Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of an immunodominant epitope on RNA polymerase III recognized by systemic sclerosis sera: application to enzyme-linked immunosorbent assay.

OBJECTIVE To characterize an immunodominant epitope on RNA polymerase III (RNAP III) recognized by systemic sclerosis (SSc) sera and to develop an enzyme-linked immunosorbent assay (ELISA) for the detection of serum anti-RNAP I/III antibodies. METHODS RNAP III-specific subunits RPC62 and RPC155 were generated in a bacterial expression system as a series of recombinant fragments. Reactivities to these recombinant fragments were examined by immunoblots and/or ELISA in 16 SSc sera containing anti-RNAP I/III antibodies, 89 SSc sera lacking anti-RNAP I/III antibodies, 61 systemic lupus erythematosus (SLE) sera, and 61 healthy control sera. RESULTS Anti-RNAP I/III-positive SSc sera recognized several distinct epitopes on RPC62 and RPC155 in various combinations, but the fragment encoding amino acids at positions 732-1166 of RPC155 was recognized by all 11 anti-RNAP I/III-positive SSc sera tested. Carboxyl- and amino-terminal deletion studies showed that at least 130 amino acids at positions 891-1020 of RPC155 were necessary for the antibody binding, but strong reactivity required an additional amino-terminal extension. When a purified recombinant fragment containing the immunodominant epitope was used as the antigen source in an ELISA, elevated antibody reactivity was detected in all 16 anti-RNAP I/III-positive SSc sera, but in no anti-RNAP I/III-negative SSc, SLE, or healthy control sera, representing a sensitivity of 100% and a specificity of 100%. CONCLUSION A major epitope commonly recognized by SSc sera containing anti-RNAP I/III antibodies was identified on RPC155. The ELISA using a recombinant fragment expressing the immunodominant epitope should be a valuable tool for routine screening for anti-RNAP I/III antibodies in clinical diagnostic laboratories.
Multivalent Pseudopeptides Targeting Cell Surface Nucleoproteins Inhibit Cancer Cell Invasion through Tissue Inhibitor of Metalloproteinases 3 (TIMP-3) Release*

Background: NucAnt 6L (N6L) binds to nucleoproteins and inhibits tumor growth. Results: N6L bound to sulfated glycosaminoglycans, induced TIMP-3 release, and inhibited cell invasion. Silencing of TIMP-3 abolished N6L effect on cell invasion. Conclusion: N6L inhibits cell invasion through the release of TIMP-3. Significance: TIMP-3 released by N6L inhibits cell invasion. Sulfated glycosaminoglycans are presented as new receptors for N6L. Blockage of the metastasis process remains a significant clinical challenge, requiring innovative therapeutic approaches. For this purpose, molecules that inhibit matrix metalloproteinases activity or induce the expression of their natural inhibitor, the tissue inhibitor of metalloproteinases (TIMPs), are potentially interesting. In a previous study, we have shown that synthetic ligands binding to cell surface nucleolin/nucleophosmin and known as HB 19 for the lead compound and NucAnt 6L (N6L) for the most potent analog, inhibit both tumor growth and angiogenesis. Furthermore, they prevent metastasis in a RET transgenic mice model which develops melanoma. Here, we investigated the effect of N6L on the invasion capacity of MDA-MB-435 melanoma cells. Our results show that the multivalent pseudopeptide N6L inhibited Matrigel invasion of MDA-MB-435 cells in a modified Boyden chamber model. This was associated with an increase in TIMP-3 in the cell culture medium without a change in TIMP-3 mRNA expression suggesting its release from cell surface and/or extracellular matrix. This may be explained by our demonstrated N6L interaction with sulfated glycosaminoglycans and consequently the controlled bioavailability of glycosaminoglycan-bound TIMP-3. The implication of TIMP-3 in N6L-induced inhibition of cell invasion was evidenced by siRNA silencing experiments showing that the loss of TIMP-3 expression abrogated the effect of N6L. The inhibition of tumor cell invasion by N6L demonstrated in this study, in addition to its previously established inhibitory effect on tumor growth and angiogenesis, suggests that N6L represents a promising anticancer drug candidate warranting further investigation.
Monoclonal Antibodies That Bind to Domain III of Dengue Virus E Glycoprotein Are the Most Efficient Blockers of Virus Adsorption to Vero Cells

