Miracle-dz/UniFAR-FTUs huggingface dataset:
NanoMonitor: a miniature electronic biosensor for glycan biomarker detection.

AIM The goal of our research is to develop an ultrasensitive diagnostic platform called 'NanoMonitor' to enable rapid label-free analysis of a highly promising class of biomarkers called glycans (oligosaccharide chains attached to proteins) with high sensitivity and selectivity. The glycosylation of fetuin - a serum protein - and extracts from a human pancreatic cancer line was analyzed to demonstrate the capabilities of the NanoMonitor. MATERIAL & METHODS The NanoMonitor device consists of a silicon chip with an array of gold electrodes forming multiple sensor sites and works on the principle of electrochemical impedance spectroscopy. Each sensor site is overlaid with a nanoporous alumina membrane that forms a high density of nanowells on top of each electrode. Lectins (proteins that bind to and recognize specific glycan structures) are conjugated to the surface of the electrode. When specific glycans from a test sample bind to lectins at the base of each nanowell, a perturbation of electrical double-layer occurs, which results in a change in the impedance. Using the lectins Sambucs nigra agglutinin (SNA) and Maackia amurensis agglutinin (MAA), subtle variations to the glycan chains of fetuin were investigated. Protein extracts from BXPC-3, a cultured human pancreatic cancer cell line were also analyzed for binding to SNA and MAA lectins. The performance of the NanoMonitor was compared to a conventional laboratory technique: lectin-based enzyme linked immunosorbent assay (ELISA). RESULTS & DISCUSSION The NanoMonitor was used to identify glycoform variants of fetuin and global differences in glycosylation of protein extracts from cultured human pancreatic cancerous versus normal cells. While results from NanoMonitor correlate very well with results from lectin-based ELISA, the NanoMonitor is rapid, completely label free, requires just 10 microl of sample, is approximately five orders of magnitude more sensitive and highly selective over a broad dynamic range of glycoprotein concentrations. CONCLUSION Based on its performance metrics, the NanoMonitor has excellent potential for development as a point-of-care handheld electronic biosensor device for routine detection of glycan biomarkers from clinical samples.
Immunoperoxidase staining for identification of Aspergillus species in routinely processed tissue sections.

AIMS: To evaluate the performance of an immunoperoxidase stain using the monoclonal antibody EB-A1 to detect Aspergillus species in formalin fixed, paraffin wax embedded tissue. METHODS: The monoclonal antibody EB-A1 directed against galactomannan was used to detect Aspergillus species in 23 patients with suspected or confirmed invasive aspergillosis. Immunostaining was performed on formalin fixed, paraffin wax embedded tissue using the streptavidin-biotin method and compared with conventional haematoxylin and eosin, periodic acid-Schiff, and Gomori-Grocott stains. Results of immunostaining were semiquantitatively analysed with regard to both intensity of staining and number of positively staining micro-organisms. Tissue sections from 16 patients with confirmed invasive mycoses due to Candida species, Apophysomyces elegans, Rhizopus oryzae, Pseudallescheria boydii and Histoplasma capsulatum were used as controls. RESULTS: In 19 (83%) of 23 cases invasive aspergillosis was confirmed by both histological examination and culture (18 Aspergillus fumigatus and one A flavus). Immunoperoxidase stains were positive in 17 (89%) of 19 cases including one case of disseminated infection due to A flavus. Furthermore, the immunoperoxidase stain was positive in a culture negative tissue section with histological evidence of mycelial development, indicating the presence of Aspergillus species. Some cross-reactivity was observed with the highly related fungus P boydii, although the number of mycelial elements that stained was low. CONCLUSIONS: Immunoperoxidase staining using the monoclonal antibody EB-A1 performs well on routinely processed tissue sections and permits detection and generic identification of Aspergillus species, although it was no better than conventional histopathology in identifying the presence of an infection. An additional advantage is that the immunostain may help to provide an aetiological diagnosis when cultures remain negative.
Invasive diagnostic procedures in twin pregnancies

