Miracle-dz/UniFAR-FTUs huggingface dataset:
Dialysis-related systemic microinflammation is associated with specific genomic patterns.

BACKGROUND Although several reports have focused on the clinical importance of the systemic microinflammatory state in the uraemic population, the relationship between the activation of a specific transcriptome and the development of this condition is still not completely defined. METHODS Thirty haemodialysis (HD), 30 peritoneal dialysis (PD) and 30 chronic kidney disease (CKD) patients were enrolled in our study. For all patients, serum C-reactive protein (CRP) and ferritin levels were determined. In addition, the expression level of 234 inflammatory responses and oxidative stress pathway genes was measured, using oligonucleotide microarray chips (HG-U133A, Affymetrix), in peripheral blood mononuclear cells of 24 randomly selected patients (8 HD, 8 PD and 8 CKD). RESULTS HD patients demonstrated higher CRP and ferritin levels compared to PD and CKD patients (P < 0.001). Statistical analysis identified 10 genes able to discriminate CKD from HD and PD patients (FDR = 5%, P < 0.001) and significantly correlated to CRP levels. All together, these genes were able to predict inflammation with an accuracy of 87% (P < 0.001). Among the selected genes there were those encoding for key regulators of inflammation and oxidative stress (e.g. RELA, GSS). Interestingly, only three inflammatory genes (MIF, IL8RB and CXCL12) were still significantly associated with inflammation when included in a multivariate analysis. RT-PCR for RELA, MIF, CXCL12 and western blots for IL8RB and GSS, using 66 patients, validated the microarray results. CONCLUSIONS This study may help to better understand the physiopathology of the systemic inflammatory state in CKD and dialysis patients and to identify new target genes potentially useful for future bio-molecular studies and therapeutic approaches.
Effects of Brood Manipulation Costs on Optimal Sex Allocation in Social Hymenoptera

In eusocial Hymenoptera, queens and workers are in conflict over optimal sex allocation. Sex ratio theory, while generating predictions on the extent of this conflict under a wide range of conditions, has largely neglected the fact that worker control of investment almost certainly requires the manipulation of brood sex ratio. This manipulation is likely to incur costs, for example, if workers eliminate male larvae or rear more females as sexuals rather than workers. In this article, we present a model of sex ratio evolution under worker control that incorporates costs of brood manipulation. We assume cost to be a continuous, increasing function of the magnitude of sex ratio manipulation. We demonstrate that costs counterselect sex ratio biasing, which leads to less female‐biased population sex ratios than expected on the basis of relatedness asymmetry. Furthermore, differently shaped cost functions lead to different equilibria of manipulation at the colony level. While linear and accelerating cost functions generate monomorphic equilibria, decelerating costs lead to a process of evolutionary branching and hence split sex ratios.
A microfluidic device for isolation and characterization of transendothelial migrating cancer cells

Transendothelial migration of cancer cells is a critical stage in cancer, including breast cancer, as the migrating cells are generally believed to be highly metastatic. However, it is still challenging for many existing platforms to achieve a fully covering endothelium and to ensure transendothelial migration capability of the extracted cancer cells for analyses with high specificity. Here, we report a microfluidic device containing multiple independent cell collection microchambers underneath an embedded endothelium such that the transendothelial-migrated cells can be selectively collected from only the microchambers with full coverage of an endothelial layer. In this work, we first optimize the pore size of a microfabricated supporting membrane for the endothelium formation. We quantify transendothelial migration rates of a malignant human breast cell type (MDA-MB-231) under different shear stress levels. We investigate characteristics of the migrating cells including morphology, cytoskeletal structures, and migration (speed and persistence). Further implementation of this endothelium-embedded microfluidic device can provide important insights into migration and intracellular characteristics related to cancer metastasis and strategies for effective cancer therapy.
Reorganizing Polymer Chains with Cyclodextrins

