Miracle-dz/UniFAR-FTUs huggingface dataset:
Lipid raft proteome of the human neutrophil azurophil granule

Detergent‐resistant membrane domains (DRMs) are present in the membranes of azurophil granules in human neutrophils (Feuk‐Lagerstedt et al., J. Leukoc. Biol. 2002, 72, 970). Using a proteomic approach, we have now identified 106 proteins in a DRM preparation from these granule membranes. Among these proteins were the lipid raft structural proteins flotillin‐1 and ‐2, cytoskeletal proteins such as actin, vimentin and tubulin, and membrane fusion promoting proteins like annexins and dysferlin. Our results suggest that the azurophil granule membrane, in similarity to the plasma membrane, is an elaborate structure that takes part in intracellular signaling and functions other than the mere delivery of bactericidal effector molecules to the phagosome.
Four-dimensional computed tomography pulmonary ventilation images vary with deformable image registration algorithms and metrics.

PURPOSE A novel pulmonary ventilation imaging technique based on four-dimensional (4D) CT has advantages over existing techniques and could be used for functional avoidance in radiotherapy. There are various deformable image registration (DIR) algorithms and two classes of ventilation metric that can be used for 4D-CT ventilation imaging, each yielding different images. The purpose of this study was to quantify the variability of the 4D-CT ventilation to DIR algorithms and metrics. METHODS 4D-CT ventilation images were created for 12 patients using different combinations of two DIR algorithms, volumetric (DIR(vol)) and surface-based (DIR(sur)), yielding two displacement vector fields (DVFs) per patient (DVF(voI) and DVF(sur)), and two metrics, Hounsfield unit (HU) change (V(HU)) and Jacobian determinant of deformation (V(Jac)), yielding four ventilation image sets (V(HU)(vol), V(HU)(sur), V(Jac)(voI), and V(Jac)(sur). First DVF(vol) and DVF(sur) were compared visually and quantitatively to the length of 3D displacement vector difference. Second, four ventilation images were compared based on voxel-based Spearman's rank correlation coefficients and coefficients of variation as a measure of spatial heterogeneity. V(HU)(vol) was chosen as the reference for the comparison. RESULTS The mean length of 3D vector difference between DVF(vol) and DVF(sur) was 2.0 +/- 1.1 mm on average, which was smaller than the voxel dimension of the image set and the variations. Visually, the reference V(HU)(vol) demonstrated similar regional distributions with V(HU)(sur); the reference, however, was markedly different from V(Jac)(vol) and V((Jac)(sur). The correlation coefficients of V(HU)(vol) with V(HU)(sur), V(Jac)(vol) and V(Jac)(sur) were 0.77 +/- 0.06, 0.25 +/- 0.06 and 0.15 +/- 0.07, respectively, indicating that the metric introduced larger variations in the ventilation images than the DIR algorithm. The spatial heterogeneities for V(HU)(vol), 'V(HU)(sur), V(Jac)(vol), and V(Jac)(sur) were 1.8 +/- 1.6, 1.8 +/- 1.5 (p = 0. 85), 0.6 +/- 0.2 (p = 0.02), and 0.7 +/- 0.2 (p = 0.03), respectively, also demonstrating that the metric introduced larger variations. CONCLUSIONS 4D-CT pulmonary ventilation images vary widely with DIR algorithms and metrics. Careful physiologic validation to determine the appropriate DIR algorithm and metric is needed prior to its applications.
Determination of Thiopurine Methyltransferase Activity in Human Erythrocytes by High-Performance Liquid Chromatography: Comparison With the Radiochemical Method

The current article describes a new assay to measure thiopurine methyltransferase (TPMT) activity from red blood cells. This method is based on the measurement of the reaction product 6-methylmercaptopurine (6-MMP) by high-performance liquid chromatography (HPLC). 6-MMP is extracted by ethyl acetate with recoveries of 85%, 80%, 80%, and 92% for 50, 250, 500, and 1,000 ng/100 &mgr;L packed red blood cells, respectively. 6-MMP was identified and measured by a Zorbax CN column installed in an HPLC system. The chromatograms were resolved using a mobile phase consisting of 40 mmol/L sodium phosphate buffer (pH 3) and methanol in a gradient from 1% to 20% of methanol. Under these conditions 6-MMP is well resolved from substrates (6-mercaptopurine and S-adenosyl- l -methionine) and endogenous peaks. When the TPMT activity from 20 patients was measured by the HPLC-linked assay and the classic radiochemical method, a linear correlation was obtained between both procedures (y = 0.99 x + 0.33;x-axis, radiochemical assay;y-axis, HPLC-linked assay;r = 0.98). In conclusion, the current report describes a new, reliable, safe, and nonradioactive method to measure TPMT activity that is shorter and simpler than the previously described ones.
Increment of CD8S6F1 cells in synovial fluid from patients with rheumatoid arthritis.