The rising rate of multiple pregnancies and its association with advanced maternal age has expanded the need for prenatal diagnosis in twins and higher order gestations. The complexity of the invasive diagnostic procedures and the risk of loss of an unaffected twin raise significant clinical, technical and ethical issues. In this review we discuss the specific issues of early scanning, counseling and determination of chorionicity prior to invasive procedures in twins. We present the available data describing the risk associated with these procedures in twins and compare data of fetal loss rate from different studies. We also discuss the issues of fetal blood sampling and late karyotyping in twin pregnancies. Copyright © 2005 John Wiley & Sons, Ltd.
Solution structure and proposed domain–domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase

Polyketides are a medicinally important class of natural products. The architecture of modular polyketide synthases (PKSs), composed of multiple covalently linked domains grouped into modules, provides an attractive framework for engineering novel polyketide‐producing assemblies. However, impaired domain–domain interactions can compromise the efficiency of engineered polyketide biosynthesis. To facilitate the study of these domain–domain interactions, we have used nuclear magnetic resonance (NMR) spectroscopy to determine the first solution structure of an acyl carrier protein (ACP) domain from a modular PKS, 6‐deoxyerythronolide B synthase (DEBS). The tertiary fold of this 10‐kD domain is a three‐helical bundle; an additional short helix in the second loop also contributes to the core helical packing. Superposition of residues 14–94 of the ensemble on the mean structure yields an average atomic RMSD of 0.64 ± 0.09 Å for the backbone atoms (1.21 ± 0.13 Å for all non‐hydrogen atoms). The three major helices superimpose with a backbone RMSD of 0.48 ± 0.10 Å (0.99 ± 0.11 Å for non‐hydrogen atoms). Based on this solution structure, homology models were constructed for five other DEBS ACP domains. Comparison of their steric and electrostatic surfaces at the putative interaction interface (centered on helix II) suggests a model for protein–protein recognition of ACP domains, consistent with the previously observed specificity. Site‐directed mutagenesis experiments indicate that two of the identified residues influence the specificity of ACP recognition.
Restricted Expression of LGR8 in Intralaminar Thalamic Nuclei of Rat Brain Suggests a Role in Sensorimotor Systems

Abstract: LGR8 was recently identified as a cognate receptor for insulin‐like peptide‐3 (INSL3), and INSL3‐LGR8 signaling is best known for its role in testis descent during development. LGR8 mRNA has been detected in various human tissues including brain, but the regional and cellular distribution of LGR8 expression in the mammalian central nervous system is unknown. Therefore, in this study we investigated the presence and localization of LGR8 mRNA in rat brain using reverse transcription‐polymerase chain reaction and in situ hybridization histochemistry. Results revealed a distinct distribution of LGR8 in forebrain, with transcripts principally restricted to the posterior thalamus and highest densities detected in the parafascicular nucleus of both adult and developing rats. Unexpectedly, INSL3 mRNA was not detected in brain by similar methods, but preliminary electrophysiologic studies of parafascicular neurons revealed that INSL3 altered their activity. These findings suggest that LGR8 signaling may be involved in sensorimotor control in the rat and perhaps other species, particularly via actions on parafascicular neurons that project to basal ganglia and are depleted in Parkinson's disease.
An assessment of the mucous component in carcinoma of the colon and rectum

It has been said that the prognosis of mucinous carcinoma of the colon and rectum is unfavorable. To determine the clinicopathologic significance of carcinomatous lesions with marked mucous production, the ratio of the area where there was significant mucous production (mucous component [MC]) to the area of the whole tumor on a tissue slice (area ratio) was determined by measurement with a digitizer in 281 patients with carcinoma of the colon and rectum. The MC was observed in the largest cross‐section of the tumor in 85 patients (30.2%). Of these 85 patients the MC area ratio was less than 10% in 42. In the 43 patients with an area ratio of 10% or more, no particular relationship was observed between the area ratio and the frequency of cases. If no MC was observed in the largest cross section of the tumor, the MC ratio in other regions of the tumor was almost 0. In the patients in whom the MC area ratio in the largest cross‐section was less than 10%, the MC area ratios in other sites of the tumor showed only a small variance, but in the patients with an MC area ratio of 10% or more, a large variance was observed according to the site. The prognosis for patients with an area ratio of 10% or more was less favorable than that for patients with no MC and with an MC area ratio of less than 10% (P < 0.05). These results suggest that it is reasonable to handle the patients with an MC area ratio of 10% or more as a group.
E‐cadherin prolongs the moment for interaction between intestinal stem cell and its progenitor cell to ensure Notch signaling in adult Drosophila midgut

