bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences
Authors: Deshayes Caroline , Perrodou Emmanuel , Euphrasie Daniel , Frapy Eric , Poch Olivier , Bifani Pablo , Lecompte Odile , Reyrat Jean-Marc 
Published: March 2008

AbstractBackgroundComputer-assisted analyses have shown that all bacterial genomes contain a small percentage of open reading frames with a frameshift or in-frame stop codon We report here a comparative analysis of these interrupted coding sequences (ICDSs) in six isolates ofM. tuberculosis, two ofM. bovisand one ofM. africanumand question their phenotypic impact and evolutionary significance.ResultsICDSs were classified as "common to all strains" or "strain-specific". Common ICDSs are believed to result from mutations acquired before the divergence of the species, whereas strain-specific ICDSs were acquired after this divergence. Comparative analyses of these ICDSs therefore define the molecular signature of a particular strain, phylogenetic lineage or species, which may be useful for inferring phenotypic traits such as virulence and molecular relationships. For instance,in silicoanalysis of the W-Beijing lineage ofM. tuberculosis, an emergent family involved in several outbreaks, is readily distinguishable from other phyla by its smaller number of common ICDSs, including at least one known to be associated with virulence. Our observation was confirmed through the sequencing analysis of ICDSs in a panel of 21 clinicalM. tuberculosisstrains. This analysis further illustrates the divergence of the W-Beijing lineage from other phyla in terms of the number of full-length ORFs not containing a frameshift. We further show that ICDS formation is not associated with the presence of a mutated promoter, and suggest that promoter extinction is not the main cause of pseudogene formation.ConclusionThe correlation between ICDSs, function and phenotypes could have important evolutionary implications. This study provides population geneticists with a list of targets, which could undergo selective pressure and thus alters relationships between the various lineages ofM. tuberculosisstrains and their host. This approach could be applied to any closely related bacterial strains or species for which several genome sequences are available.
Basis for treatment of tuberculosis among HIV-infected patients in Tanzania: the role of chest x-ray and sputum culture
Authors: Bakari Muhammad , Arbeit Robert D , Mtei Lillian , Lyimo Johnson , Waddell Richard , Matee Mecky , Cole Bernard F , Tvaroha Susan , Horsburgh C Robert , Soini Hanna , Pallangyo Kisali , von Reyn C Fordham 
Published: March 2008

Abstract

Background
Active tuberculosis (TB) is common among HIV-infected persons living in tuberculosis endemic countries, and screening for tuberculosis (TB) is recommended routinely. We sought to determine the role of chest x-ray and sputum culture in the decision to treat for presumptive TB using active case finding in a large cohort of HIV-infected patients.

Methods
Ambulatory HIV-positive subjects with CD4 counts ≥ 200/mm3 entering a Phase III TB vaccine study in Tanzania were screened for TB with a physical examination, standard interview, CD4 count, chest x-ray (CXR), blood culture for TB, and three sputum samples for acid fast bacillus (AFB) smear and culture.

Results
Among 1176 subjects 136 (12%) were treated for presumptive TB. These patients were more frequently male than those without treatment (34% vs. 25%, respectively; p = 0.049) and had lower median CD4 counts (319/μL vs. 425/μL, respectively; p < .0001). Among the 136 patients treated for TB, 38 (28%) had microbiologic confirmation, including 13 (10%) who had a normal CXR and no symptoms. There were 58 (43%) treated patients in whom the only positive finding was an abnormal CXR. Blood cultures were negative in all patients.

Conclusion
Many ambulatory HIV-infected patients with CD4 counts ≥ 200/mm3 are treated for presumptive TB. Our data suggest that optimal detection requires comprehensive evaluation, including CXR and sputum culture on both symptomatic and asymptomatic subjects.
CDKN1C/p57kip2is a candidate tumor suppressor gene in human breast cancer
Authors: Larson Pamela S , Schlechter Benjamin L , King Chia-Lin , Yang Qiong , Glass Chelsea N , Mack Charline , Pistey Robert , de las Morenas Antonio , Rosenberg Carol L 
Published: March 2008

Abstract

Background
CDKN1C (also known as p57KIP2) is a cyclin-dependent kinase inhibitor previously implicated in several types of human cancer. Its family members (CDKN1A/p21CIP1 and B/p27KIP1) have been implicated in breast cancer, but information about CDKN1C's role is limited. We hypothesized that decreased CDKN1C may be involved in human breast carcinogenesis in vivo.