OBJECTIVE--To investigate the role of CD8 cell subsets in the pathogenesis of rheumatoid arthritis (RA) and the phenotypes of T cells adherent or non-adherent to the target cells (endothelial cells and synovial cells) pre-treated with IL-1 beta. METHODS--The expression of S6F1 on CD8 cells and that of an activation marker on CD8 cells and CD8 cell subsets was evaluated in specimens of peripheral blood and synovial fluid obtained from 15 patients with RA and 10 with osteoarthritis (OA) using a two- or three-colour immunofluorescence method for analysis. RESULTS--The percentage of CD8S6F1 cells among CD8 cells in synovial fluid was significantly greater than that of peripheral blood. Synovial fluid from RA patients had a greater percentage of CD8S6F1 cells compared with either peripheral blood of matched patients or synovial fluid of OA patients. The percentage of CD8HLA-DR cells in synovial fluid was markedly greater than that in paired samples of peripheral blood in patients with RA. In the CD8S6F1 cells from both groups of patients, synovial fluid showed an increased percentage of HLA-DR cells compared with peripheral blood. Similar results were observed in CD8 cells lacking S6F1 expression (CD8S6F1-) from both groups of patients. There was no significant difference in the percentage of HLA-DR cells between CD8S6F1 and CD8S6F1- cell populations in peripheral blood. In contrast with peripheral blood, in synovial fluid of RA patients the percentage of HLA-DR cells in the CD8S6F1 cell population was markedly greater than that in the CD8S6F1- population. However, the percentage of HLA-DR cells in both cell populations was similar in synovial fluid of OA patients. In both the endothelial and the synovial cell adhesion assays, the percentage of CD8S6F1 among CD8 cells and the mean fluorescence intensity of S6F1 antigen on CD8S6F1 cells were significantly greater in the adherent T cell population than that in the non-adherent T cell population. CONCLUSION--These results suggest that increased expression of S6F1 antigen and the increased percentage of HLA-DR cells on CD8 cells in synovial fluid may be responsible for the migration of these cells into inflamed synovial tissues, and for cellular interactions between these cells and synovial cells or the extracellular matrix.
Characterization of Dominantly Negative Mutant ClyA Cytotoxin Proteins in Escherichia coli

ABSTRACT We report studies of the subcellular localization of the ClyA cytotoxic protein and of mutations causing defective translocation to the periplasm in Escherichia coli. The ability of ClyA to translocate to the periplasm was abolished in deletion mutants lacking the last 23 or 11 amino acid residues of the C-terminal region. A naturally occurring ClyA variant lacking four residues (183 to 186) in a hydrophobic subdomain was retained mainly in the cytosolic fraction. These mutant proteins displayed an inhibiting effect on the expression of the hemolytic phenotype of wild-type ClyA. Studies in vitro with purified mutant ClyA proteins revealed that they were defective in formation of pore assemblies and that their activity in hemolysis assays and in single-channel conductance tests was at least 10-fold lower than that of the wild-type ClyA. Tests with combinations of the purified proteins indicated that mutant and wild-type ClyA interacted and that formation of heteromeric assemblies affected the pore-forming activity of the wild-type protein. The observed protein-protein interactions were consistent with, and provided a molecular explanation for, the dominant negative feature of the mutant ClyA variants.
The expectancies of living kidney donors: do they differ as a function of relational status and gender?