During the past several years, we have been utilizing cyclodextrins (CDs) to nanostructure polymers into bulk samples whose chain organizations, properties, and behaviors are quite distinct from neat bulk samples obtained from their solutions and melts. We first form non-covalently bonded inclusion complexes (ICs) between CD hosts and guest polymers, where the guest chains are highly extended and separately occupy the narrow channels (~0.5–1.0 nm in diameter) formed by the columnar arrangement of CDs in the IC crystals. Careful removal of the host crystalline CD lattice from the polymer-CD-IC crystals leads to coalescence of the guest polymer chains into bulk samples, which we have repeatedly observed to behave distinctly from those produced from their solutions or melts. While amorphous polymers coalesced from their CD-ICs evidence significantly higher glass-transition temperatures, Tgs, polymers that crystallize generally show higher melting and crystallization temperatures (Tms, Tcs), and some-times different crystalline polymorphs, when they are coalesced from their CD-ICs. Formation of CD-ICs containing two or more guest homopolymers or with block copolymers can result in coalesced samples which exhibit intimate mixing between their common homopolymer chains or between the blocks of the copolymer. On a more practically relevant level, the distinct organizations and behaviors observed for polymer samples coalesced from their CD-ICs are found to be stable to extended annealing at temperatures above their Tgs and Tms. We believe this is a consequence of the structural organization of the crystalline polymer-CD-ICs, where the guest polymer chains included in host-IC crystals are separated and confined to occupy the narrow channels formed by the host CDs during IC crystallization. Substantial degrees of the extended and un-entangled natures of the IC-included chains are apparently retained upon coalescence, and are resistant to high temperature annealing. Following the careful removal of the host CD lattice from each randomly oriented IC crystal, the guest polymer chains now occupying a much-reduced volume may be somewhat “nematically” oriented, resulting in a collection of randomly oriented “nematic” regions of largely extended and un-entangled coalesced guest chains. The suggested randomly oriented nematic domain organization of guest polymers might explain why even at high temperatures their transformation to randomly-coiling, interpenetrated, and entangled melts might be difficult. In addition, the behaviors and uses of polymers coalesced from their CD-ICs are briefly described and summarized here, and we attempted to draw conclusions from and relationships between their behaviors and the unique chain organizations and conformations achieved upon coalescence.
Primary sclerosing cholangitis as a cause of false positive bile duct brushing cytology: Report of two cases.

Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease of unknown etiology characterized by ongoing inflammation, destruction, and fibrosis of intrahepatic and extrahepatic bile ducts. Irregular narrowing and dilation of the biliary duct system produces the characteristic beaded pattern seen on cholangiogram. Malignant degeneration resulting in cholangiocarcinoma is a well‐recognized sequela of PSC. Bile duct brushing cytology is the primary screening technique for cholangiocarcinoma. It is associated with a relatively low sensitivity but high specificity. Few false positive bile duct brushings have been reported in the literature, with the majority of these having occurred in a background of PSC. We report two patients with PSC in whom bile duct brush cytologies were falsely positive for carcinoma. Diagn. Cytopathol. 2005;32:119–124. © 2005 Wiley‐Liss, Inc.
Optimising Clinical Trial Design for Proof of Neuroprotection in Acute Ischaemic Stroke: The SAINT Clinical Trial Programme

The development of effective therapies for acute ischaemic stroke has proven to be a challenging task. The only approved therapy for acute ischaemic stroke remains intravenous recombinant tissue plasminogen activator initiated within 3 h of stroke onset, following a CT scan to exclude intracerebral haemorrhage. Many other therapies have been evaluated in Phase III clinical trials, including more than 50 neuroprotective agents, but the results have either been inconclusive or negative. These trials have provided valuable lessons for the design of future studies in acute ischaemic stroke, including the importance of adequate testing in preclinical studies, time to treatment from symptom onset, target dose, patient selection, sample size and the outcome measures used. These key criteria have been captured in the Stroke Therapy Academic Industry Roundtable (STAIR) recommendations for the preclinical and clinical development of acute stroke therapies. NXY-059 is a novel free radical-trapping neuroprotectant that reduces infarct size and preserves brain function in animal models of acute ischaemic stroke. It is one of the first compounds to have progressed to Phase III clinical trials, having fulfilled the STAIR recommendations for the preclinical development of neuroprotective agents. The efficacy and safety of NXY-059 in patients with acute ischaemic stroke is currently being evaluated in the Stroke Acute Ischaemic NXY-059 Treatment (SAINT) clinical trial programme, which was designed in accordance with the STAIR clinical recommendations. The final results from the first of these studies, SAINT I, have recently been reported.
Development of 16S rRNA-Based Probes for theCoriobacterium Group and the Atopobium Cluster and Their Application for Enumeration of Coriobacteriaceaein Human Feces from Volunteers of Different Age Groups

