)

X([0,t])

.
10-11 bp periodicities in complete genomes reflect protein structure and DNA folding.
Authors: Herzel H , Weiss O , Trifonov E N 
Published: July 2002

Abstract
MOTIVATION: Completely sequenced genomes allow for detection and analysis of the relatively weak periodicities of 10-11 basepairs (bp). Two sources contribute to such signals: correlations in the corresponding protein sequences due to the amphipatic character of alpha-helices and the folding of DNA (nucleosomal patterns, DNA supercoiling). Since the topological state of genomic DNA is of importance for its replication, recombination and transcription, there is an immediate interest to obtain information about the supercoiled state from sequence periodicities. RESULTS: We show that correlations within proteins affect mainly the oscillations at distances below 35 bp. The long-ranging correlations up to 100 bp reflect primarily DNA folding. For the yeast genome these oscillations are consistent in detail with the chromatin structure. For eubacteria and archaea the periods deviate significantly from the 10.55 bp value for free DNA. These deviations suggest that while a period of 11 bp in bacteria reflects negative supercoiling, the significantly different period of thermophilic archaea close to 10 bp corresponds to positive supercoiling of thermophilic archaeal genomes. AVAILABILITY: Protein sets and C programs for the calculation of correlation functions are available on request from the authors (see http://itb.biologie.hu-berlin.de).
Protein analyst--a distributed object environment for protein sequence and structure analysis.
Authors: Saqi M A , Wild D L , Hartshorn M J 
Published: July 2002

Abstract
SUMMARY: Protein Analyst is a flexible tool for the analysis of protein sequences with emphasis on the integration of sequence and structural information. AVAILABILITY: The software will be available from the Oxford Molecular Biolib web site (http://www. oxmol.co.uk/biolib) and will be free to the academic research community.
Immunocytochemical Localization of the Menkes Copper Transport Protein (ATP7A) to the Trans-Golgi Network
Authors: Dierick Herman A. , Adam Ayla N. , Escara-Wilke June F. , Glover Thomas W. 
Published: July 2002

AbstractWe have generated polyclonal antibodies against the amino-terminal third of the Menkes protein (ATP7A; MNK) by immunizing rabbits with a histidine-tagged MNK fusion construct containing metal-binding domains 1–4. The purified antibodies were used in Western analysis of cell lysates and in indirect immunofluorescence experiments on cultured cells. On Western blots, the antibodies recognized the ∼165 kDa MNK protein in CHO cells and human fibroblasts. No MNK signal could be detected in fibroblasts from a patient with Menkes disease or in Hep3B hepatocellular carcinoma cells, confirming the specificity of the antibodies. Immunocytochemical analysis of CHO cells and human fibroblasts showed a distinct perinuclear signal corresponding to the pattern of the Golgi complex. This staining pattern was similar to that of α-mannosidase II which is a known resident enzyme of the Golgi complex. Using brefeldin A, a fungal inhibitor of protein secretion, we further demonstrated that the MNK protein is localized to the trans-Golgi network. This data provides direct evidence for a subcellular localization of the MNK protein which is similar to the proposed vacuolar localization of Ccc2p, the yeast homolog of MNK and WND (ATP7B), the Wilson disease gene product. In light of the proposed role of MNK both in subcellular copper trafficking and in copper efflux, these data suggest a model for how these two processes are linked and represent an important step in the functional analysis of the MNK protein.
A comparison of position‐specific score matrices based on sequence and structure alignments
Authors: Panchenko Anna R. , Bryant Stephen H. 
Published: July 2002

AbstractSequence comparison methods based on position‐specific score matrices (PSSMs) have proven a useful tool for recognition of the divergent members of a protein family and for annotation of functional sites. Here we investigate one of the factors that affects overall performance of PSSMs in a PSI‐BLAST search, the algorithm used to construct the seed alignment upon which the PSSM is based. We compare PSSMs based on alignments constructed by global sequence similarity (ClustalW and ClustalW‐pairwise), local sequence similarity (BLAST), and local structure similarity (VAST). To assess performance with respect to identification of conserved functional or structural sites, we examine the accuracy of the three‐dimensional molecular models predicted by PSSM‐sequence alignments. Using the known structures of those sequences as the standard of truth, we find that model accuracy varies with the algorithm used for seed alignment construction in the pattern local‐structure (VAST) > local‐sequence (BLAST) > global‐sequence (ClustalW). Using structural similarity of query and database proteins as the standard of truth, we find that PSSM recognition sensitivity depends primarily on the diversity of the sequences included in the alignment, with an optimum around 30–50% average pairwise identity. We discuss these observations, and suggest a strategy for constructing seed alignments that optimize PSSM‐sequence alignment accuracy and recognition sensitivity.
Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein–protein cooperative interactions
Authors: Mou Tung‐Chung , Sreerama Narasimha , Terwilliger Thomas C. , Woody Robert W. , Gray Donald M. 
Published: July 2002