BACKGROUND While two-thirds of the living kidney donors continue to be genetically related to the recipient, there has been a 300% increase in unrelated living donors over the last 10 years. Also, women continue to represent more than half of all the living kidney donors. This study examined whether donor expectancies varied as a function of relational status or gender. METHODS 362 kidney donor candidates (232 related, 130 unrelated) completed the Living Donation Expectancies Questionnaire (LDEQ). A 2 (relational status: related or unrelated) x 2 (gender: male or female) multivariate analysis of variance was conducted to examine main and interaction effects across the six domains of the LDEQ: interpersonal benefit (IB), personal growth (PG), spiritual benefit (SB), quid pro quo (QPQ), health consequences (HC) and miscellaneous consequences (MC). RESULTS The highest expectancies were for PG (54.1%) and IB (29.8%), followed by expectations of MC (18.2%), SB (16.9%), HC (14.4%), and QPQ (4.4%). Multivariate analyses showed a relational main effect [F = 4.18, P = 0.02] and a gender main effect [F = 5.09, P = 0.01]. Subsequent univariate analyses showed significant effects (P<0.05) for IB (related>unrelated), QPQ (men>women), HC (unrelated>related, men > women) and MC (unrelated > related). CONCLUSION Overall, donor candidate expectancies appear to be realistic in light of previous findings of donor benefit. However, some living donor expectancies may vary as a function of donor relational status and gender. It may be important to assess and appropriately address both positive and negative expectancies at the time of donor evaluation. The LDEQ may be a useful clinical tool for assessing such expectancies.
Circulating complement proteins in patients with sepsis or systemic inflammatory response syndrome

The systemic inflammatory response of the body to invading microorganisms, termed sepsis, leads to profound activation of the complement system. Pathophysiological concepts suggest that complement activation occurs very early in this syndrome. Thus, we discuss whether the determination of concentrations of the complement components C3a, C5a, and C3 in plasma as well as of the C3a/C3 ratio might be helpful to diagnose sepsis early. For this purpose, 33 patients from an intensive care unit were monitored for 10 days. In comparison with healthy donors, C3a levels and the C3a/C3 ratio of intensive-care-unit patients were significantly elevated (P < 0.0001) on admission. In contrast, C3 levels were significantly reduced (P < 0.0001) but increased during the study. C5a levels in the plasma of healthy donors and patients were identical. Twenty-two of 33 patients fulfilled microbiological and clinical criteria of sepsis. Eleven patients had signs of systemic inflammatory response syndrome but no microbiological evidence of sepsis. The groups could be differentiated from each other by their C3a levels or their C3a/C3 ratios during the first 24 h after the clinical onset of sepsis (P < 0.05). Septic patients in shock had higher C3a levels than normotensive septic patients, although the differences were not significant. Nonsurvivors had significantly higher C3a levels on admission than survivors (P = 0.0185). No differences were found between septic patients who developed adult respiratory distress syndrome and those who did not. Thus, determination of C3a concentrations in plasma may prove useful (i) to diagnose sepsis early, (ii) to differentiate between patients with sepsis and those with systemic inflammatory response syndrome, and (iii) to assess prognosis.
Toxicological studies on aqueous extract of Gmelina arborea in rodents

Context: Gmelina arborea Roxb. (Verbenaceae) is an important medicinal plant in the traditional system of medicine of India. The plant is used in the treatment of snake-bites, fever, piles, and diabetes. However, there is little toxicological information available regarding its safety after exposure. The present study was designed to evaluate acute and repeated dose toxicity of the aqueous extract of Gmelina arborea stem bark. Materials and methods: In the acute toxicity test, Swiss albino mice were treated with aqueous extract (300, 2000, and 5000 mg/kg), orally. Animals were observed periodically during the first 24 h after administration of the extract, and daily thereafter for 14 days. In the repeated dose toxicity study, the aqueous extract of Gmelina arborea (300, 1000, and 2000 mg/kg per day) was administered orally for a period of 28 days in Wistar rats. The effects on body weight, food and water consumption, organ weight, hematology, clinical biochemistry, as well as histology, were studied. Results and conclusion: Aqueous extract did not produce mortality, changes in behavior or any other physiological activities in mice, for any of the selected doses. There were no significant differences in the body weight, organ weights and feeding habits between control and treated animals. Hematological and biochemical analysis showed no marked differences in any of the parameters examined in either the control or treated groups. Pathologically, neither gross abnormalities nor histopathological changes were observed. The aqueous extract of Gmelina arborea was found safe in acute and repeated dose toxicity studies when tested in rodents.
The clinical picture of Alzheimer's disease in the decade before diagnosis: clinical and biomarker trajectories.