Methods
We determined rates of allele imbalance or loss of heterozygosity (AI/LOH) in CDKN1C, using an intronic polymorphism, and in the surrounding 11p15.5 region in 82 breast cancers. We examined the CDKN1C mRNA level in 10 cancers using quantitative real-time PCR (qPCR), and the CDKN1C protein level in 20 cancers using immunohistochemistry (IHC). All samples were obtained using laser microdissection. Data were analyzed using standard statistical tests.

Results
AI/LOH at 11p15.5 occurred in 28/73 (38%) informative cancers, but CDKN1C itself underwent AI/LOH in only 3/16 (19%) cancers (p = ns). In contrast, CDKN1C mRNA levels were reduced in 9/10 (90%) cancers (p < 0.0001), ranging from 2–60% of paired normal epithelium. Similarly, CDKN1C protein staining was seen in 19/20 (95%) cases' normal epithelium but in only 7/14 (50%) cases' CIS (p < 0.004) and 5/18 (28%) cases' IC (p < 0.00003). The reduction appears primarily due to loss of CDKN1C expression from myoepithelial layer cells, which stained intensely in 17/20 (85%) normal lobules, but in 0/14 (0%) CIS (p < 0.00001). In contrast, luminal cells displayed less intense, focal staining fairly consistently across histologies. Decreased CDKN1C was not clearly associated with tumor grade, histology, ER, PR or HER2 status.

Conclusion
CDKN1C is expressed in normal epithelium of most breast cancer cases, mainly in the myothepithelial layer. This expression decreases, at both the mRNA and protein level, in the large majority of breast cancers, and does not appear to be mediated by AI/LOH at the gene. Thus, CDKN1C may be a breast cancer tumor suppressor.
Cracked mercury dental amalgam as a possible cause of fever of unknown origin: a case report
Authors: Bamonti Fabrizia , Guzzi Gianpaolo , Ferrero Maria Elena 
Published: March 2008

Abstract

Introduction
Sudden fever of unknown origin is quite a common emergency and may lead to hospitalization. A rise in body temperature can be caused by infectious diseases and by other types of medical condition. This case report is of a woman who had fever at night for several days and other clinical signs which were likely related to cracked dental mercury amalgam.

Case presentation
A healthy women developed fever many days after had cracked a mercury dental amalgam filling. Blood tests evidenced increased erythrocyte sedimentation rate, anemia and elevated white cell count; symptoms were headache and palpitations. Blood tests and symptoms normalized within three weeks of removal of the dental amalgam.

Conclusion
This case highlights the possible link between mercury vapor exposure from cracked dental amalgam and early activation of the immune system leading to fever of unknown origin.
Dysfunctional interferon-α production by peripheral plasmacytoid dendritic cells upon Toll-like receptor-9 stimulation in patients with systemic lupus erythematosus
Authors: Kwok Seung-Ki , Lee June-Yong , Park Se-Ho , Cho Mi-La , Min So-Youn , Park Sung-Hwan , Kim Ho-Youn , Cho Young-Gyu 
Published: March 2008

Abstract
Background
It is well known that interferon (IFN)-α is important to the pathogenesis of systemic lupus erythematosus (SLE). However, several reports have indicated that the number of IFN-α producing cells are decreased or that their function is defective in patients with SLE. We studied the function of plasmacytoid dendritic cells (pDCs) under persistent stimulation of Toll-like receptor (TLR)9 via a TLR9 ligand (CpG ODN2216) or SLE serum.

Methods
The concentrations of IFN-α were determined in serum and culture supernatant of peripheral blood mononuclear cells (PBMCs) from SLE patients and healthy controls after stimulation with CpG ODN2216 or SLE serum. The numbers of circulating pDCs were analyzed by fluoresence-activated cell sorting analysis. pDCs were treated with CpG ODN2216 and SLE serum repeatedly, and levels of produced IFN-α were measured. The expression of IFN-α signature genes and inhibitory molecules of TLR signaling were examined in PBMCs from SLE patients and healthy control individuals.

Results
Although there was no significant difference in serum concentration of IFN-α and number of circulating pDCs between SLE patients and healthy control individuals, the IFN-α producing capacity of PBMCs was significantly reduced in SLE patients. Interestingly, the degree which TLR9 ligand-induced IFN-α production in SLE PBMCs was inversely correlated with the SLE serum-induced production of IFN-α in healthy PMBCs. Because repeated stimulation pDCs with TLR9 ligands showed decreased level of IFN-α production, continuous TLR9 stimulation may lead to decreased production of IFN-α in SLE PBMCs. In addition, PBMCs isolated from SLE patients exhibited higher expression of IFN-α signature genes and inhibitory molecules of TLR signaling, indicating that these cells had already undergone IFN-α stimulation and had become desensitized to TLR signaling.