ABSTRACT Two 16S rRNA-targeted probes were developed: one for theCoriobacterium group and the other for theAtopobium cluster (which comprises most of theCoriobacteriaceae species, including theCoriobacterium group). The new probes were based on sequences of three new Coriobacteriaceae strains isolated from human feces and clinical material and sequences from databases. Application of the probes to fecal samples showed that formula-fed infants had higher numbers of Coriobacterium group cells in their feces than breast-fed infants. In addition, based on the presented results, it is hypothesized that with the increasing age of a person, the diversity of Atopobium cluster species present in the feces increases.
Smokey: Automatic Recognition of Hostile Messages

Abusive messages (flames) can be both a source of frustration and a waste of time for Internet users. This paper . describes some approaches to flame recognition, mcluding a prototype system, Smokey. Smokey builds a 47-element feature vector based on the syntax and semantics of each sentence, combining the vectors for the sentences within each message. A training set of 720 messages was used by Quinlan's C4.5 decision-tree generator to determine feature-based rules that were able to correctly categorize 64% of the flames and 98% of the nonflames in a separate test set of 460 messages. Additional techniques for greater accuracy and user customization are also discussed.
Brazilian version of the Overall Assessment of the Speaker's Experience of Stuttering - Adults protocol (OASES-A).

PURPOSE To verify the applicability of the protocol Overall Assessment of the Speaker's Experience of Stuttering - Adults (OASES-A), translated into Brazilian Portuguese, in a sample of adults who stutter. METHODS The Brazilian Portuguese version of the OASES-A protocol was individually applied to 18 people who stutter. The classification of stuttering severity was based on the Stuttering Severity Instrument for Children and Adults (SSI-3) protocol. Translation and back-translation processes were carried out by specialists, considering semantic, conceptual, cultural, and idiomatic equivalences. RESULTS There was no correlation between the severity degrees of stuttering assessed by the SSI-3 protocol and the self-assessment performed using the OASES-A. Subjects reported impairments in perceived fluency; speech ability; level of knowledge about stuttering and treatment options; use of confrontational techniques; quality of life. They also mentioned having difficulty coping with emotional states such as anxiety and embarrassment, and with communication in daily situations. CONCLUSION The OASES-A protocol is useful in the assessment and treatment of stutterers, as it provides specialized speech-language pathologists with sutterers' self-perception regarding their communication difficulties and the impact of stuttering on their quality of life.
A Two-Phase Model for Evaporating Solvent-Polymer Mixtures

Evaporating solvent-polymer mixtures play an important role in a number of modern industrial applications. We focus on developing a two-phase model for a fluid composed of a volatile solvent and a nonvolatile polymer in a thin-film geometry. The model accounts for density differences between the phases as well as evaporation at a fluid-air interface. We use the model in one dimension to explore the interplay between evaporation and compositional buoyancy; the former promotes the growth of a polymer-rich skin at the free surface while the latter tends to pull the denser polymeric phase to the substrate. We also examine how these mechanisms influence the drying time of the film. In the limit of dilute polymer, the model can be reduced to a single nonlinear boundary value problem. The nondilute problem has a rich asymptotic structure. We find that the shortest drying times occur in the limit of strong gravitational effects due to the rapid formation of a bilayer with a polymer-rich lower layer and a solvent-rich upper layer. In addition, gravity plays a key role in inhibiting the formation of a skin and can prevent substantial increases in the drying time of the film.
The Low Lumbar Spine Below Cotrel–Dubousset Instrumentation: Long-Term Findings