OBJECTIVE Increasing evidence suggests that Alzheimer's disease begins at least a decade before the diagnosis of dementia. Earlier identification of the disease will have important implications for intervention; however, current models of preclinical changes are theoretical and require verification from empirical observations. Furthermore, these models have not incorporated psychiatric features. METHOD Clinical and biological markers were examined at baseline (1999-2001) in 9,076 people aged 65 years and older. A nested case-control study included 830 cases with Alzheimer's disease diagnosed by DSM-IV criteria during the 10-year follow-up and twice as many controls. By taking the distance between baseline and diagnosis as the length of the preclinical period, disease marker trajectories were estimated using nonparametric locally weighted smoothing analysis. RESULTS Significant differences for the cases compared to the controls were observed on both intercept and slope for truncated amyloid β40 (P = .006; P = .003, respectively), C-reactive protein (P = .03; P = .05), verbal fluency (P < .0001; P < .0001), visual recall (P < .0001; P = .007), and hippocampal volume (P = .0002; P = .04) and on the slope only for truncated amyloid β42 (P = .01). The cases showed higher levels of depressive symptoms (P = .003), which remained stable over the 10 years to diagnosis. CONCLUSIONS As hypothesized by existing theoretical models, changes in plasma amyloid β levels, hippocampal atrophy, cognitive loss, and C-reactive protein are already observed up to 10 years before diagnosis. An acceleration in cognitive decline appears to follow a significant increase in amyloid accumulation, and depressive symptomatology remains at a constantly higher level. Overall, clinical and biological markers do not follow the same trajectories; the clinical picture changes according to distance from dementia.
Understanding the physical basis for the side‐chain conformational preferences of methionine

Methionine (Met) is a structurally versatile amino acid most commonly found in protein cores and at protein–protein interfaces. Thus, a complete description of the structure of Met is important for a fundamental understanding of protein structure and design. In previous work, we showed that the hard‐sphere dipeptide model is able to recapitulate the side‐chain dihedral angle distributions observed in high‐resolution protein crystal structures for the nine amino acids we have studied to date: Val, Thr, Ser, Leu, Ile, Cys, Tyr, Trp, and Phe. Using the same approach, we are also able to predict the observed χ1 and χ2 side‐chain dihedral angle distributions for Met. However, the form of the side‐chain dihedral angle distribution P(χ3) predicted by the hard‐sphere model does not match the observed distribution. We investigate the possible origins of the discrepancy and find that specific bond lengths and angles in Met side chains strongly influence P(χ3). We then identify minimal additions to the hard‐sphere dipeptide model necessary to quantitatively predict P(χ3) of Met, and its near isosteres norleucine (Nle) and selenomethionine (Mse). We find that adding weak attractive interactions between hydrogen atoms to the model is sufficient to achieve predictions for P(χ3) that closely match the observed P(χ3) distributions for Met, Nle, and Mse. We explicitly show that weak attractive interactions between hydrogens do not negatively affect the agreement between the predicted and observed side‐chain dihedral angle distribution for Val, Leu, Ile, and Phe, as we expect for other amino acids. Proteins 2016; 84:900–911. © 2016 Wiley Periodicals, Inc.
Altered tumor formation and evolutionary selection of genetic variants in the human MDM4 oncogene

A large body of evidence strongly suggests that the p53 tumor suppressor pathway is central in reducing cancer frequency in vertebrates. The protein product of the haploinsufficient mouse double minute 2 (MDM2) oncogene binds to and inhibits the p53 protein. Recent studies of human genetic variants in p53 and MDM2 have shown that single nucleotide polymorphisms (SNPs) can affect p53 signaling, confer cancer risk, and suggest that the pathway is under evolutionary selective pressure (1–4). In this report, we analyze the haplotype structure of MDM4, a structural homolog of MDM2, in several different human populations. Unusual patterns of linkage disequilibrium (LD) in the haplotype distribution of MDM4 indicate the presence of candidate SNPs that may also modify the efficacy of the p53 pathway. Association studies in 5 different patient populations reveal that these SNPs in MDM4 confer an increased risk for, or early onset of, human breast and ovarian cancers in Ashkenazi Jewish and European cohorts, respectively. This report not only implicates MDM4 as a key regulator of tumorigenesis in the human breast and ovary, but also exploits for the first time evolutionary driven linkage disequilibrium as a means to select SNPs of p53 pathway genes that might be clinically relevant.
Path loss prediction in durian orchard using uniform geometrical theory of diffraction

The analysis of path loss in scattering zone by using UTD is presented. The results of the total field results from the UTD solution agree very well with that from NEC-BSC. Around the vicinity of the source, the UTD results agree with experimental results but not in the further region. This is due to the fact that the line-of-sight and reflected field components are very strong in this region. For the further distance, the path loss of the UTD is stronger than the experimental results. The error comes from the present UTD propagation model which is under assumption that the trees and ground surface are PEC. Therefore, the effects of the actual surface of trees and ground must be included in the calculation to treat the actual environment. The results with the effects of the actual surface will be presented in the next meeting.
Environmental and developmental signals modulate proline homeostasis: evidence for a negative transcriptional regulator.