Intestinal stem cells (ISCs) are required for maintenance of the proper cell composition in the adult intestine. To ensure permanent recruitment of newly differentiated cells, the ISC undergoes asymmetric cell division that generates an ISC itself and a progenitor cell. In the Drosophila midgut, cell fate for the absorptive cell is determined by Notch (N) signal in the progenitor cells that receive a ligand Delta (Dl) produced by the ISCs. Although most of the ISCs and progenitor cells are distantly located, they should retain their attachment when N is activated because the Dl–N interaction requires cell adhesion. Furthermore, N cannot be activated before completion of cell division. Thus, the moment after cell division and before cell separation should be prolonged for certain N activation, although the mechanism for this remains unclear. Here, we demonstrate that E‐cadherin (E‐cad) is required for stable attachment between the two cells. When E‐cad does not function, N is not activated and cell differentiation is attenuated. We also show that the ISC tumor by N inactivation is assisted by a defect in E‐cad down‐regulation. These findings reveal one of the normal N functions used to inhibit tumorigenesis through lowering of E‐cad for proper midgut cell turnover.
Granzyme B in Atherosclerosis and Transplant Vascular Disease: Association with Cell Death and Atherosclerotic Disease Severity

Apoptosis of intimal cells is an important contributor to the pathogenesis of atherosclerosis and transplant vascular disease (TVD). Since the activated immune response may be a key regulator of apoptosis in these lesions, we used immunohistochemistry to characterize the presence and localization of granzyme B, a major mediator of the cytotoxic immune response, in advanced atherosclerosis and TVD. Formalin-fixed, paraffin-embedded transverse sections from human left anterior descending coronary arteries were cut serially and stained with antibodies specific for granzyme B, smooth muscle α-actin, CD68, and CD3. The amount of granzyme B staining was semi-quantitated on a 0–5+/5+ scale. Also, TUNEL staining and in situ hybridization was performed to visualize cells undergoing cellular damage suggestive of apoptosis, and to localize granzyme B mRNA, respectively. Granzyme B localization was similar in both diseases. This protease was absent in arteries with mild atherosclerosis, but was abundant in the intima and media of vessels with advanced atherosclerosis and TVD. Within the intima, granzyme B localized to TUNEL-positive foam cells surrounding lipid-rich atheromas. Staining of serial sections with granzyme B and either smooth muscle α-actin, anti-CD68, or anti-CD3 showed that granzyme B localized to smooth muscle cells, macrophages, and T-cells. Further, in situ hybridization for granzyme B mRNA in TVD cases localized its expression to infiltrating leukocytes and not foam cells. In conclusion, the presence of granzyme B in advanced atherosclerotic lesions and TVD is associated with increasing disease severity and cell death. These observations suggest that granzyme B-mediated apoptosis may contribute to the pathogenesis of these diseases.
Quantitative Structure-Based Design: Formalism and Application of Receptor-Dependent RD-4D-QSAR Analysis to a Set of Glucose Analogue Inhibitors of Glycogen Phosphorylase

A method for performing quantitative structure-based design has been developed by extending the current receptor-independent RI-4D-QSAR methodology to include receptor geometry. The resultant receptor-dependent RD-4D-QSAR approach employs a novel receptor-pruning technique to permit effective processing of ligands with the lining of the binding site wrapped about them. Data reduction, QSAR model construction, and identification of possible pharmacophore sites are achieved by a three-step statistical analysis consisting of genetic algorithm optimization followed by backward elimination multidimensional regression and ending with another genetic algorithm optimization. The RD-4D-QSAR method is applied to a series of glucose inhibitors of glycogen phosphorylase b, GPb. The statistical quality of the best RI- and RD-4D-QSAR models are about the same. However, the predictivity of the RD- model is quite superior to that of the RI-4D-QSAR model for a test set. The superior predictive performance of the RD- model is due to its dependence on receptor geometry. There is a unique induced-fit between each inhibitor and the GPb binding site. This induced-fit results in the side chain of Asn-284 serving as both a hydrogen bond acceptor and donor site depending upon inhibitor structure. The RD-4D-QSAR model strongly suggests that quantitative structure-based design cannot be successful unless the receptor is allowed to be completely flexible.
Differential Recognition of Mycobacterium tuberculosis‐Specific Epitopes as a Function of Tuberculosis Disease History