Study Design. Retrospective review of long instrumented fusions down to the low lumbar spine for the treatment of adolescent idiopathic scoliosis. Objectives. To evaluate whether the use of instrumentation systems that preserve the sagittal profile could reduce the incidence of early degenerative changes. Summary of Background Data. Long fusions and distractive Harrington instrumentation in the surgical treatment of adolescent idiopathic scoliosis (AIS) are known to produce pain and degenerative changes in the free lumbar segments. Reports on the use of Cotrel–Dubousett instrumentation (CDI) confirm that the instrumentation maintains physiologic lumbar lordosis, but the evolution of the spine below the fusion is not addressed. Method. Thirty-five patients with AIS and CDI were studied. Their spines were fused to L3 or lower, and they had a minimum follow-up of 10 years. Radiologic measurements were recorded from frontal and lateral radiographs. At the time of last examination, lateral flexion–extension dynamic radiographs and magnetic resonance imaging evaluated the health of the disks below the fusion. Clinical outcome was assessed with the Scoliosis Research Society instrument. A control group consisting of 35 peers without scoliosis served as a reference for the outcome questionnaire. Results. Surgery kept the sagittal profile in a physiologic range. All but two patients were satisfied with the results of surgery. There were no differences between patients and control group insofar as pain, self-image, general function, and daily activity were concerned. Eleven patients showed instability signs in dynamic radiographs and more than half of patients showed incipient degeneration on magnetic resonance images. These findings are similar to those found in the general population, according to the literature, and could evidence normal aging processes. Conclusions. Cotrel–Dubousset instrumentation maintains the physiologic sagittal contour. Although there are some degenerative changes in magnetic resonance images and dynamic radiographs, the quality of life and daily activities of the patients after surgery are similar to those of a normal population of the same age.
Hydroxyl radical rate constants and photolysis rates of .alpha.-dicarbonyls.

38, 811. (37) Matthess, G. ; Pekdeger, A. GWF, GasWasserfach: WasserlAbwasser 1980, 121, 214. (38) Davis, J. In “Contaminants and Sediments”: Baker, R. A,, Ed.; Ann Arbor Science: Ann Arbor, MI 1980; p 279. (39) Hansch, C. ; Leo, A. In “Substituent Constants for Correlation Analysis in Chemistry and Biology”; Elsevier: Amsterdam, 1979. (40) Tute, M. S. Adv. Drug. Res. 1971, 6 , 1. (41) Mackay, D. ; Bobra, A,; Shin, W. Y. ; Yalkowsky, S. H.
The coronal pulp cavity index: a biomarker for age determination in human adults.

The correlation between reduction of the coronal pulp cavity and chronological age was examined in a sample of 846 intact teeth from 433 individuals of known age and sex. Panoramic (rotational) radiography was used to measure the height (mm) of the crown (CH = coronal height) and the height (mm) of the coronal pulp cavity (CPCH = coronal pulp cavity height) of 425 premolars and 421 molars from 213 males and 220 females. The tooth-coronal index (TCI) after Ikeda et al. [1985] Jpn. J. For. Med. 39:244-250) was computed for each tooth and regressed on real age. The correlation coefficients ranged from -0.92 (molars, combined sample, right side) to -0.87 (female molars), with an S.E. of the estimate ranging from 5.88-6.66 years. Correlations were slightly higher in males than females. The equations obtained allowed estimation of age in a sample of 100 teeth from both sexes (not used for the regression) with an error of +/- 5 years in 81.4% of cases for male molars. The regression formulae for estimating age obtained from the recent sample were tested on a historical sample of 100 teeth from 100-year-old skeletons with an error of +/- 5 years in 70.3% of cases for male molars. This study illustrates the potential value of a little-known aging method which can be easily applied to estimate age in both living individuals and skeletal material of unknown age.
The molecular basis of factor V and VIII procofactor activation