In many plants, osmotic stress induces a rapid accumulation of proline through de novo synthesis from glutamate. This response is thought to play a pivotal role in osmotic stress tolerance [Kishor, P. B. K. , Hong, Z. , Miao, G. -H. , Hu, C. -A. A. and Verma, D. P. S. (1995) Plant Physiol. 108, 1387-1394]. During recovery from osmotic stress, accumulated proline is rapidly oxidized to glutamate and the first step of this process is catalyzed by proline oxidase. We have isolated a full-length cDNA from Arabidopsis thaliana, At-POX, which maps to a single locus on chromosome 3 and that encodes a predicted polypeptide of 499 amino acids showing significant similarity with proline oxidase sequences from Drosophila and Saccharomyces cerevisiae (55.5% and 45.1%, respectively). The predicted location of the encoded polypeptide is the inner mitochondrial membrane. RNA gel blot analysis revealed that At-POX mRNA levels declined rapidly upon osmotic stress and this decline preceded proline accumulation. On the other hand, At-POX mRNA levels rapidly increased during recovery. Free proline, exogenously added to plants, was found to be an effective inducer of At-POX expression; indeed, At-POX was highly expressed in flowers and mature seeds where the proline level is higher relative to other organs of Arabidopsis. Our results indicate that stress- and developmentally derived signals interact to determine proline homeostasis in Arabidopsis.
Who Cares: Stakeholder Participation and the Use of Performance Information in Strategic Planning

Performance measurement translates organizational goals into objectives and actions. In empirical performance information scores and ranks functional departments and subordinates based on their implementation capacity— such capacity indexes could be linked to strategic planning and its adjustment. Previous research in strategic plans and performance measurement focused on the nature of performance information. This study further detects how it relates to different stakeholders’ interests and capacity. Does various stakeholders’ participation in strategic plans enhance the use of performance information in the planning process? Do external stakeholders generate different effect on the use of performance information if compared to internal stakeholders? The author attempts to answer these questions by examining whether external stakeholders (including interest groups and citizen groups) and internal stakeholders (including Chief Administrative Officers, local government staffs and elected officials’) participation in strategic plans could positively influence the application of performance information in strategic planning. Data are mainly from International City/County Management Association (ICMA) “State of the Profession” survey in 2006. The methods of logistic regression and predicted probability are employed. The statistical results show that the participation of CAOs, local government staffs and elected officials are positively and significantly influence the application of performance information to strategic planning. Based on technical rationality, managerial effectiveness and political accountability, internal stakeholders can generate a more significant effect on the use of performance information than external stakeholders. 성과 측정은 조직 목표를 의제와 행동으로 전환한다. 실증적 성과 정보는 각 부서와 부하 직원들을 채점하고 순위 매긴다. 그러한 능력 지표는 전략 기획과 그 적응에 연결될 수 있다. 전략적 기획과 성과 측정에 관한 선행 연구는 성과 정보의 본질에 초점을 맞추고 있다. 본 연구는 더 나아가 그것이 다양한 이해관계와 능력에 어떻게 관련되는지를 탐구한다. 전략적 기획에서의 다양한 이해 관계자 참여가 기획 단계에서의 성과 정보 이용을 축진하는가? 내적 이해관계자에 비하여 외적 이해관계자가 성과정보 이용에 다양한 영향을 미치는가? 저자는 외적 이해관계자 (이해 단체와 시민 단체를 포함)과 내적 이해관계자 (행정 부서장, 지방 정부 공무원, 지방 의회 의원)의 전략적 기획에의 참여가 전략적 기획에서의 성과 정보 이용에 긍정적 영향을 미치는지를 연구함으로써 이러한 질문에 답하고자 하였다. 데이터는 주로 국제 도시/카운티 연합(ICMA)의 2006 직업의 상태 설문 조사에 의거하였다. 로짓 회귀분석과 예측 확률 방법론을 이용하였다. 통계 결과에 따르면 행정 부서장, 지방 정부 공무원, 지방 의회 의원의 참여는 전략적 기획에서의 성과 정보 적용에 긍정적이고 통계적으로 유의미한 영향을 미쳤다. 기술적 합리성, 관리적 효율성, 그리고 정치적 책무성에 의거하여 내적 이해관계자들은 외적 이해관계자들에 비하여 성과 정보 이용에 보다 유의미한 영향을 미쳤다.