Conclusion
We suggest that the persistent presence of endogenous IFN-α inducing factors induces TLR tolerance in pDCs of SLE patients, leading to impaired production of IFN-α.
The histopathology of septic acute kidney injury: a systematic review
Authors: Langenberg Christoph , Bagshaw Sean M , May Clive N , Bellomo Rinaldo 
Published: March 2008

Abstract
Introduction
Sepsis is the most common trigger of acute kidney injury (AKI) in critically ill patients; understanding the structural changes associated with its occurrence is therefore important. Accordingly, we systematically reviewed the literature to assess current knowledge on the histopathology of septic AKI.

Methods
A systematic review of the MEDLINE, EMBASE and CINHAL databases and bibliographies of the retrieved articles was performed for all studies describing kidney histopathology in septic AKI.

Results
We found six studies reporting the histopathology of septic AKI for a total of only 184 patients. Among these patients, only 26 (22%) had features suggestive of acute tubular necrosis (ATN). We found four primate studies. In these, seven out of 19 (37%) cases showed features of ATN. We also found 13 rodent studies of septic AKI. In total, 23% showed evidence of ATN. In two additional studies performed in a dog model and a sheep model there was no evidence of ATN on histopathologic examination. Overall, when ATN was absent, studies reported a wide variety of kidney morphologic changes in septic AKI – ranging from normal (in most cases) to marked cortical tubular necrosis.

Conclusion
There are no consistent renal histopathological changes in human or experimental septic AKI. The majority of studies reported normal histology or only mild, nonspecific changes. ATN was relatively uncommon.
How Should We Design Supportive Cancer Care? The Patient's Perspective
Authors: Casarett David , Fishman Jessica , O'Dwyer Peter J. , Barg Frances K. , Naylor Mary , Asch David A. 
Published: March 2008

Purpose Hospice services are designed to meet the needs of patients near the end of life. Although so-called open-access hospice programs and bridge programs are beginning to offer these services to patients who are still receiving treatment, it is not known whether they best meet patients’ needs. Patients and Methods Three hundred adult patients receiving treatment for cancer completed interviews in which each patient's value or ability for supportive care services were calculated from the choices that they made among combinations of those services. Preferences for five traditional hospice services and six alternative supportive care services were measured, and patients were followed up for 6 months or until death. Results Patients’ utilities for alternative services were higher than those for traditional hospice services (0.53 v 0.39; sign-rank test P < .001). Alternative services were also preferred among patients with poor functional status (Eastern Cooperative Oncology Group performance score > 2; n = 54; 0.65 v 0.48; P < .001) and among those who were in the last 6 months of life (0.68 v 0.56; sign-rank test P = .003). Even patients who were willing to forgo cancer treatment (n = 38; 13%) preferred alternative services (3.1 v 1.8; P < .001). Conclusion Patients who are receiving active treatment for cancer, and even those who are willing to stop treatment, express a clear preference for alternative supportive care services over traditional hospice services. Supportive care programs for patients with advanced cancer should reconsider the services that they offer and might seek to include novel services in addition to, or perhaps instead of, traditional hospice services.
Use of Different Postmenopausal Hormone Therapies and Risk of Histology- and Hormone Receptor–Defined Invasive Breast Cancer
Authors: Fournier Agnès , Fabre Alban , Mesrine Sylvie , Boutron-Ruault Marie-Christine , Berrino Franco , Clavel-Chapelon Françoise 
Published: March 2008