Summary. Activation of precursor proteins by specific and limited proteolysis is a hallmark of the hemostatic process. The homologous coagulation factors (F)V and FVIII circulate in an inactive, quiescent state in blood. In this so‐called procofactor state, these proteins have little, if any procoagulant activity and do not participate to any significant degree in their respective macromolecular enzymatic complexes. Thrombin is considered a key physiological activator, cleaving select peptide bonds in FV and FVIII which ultimately leads to appropriate structural changes that impart cofactor function. As the active cofactors (FVa and FVIIIa) have an enormous impact on thrombin and FXa generation, maintaining FV and FVIII as inactive procofactors undoubtedly plays an important regulatory role that has likely evolved to maintain normal hemostasis. Over the past three decades there has been widespread interest in studying the proteolytic events that lead to the activation of these proteins. While a great deal has been learned, mechanistic explanations as to how bond cleavage facilitates conversion to the active cofactor species remain incompletely understood. However, recent advances have been made detailing how thrombin recognizes FV and FVIII and also how the FV B‐domain plays a dominant role in maintaining the procofactor state. Here we review our current understanding of the molecular process of procofactor activation with a particular emphasis on FV.
The effect of different type of vermicompost organic fertilizer litter on quantitive , qualitative and biochemical characteristics of green mung bean ( Vigna radiata L . ) in drought stress conditions in Varamin

Vermicompost in sustainable agriculture is very useful for improving soil porosity and thereby providing more nutrients to plants; accordingly, a split plot experiment was performed on mung bean in a randomized complete block design from with three replications in research farm of Islamic Azad University, Varamin – Pishva. The first factor was drought stress including lack of drought stress, irrigation cut in podding stage and irrigation cut in grain filling stage as the main plot and the second factor was vermicompost including non-consumption, vermicompost with cattle litter, vermicompost with cattle and equine litter, as well as vermicompost with cattle, poultry and equine litter as sub plot. Based on the results of analysis of variance, the main effect of drought stress and grain yield vermicompost, biological yield, protein yield, proline and cell membrane stability was significant at one percent probability level. Additionally, drought stress was significantly effective on protein percentage at one percent probability level as well as on leaf relative water content and protein percentage at five percent probability level. The results showed that with increase in drought stress, grain yield, biological yield, protein yield, leaf relative water content and membrane stability decrease and protein and proline percentage are added, so that the most negative effect in irrigation cut occurred in podding stage. It was also found that vermicompost in the presence or absence of drought stress improves yield and drought yield components, so that vermicompost with cattle and equine litter, as well as with cattle, poultry and equine litter had the greatest impact.
Glucocorticoid Receptor and Molecular Chaperones in the Pathogenesis of Adrenal Incidentalomas: Potential Role of Reduced Sensitivity to Glucocorticoids

Glucocorticoid (GC) sensitivity depends on glucocorticoid receptor (GR) and heat shock proteins (Hsps). We investigated whether common GR genes (ER22/23EK N363S, Bcl I, and 9β) and adrenocorticotropin receptor promoter polymorphisms influence susceptibility for unilateral adrenal incidentaloma (AI), plus GR and Hsp expression in tumorous (n = 19), peritumorous (n = 13) and normal adrenocortical (n = 11) tissues. Patients (n = 112), population-matched controls (n = 100) and tumor tissues (n = 32) were genotyped for these polymorphisms. Postdexamethasone serum cortisol was higher in patients (p < 0.001). GR gene variants, larger allele of Bcl I (odds ratio (OR) 2.9; 95% confidence interval (CI) 1.7–5.1; p < 0.001] and minor allele of 9β (OR 3.0; 95% CI 1.6–5.7; p < 0.001) were independent predictors of AI. In patients, the first allele is linked with larger tumors (p = 0.002) and the latter with higher postdexamethasone cortisol levels (p = 0.025). Both allele carriers had lesser waist circumference (p = 0.02), similar adrenocorticotropin and higher basal (p = 0.024) and postdexamethasone cortisol concentrations (p < 0.001). Tumorous and constitutional genotypes were similar. GR-D is the major receptor isoform in normal adrenal cortex by Western blotting. Loss of other receptor iso-forms, decrease in immunostaining for GR (p < 0.0001), underexpression of chaperones (p ≤ 0.01) and the presence of inducible Hsp70 were found in adenomas. In conclusion, GR gene variants, C allele of Bcl I and minor allele of 9β, are associated with Als. Their concurrent presence in patients reduces GC sensitivity. Normal adrenal cortex preferentially expresses GR-D. In adenomas, the lack of other GR isoforms and underexpression of heat shock proteins perhaps permanently impair GC signaling, which could promote dysregulated cortisol production and tumor growth. The innate GC sensitivity probably modifies these effects.