Rationale: Individuals with a history of tuberculosis (TB) disease are at elevated risk of disease recurrence. The underlying cause is not known, but one explanation is that previous disease results in less‐effective immunity against Mycobacterium tuberculosis (Mtb). Objectives: We hypothesized that the repertoire of Mtb‐derived epitopes recognized by T cells from individuals with latent Mtb infection differs as a function of previous diagnosis of active TB disease. Methods: T‐cell responses to peptide pools in samples collected from an adult screening and an adolescent validation cohort were measured by IFN‐&ggr; enzyme‐linked immunospot assay or intracellular cytokine staining. Measurements and Main Results: We identified a set of “type 2” T‐cell epitopes that were recognized at 10‐fold‐lower levels in Mtb‐infected individuals with a history of TB disease less than 6 years ago than in those without previous TB. By contrast, “type 1” epitopes were recognized equally well in individuals with or without previous TB. The differential epitope recognition was not due to differences in HLA class II binding, memory phenotypes, or gene expression in the responding T cells. Instead, “TB disease history‐sensitive” type 2 epitopes were significantly (P < 0.0001) more homologous to sequences from bacteria found in the human microbiome than type 1 epitopes. Conclusions: Preferential loss of T‐cell reactivity to Mtb epitopes that are homologous to bacteria in the microbiome in persons with previous TB disease may reflect long‐term effects of antibiotic TB treatment on the microbiome.
Epstein–Barr viral load as a marker of lymphoma in AIDS patients

Epstein–Barr virus (EBV) is implicated in the pathogenesis of acquired immunodeficiency syndrome (AIDS) lymphoma, and viral DNA is present within the malignant cells in about half of affected patients. We examined the extent to which EBV viral load is elevated in the plasma of AIDS lymphoma patients compared to AIDS patients with opportunistic infections. Sixty‐one AIDS patients were studied including 35 with lymphoma (24 non‐Hodgkin, six Hodgkin, and five brain lymphoma) and 26 with various opportunistic infections. In situ hybridization revealed EBV encoded RNA (EBER) expression in the malignant cells of 17/28 AIDS lymphomas (61%). In 232 serial plasma samples from 35 lymphoma patients and in 128 samples from AIDS controls, EBV viral load was assayed by quantitative‐polymerase chain reaction (Q‐PCR) using a TaqMan probe targeting the BamH1W sequence. EBV was detected in plasma from all 17 EBER‐positive AIDS lymphoma patients, with viral loads ranging from 34 to 1,500,000 copies per ml (median 3,210). Viral load usually fell rapidly upon initiation of lymphoma therapy and remained undetectable except in two patients with persistent tumor. In 11 AIDS patients, whose lymphoma lacked EBER expression, and in 26 control patients without lymphoma, levels of EBV in plasma were usually low or undetectable (range 0–1,995 and 0–2,409, median 0 and 0, respectively). There was no association between EBV viral load and human immunodeficiency virus (HIV) load or CD4 count. In conclusion, EBV viral load shows promise as a tool to assist in diagnosis and management of EBV‐related lymphoma patients. J. Med. Virol. 75:59–69, 2005. © 2005 Wiley‐Liss, Inc.
AKT1 mediates bypass of the G1/S checkpoint after genotoxic stress in normal human cells