PurposeWe previously found that the risk of invasive breast cancer varied according to the progestagen component of combined postmenopausal hormone therapy (CHT): progesterone, dydrogesterone, or other progestagens. We conducted the present study to assess how these CHTs were associated with histology- and hormone receptor-defined breast cancer.Patients and MethodsWe used data from the French E3N cohort study, with 80,391 postmenopausal women followed for a mean duration of 8.1 years; 2,265 histologically confirmed invasive breast cancers were identified through biennial self-administered questionnaires completed from 1990 to 2002. The relative risks (RRs) were estimated using Cox proportional hazards models.ResultsCompared with postmenopausal hormone therapy (HT) never-use, ever-use of estrogen+progesterone was not significantly associated with the risk of any breast cancer subtype, but increasing duration of estrogen+progesterone was associated with increasing risks of lobular (P = .06) and estrogen receptor–positive/progesterone receptor–negative (ER+/PR−; P = .02). Estrogen+dydrogesterone was associated with a significant increase in risk of lobular carcinoma (RR, 1.7; 95% CI, 1.1 to 2.6). Estrogen+other progestagens was associated with significant increases in risk of ductal and lobular carcinomas (RR, 1.6; 95% CI, 1.3 to 1.8; and 2.0; 95% CI, 1.5 to 2.7, respectively), of ER+/PR+ and ER+/PR− carcinomas (RR, 1.8; 95% CI, 1.5 to 2.1; and 2.6; 95% CI, 1.9 to 3.5, respectively), but not of ER−/PR+ or ER−/PR− carcinomas (RR, 1.0; 95% CI, 0.5 to 2.1; and 1.4; 95% CI, 0.9 to 2.0, respectively).ConclusionThe increase in risk of breast cancer observed with the use of CHTs other than estrogen+progesterone and estrogen+dydrogesterone seems to apply preferentially to ER+ carcinomas, especially those ER+/PR−, and to affect both ductal and lobular carcinomas.
Targeting Vascular Endothelial Growth Factor in Advanced Carcinoid Tumor: A Random Assignment Phase II Study of Depot Octreotide With Bevacizumab and Pegylated Interferon Alfa-2b
Authors: Yao James C. , Phan Alexandria , Hoff Paulo M. , Chen Helen X. , Charnsangavej Chusilp , Yeung Sai-Ching J. , Hess Kenneth , Ng Chaan , Abbruzzese James L. , Ajani Jaffer A. 
Published: March 2008

Purpose Effective systemic therapy for advanced carcinoid is lacking. The combination of bevacizumab (BEV) and pegylated (PEG) interferon alfa-2b was evaluated among patients with metastatic or unresectable carcinoid tumors. Patients and Methods Forty-four patients on stable doses of octreotide were randomly assigned to 18 weeks of treatment with bevacizumab or PEG interferon alfa-2b. At disease progression (PD) or at the end of 18 weeks (whichever occurred earlier), patients received bevacizumab plus PEG interferon until progression. Functional computer tomography (CT) scans were performed to measure effect on tumor blood flow. Results In the bevacizumab arm, four patients (18%) achieved confirmed partial response (PR), 17 patients (77%) had stable disease (SD), and one patient (5%) had PD. In the PEG interferon arm, 15 patients (68%) had SD and six patients (27%) had PD. Progression-free survival (PFS) rates after 18 weeks of monotherapy were 95% in bevacizumab versus 68% on the PEG interferon arm. The overall median PFS for all 44 patients is 63 weeks. Compared with paired baseline measurements on functional CT scans, we observed a 49% (P < .01) and 28% (P < .01) decrease in tumor blood flow at day 2 and week 18 among patients treated with bevacizumab. No significant changes in tumor blood flow were observed following PEG interferon. PEG interferon alfa-2b treatment was associated with decrease in plasma basic fibroblast growth factor (bFGF; P = .04) and increase in plasma interleukin-18 (IL-18; P < .01). No significant changes in bFGF or IL-18 following treatment with bevacizumab were observed. Conclusion Bevacizumab therapy resulted in objective responses, reduction of tumor blood flow, and longer PFS in patients with carcinoid than PEG interferon treatment.
Cation mass-valence sum (CM-VS) approach to assigning OH-bending bands in dioctahedral smectites
Authors: Gates Will P. 
Published: March 2008

AbstractThe assignments of OH-bending bands in the infrared (IR) spectra of dioctahedral smectites (montmorillonites, ferruginous smectites, and nontronites) have been revisited using a cation mass-valence sum (CM-VS) approach to quantify octahedral cation occupancy. The CM-VS approach enabled prediction of OH-bending band positions (in wavenumbers) related to OH-sharing octahedral cation pairs that had valence sums of 4 and 5, and cation masses associated with Fe(II) and Mg. Application of rules for the relationship enabled determination of the location of OH-sharing octahedral cation pairs containing Mg and Fe(II) for which previous assignments have been considered controversial, e.g. Fe(III)Mg-OH and MgMg-OH, or for which assignments have been missing due to lack of spectroscopic evidence, e.g. AlFe(II)-OH, Fe(III)Fe(II)-OH, Fe(II)Mg-OH, and Fe(II)Fe(II)-OH. Examples of these bands from several natural ferruginous smectites and nontronites are discussed. Quantification of IR spectra was used to develop a better understanding of the octahedral cation occupancy of this important class of Fe(III)-enriched smectites. While Fe(II) contents may be somewhat overestimated by the IR technique, those for four of the six ferruginous smectites studied here agree well with data from Mössbauer spectroscopy.
Geochemical records of a bentonitic acid-tuff succession related to a transgressive systems tract — Indication of changes in the volcanic sedimentation rate
Authors: Püspöki Z. , Kozák M. , Kovács-Pálffy P. , Szepesi J. , McIntosh R. , Kónya P. , Vincze L. , Gyula G. 
Published: March 2008