AbstractThe gene 5 protein (g5p) of the Ff virus contains five Tyr, individual mutants of which have now all been characterized by CD spectroscopy. The protein has a dominant tyrosyl 229‐nm La CD band that is shown to be approximately the sum of the five individual Tyr contributions. Tyr41 is particularly important in contributing to the high cooperativity with which the g5p binds to ssDNA, and Y41F and Y41H mutants are known to differ in dimer–dimer packing interactions in crystal structures. We compared the solution structures and binding properties of the Y41F and Y41H mutants using CD spectroscopy. Secondary structures of the mutants were similar by CD analyses and close to those derived from the crystal structures. However, there were significant differences in the binding properties of the two mutant proteins. The Y41H protein had an especially low binding affinity and perturbed the spectrum of poly[d(A)] in 2 mM Na+ much less than did Y41F and the wild‐type gene 5 proteins. Moreover, a change in the Tyr 229 nm band, assigned to the perturbation of Tyr34 at the dimer–dimer interface, was absent in titrations with the Y41H mutant under low salt conditions. In contrast, titrations with the Y41H mutant in 50 mM Na+ exhibited typical CD changes of both the nucleic acid and the Tyr 229‐nm band. Thus, protein–protein and g5p–ssDNA interactions appeared to be mutually influenced by ionic strength, indicative of correlated changes in the ssDNA binding and cooperativity loops of the protein or of indirect structural constraints.
Association of Medicaid Expansion With Postpartum Depression Treatment in Arkansas
Authors: Steenland Maria W. , Trivedi Amal N. 
Published: February 2023

ImportancePostpartum depression affects approximately 1 in every 8 postpartum individuals in the US. Antidepressant medication can effectively treat postpartum depression. However, gaps in postpartum insurance coverage after the end of Medicaid pregnancy coverage at 60 days postpartum may limit treatment uptake and decrease continuity of postpartum depression treatment.ObjectiveTo examine the association of Medicaid expansion in Arkansas with postpartum antidepressant prescription fills and antidepressant continuation and supply during the first 6 months postpartum.Design, Setting, and ParticipantsCohort study with a difference-in-differences analysis comparing persons with Medicaid and commercially financed childbirth using Arkansas’ All-Payer Claims Database (2013-2016). Analysis was completed between July 2021 and June 2022.ExposuresMedicaid-paid childbirth after January 1, 2014.Main Outcomes and MeasuresAntidepressant medication prescription fills and the number of days of antidepressant supply in the early (first 60 days after childbirth) and the late (61 days to 6 months after childbirth) postpartum periods.ResultsIn this cohort study with a difference-in-differences analysis of 60 990 childbirths (mean [SD] birthing parent’s age, 27 [5.3] years; 22% Black, 7% Hispanic, 67% White individuals), 72% of births were paid for by Medicaid and 28% were paid for by a commercial payer. Before expansion, 4.2% of people with a Medicaid-paid birth filled an antidepressant prescription in the later postpartum period. Medicaid expansion was associated with a 4.6 percentage point (95% CI, 2.9-6.3) increase in the likelihood, or a relative change of 110%, in this outcome. Before expansion, among people with postpartum depression in the early postpartum period with a Medicaid-paid birth, 32.7% filled an antidepressant prescription in the later postpartum period, and had an average of 23 days of antidepressant prescription supply during the later postpartum period. Among people with early postpartum depression, Medicaid expansion increased the continuity of antidepressant treatment by 20.5 percentage points (95% CI, 14.1-26.9) and the number of days with antidepressant supply in the later postpartum period by 14.1 days (95% CI, 7.2-20.9).Conclusions and RelevanceMedicaid expansion in Arkansas was associated with an increase in postpartum antidepressant prescription fills, and an increase in antidepressant treatment continuity and medication supply in the period after Medicaid pregnancy-related eligibility ended.