Certain forms of hexavalent chromium [Cr(VI)] are human carcinogens. Our recent work has shown that a broad range protein tyrosine phosphatase (PTP) inhibitor, sodium orthovanadate (SOV), abrogated both Cr(VI)-induced growth arrest and clonogenic lethality. Notably, SOV enhanced Cr(VI) mutation frequency, ostensibly through forced survival of genetically damaged cells. In the present study, co-treatment with this PTP inhibitor bypassed the Cr(VI)-induced G1/S checkpoint arrest in diploid human lung fibroblasts (HLF). Moreover, the PTP inhibitor abrogated the Cr(VI)-induced decrease in the expression of key effectors of the G1/S checkpoint [Cyclin D1, phospho Ser 807/811 Rb (pRB), p27]. Cr(VI)-induced G1 arrest was associated with the cytoplasmic appearance of pRb and the nuclear localization of p27, both of which were reversed by the PTP inhibitor. The PTP inhibitor’s reversal of G1/S checkpoint effector localization after Cr exposure was found to be Akt1-dependent, as this was abrogated by transfection with either akt1 siRNA or an Akt1-kinase dead plasmid. Furthermore, Akt1 activation alone was sufficient to induce G1/S checkpoint bypass and to prevent Cr(VI)-induced changes in pRb and p27 localization. In conclusion, this work establishes Akt1 activation to be both sufficient to bypass the Cr(VI)-induced G1/S checkpoint, as well as necessary for the observed PTP inhibitor effects on key mediators of the G1/S transition. The potential for Akt to bypass G1/S checkpoint arrest in the face of genotoxic damage could increase genomic instability, which is a hallmark of neoplastic progression.
The opacity proteins of Neisseria gonorrhoeae strain MS11 are encoded by a family of 11 complete genes

Variants of Neisseria gonorrhoeae MS11 show distinct colony morphologies because of the expression of a class of surface components called opacity (Opa, PII) proteins. Southern analyses combined with molecular cloning of genomic DNA from a single variant of MS11 has identified 11 opa genes contained in separate loci. These opa genes code for distinct opacity proteins which are distinguishable at their variable domains. The opa gene analyses were also extended to divergent variants of MS11. These studies have shown that, during in vitro and in vivo culture, 10 of the 11 opa genes did not undergo significant change in their primary sequence. However, in these variants, one gene (opaE) underwent non‐reciprocat inter‐opa recombinations to generate newer Opa variants. Phylogenic analysis of the opa gene sequences suggests that the opa gene family have evolved by a combination of gene duplication, gene replacement and partial inter‐opa recombination events.
Retirement intentions and spousal support: a multi-actor approach.

OBJECTIVES This study investigates the role of the partner in the retirement decision-making process. It determines the extent to which the support and intentions of partners regarding early retirement influence each other, and which partner dominates. METHODS Data have been collected directly from 1,052 older employees working in Dutch industry and trade, and from their spouses. Because it is conceptualized that husbands' and wives' retirement intentions/support are related in a reciprocal way, a two-stage least squares regression analysis (2SLS) is used to establish the specified mutual relationships. RESULTS Intentions and support of both partners concerning retirement are strongly related. The results of the 2SLS suggest that early retirement of one of the spouses is the result of influence processes within the household, and that early retirement can be considered, to a certain extent, a household decision. This holds for married men's early retirement in particular. There seems to be no direct causal relationship between a couple's own decision making with respect to early retirement and the retirement behavior of a couple's social network. DISCUSSION Future research on the retirement decision-making process should focus on the family unit rather than simply on the individual worker, and be extended to different types of retirement behavior.
A wideband planar array antenna for Ka-band wireless communication applications

A wideband planar array antenna is proposed for Ka-band wireless communication applications in this paper. It consists of several rectangular radiating cavities and a stripline feeding network. Metalized posts are employed to improve the impedance matching. Besides, higher harmonic mode can be suppressed by these metalized posts. A transition from a standard waveguide to a strip line is designed based on the same method. Finally, a 2×2 array prototype is fabricated by pressing three PCB boards together. Simulated results of the element show reflection coefficient bandwidth (|S11|<;-10dB) of 46.6% and gain more than 5dBi ranging from 23GHz to 37 GHz. Measured results of the array demonstrate more than 20% of reflection coefficient bandwidth within the frequency band of 24~32 GHz. The gain fluctuates less than 1.6 dB within the same band. The height of the antenna is 0. 21λ0 (λ0 is the free space wavelength of the center frequency).