AbstractA detailed stratigraphic and facies reconstruction of a bentonitized acid-tuff succession, deposited within the transgressive systems tract of the Upper Miocene-Sarmatian Ser-3 eustatic cycle, at Sajóbábony, northern Hungary, was performed via petrographic, mineralogical and geochemical analyses. The purpose of the work was to analyze the degree of alteration of the volcanogenic sediments, as an indicator of the relative volcanic sedimentation rate. This may have an important role in indicating volcanic periods synchronous with sedimentation or reconstructing the volcanosedimentary paleoconditions. Sample pairs were collected from each bentonite and tuff layer, and, to facilitiate microstratigraphic relations, samples were collected every 10 cm within bentonite layers. Mineralogical analyses were performed by X-ray diffraction and geochemical analyses by inductively coupled plasma-mass spectroscopy.The CaO/K2O and Eu/La ratios correlate with each other and with a montmorillonite/X-ray-amorphous phase ratio, reflecting Ca and Eu incorporation associated with devitrification and smectite formation. In accordance with the current literature, these mineralogical and geochemical proxies can be related primarily to the weathering processes. Considering vertical distributions in a sequence-stratigraphic context, the Ca content and Eu/La values show that local peaks and Eu anomalies characteristic of acid tuffs show minima at flooding surfaces (FS). Within a bentonite layer, representing a single transgressive period, the repeated events of dust-tuff accumulations have been determined by K2O/CaO and La/Eu peaks, confirmed also by the Eu anomalies in the rare earth element (REE) patterns, thus leading to the conclusion that the level of alteration is closely correlated with the elimination of terrigenous input and a minimum in volcanic sedimentation rate allowing more intensive alteration of the deposited volcanic material. In the case of fine tuff beds, Eu anomalies on REE patterns reflect limited alteration at the bottom and more intensive alteration in the upper parts of the beds, reflecting the effect of infiltration of sea water into the pores.
The viscosity of organic liquid suspensions of trimethyldococylammonium-montmorillonite complexes
Authors: Minase Makoto , Kondo Mitsuji , Onikata Masanobu , Kawamura Katsuyuki 
Published: March 2008

AbstractAn organophilic bentonite was prepared by means of a reaction of natural Na-montmorillonite with trimethyldococylammonium which has an especially longn-alkyl chain. The addition of trimethyldococylammonium to montmorillonite was in the range 0.25–3.0 times the cation exchange capacity (CEC) of the clay (i.e.0.23–2.82 mmol/g clay). The particle morphology in organic liquid suspensions of organoclay complexes was studied by measuring the viscosity based on Eyring’s rate process and Robinson’s relative sediment volume. In toluene, montmorillonite with 1.17 mmol/g clay trimethyldococylammonium (1.25 times the CEC) had the largest specific gel volume, relative sediment volume, andK-factor. The results of the stoichiometry for trimethyldococylammonium-montmorillonite show that practically all of the quaternary ammonium was adsorbed to montmorillonite. Maximum half widths of 001 reflections from X-ray diffraction patterns were obtained in the range 0.74–1.17 mmol/g clay, indicating a disordered arrangement of the organic cation molecules intercalated between the layers. Appreciable shifts to lower-frequency regions in the Fourier transform infrared absorption spectra as a result of CH2-stretching vibrations were observed with increasing amounts of the organic cation. When increasing the amount of organic cation added to the clay from 0.94 to 1.41 mmol/g clay, a large shift occurred to the lower-frequency side, approaching the frequency of the organic cation alone. This indicates that the interaction between adjacent hydrocarbon chains becomes progressively stronger, due to van der Waals attraction, with increases in the amount of organic cation. Interactions of the alkyl chains in trimethyldococylammonium-montmorillonite complexes with irregularly distributed and randomly arranged alkyl chains between the silicate layers were weak, and, as a result, solvation with external organic liquids occurred and gel formation developed through macroscopic swelling of the organoclay.