ABSTRACT The specific mechanisms by which antibodies neutralize flavivirus infectivity are not completely understood. To study these mechanisms in more detail, we analyzed the ability of a well-defined set of anti-dengue (DEN) virus E-glycoprotein-specific monoclonal antibodies (MAbs) to block virus adsorption to Vero cells. In contrast to previous studies, the binding sites of these MAbs were localized to one of three structural domains (I, II, and III) in the E glycoprotein. The results indicate that most MAbs that neutralize virus infectivity do so, at least in part, by the blocking of virus adsorption. However, MAbs specific for domain III were the strongest blockers of virus adsorption. These results extend our understanding of the structure-function relationships in the E glycoprotein of DEN virus and provide the first direct evidence that domain III encodes the primary flavivirus receptor-binding motif.
Enculturation and Alcohol Use Problems among Aboriginal University Students

Objective: To examine associations between Aboriginal enculturation, Canadian acculturation, and alcohol problems among Aboriginal university students living in an urban area in Canada. Methods: Data for this mixed methods study were collected through in-person surveys with a convenience sample of Aboriginal university students (n = 60) in 2008/2009. Results: Students evidenced high levels of Aboriginal enculturation and Canadian acculturation. Aboriginal enculturation was significantly associated with reduced alcohol problems for Aboriginal university students. There was no association between Canadian acculturation and alcohol problems. Qualitative findings suggest Aboriginal cultural practices helped students cope with problems in their daily lives and provided them with both personal and social rewards. Conclusions: This study found Aboriginal enculturation was significantly associated with reduced alcohol problems among Aboriginal university students. Results support the growth of programs and services that encourage Aboriginal students to maintain their cultural identity within the university setting.
Behavior of Surface-Anchored Poly ( acrylic acid ) Brushes with Grafting Density Gradients on Solid Substrates : 2 . Theory

We apply a molecular theory to predict the structural properties of poly(acrylic acid) macromolecules grafted via one of their ends to solid surfaces. The theory explicitly incorporates the acid-base equilibrium responsible for the charge regulation of the acrylic groups, as well as the conformations, size, shape, and charge distributions of all the molecular species present. We compare the predictions of the theory with experimental observations presented in the preceding article for the height of the layer as a function of ionic strength for different polymer molecular weight and polymer surface coverage. The calculated heights are found to be in good agreement with the experimental observations. The theory predicts the distribution of charges within the layer. We find that the counterions adsorb to the grafting surface, overcompensating the charge of the polymer. The charge regulation within the polymer layer is determined by the interplay between the bulk pH, the ionic strength, and the density of polymer. The system tends to become uncharged with decreasing ionic strength of the solution and increasing polymer density. In all cases the charge regulation acts in order to minimize the electrostatic repulsions in the system. The local distribution of protons within the polymer layer is predicted to be very different from that of the bulk solution. The local pH within the polymer layer can be tuned by varying the solution ionic strength and the polymer surface coverage; the variation can be large as two pH units, relative to the bulk pH. This large variation of the local pH within a couple of nanometers within the brush can be used in the design of biosensors.
RETROLENTAL FIBROPLASIA

In the period 1956–1974, 31 new cases of retrolental fibroplasia (RLF) were diagnosed at the Helsinki University Eye Hospital. All were alive in 1974. 90% weighed less than 1500 g at birth and the gestational age of less than 30 weeks at birth was present in 85%. All patients had required supplementary oxygen during the first weeks of life. 84% of the eyes had visual acuity of finger counting 1 m or less and when classified according to the corrected visual acuity in the better eye, 71% of the patients were practically blind according to the classification by Rintelen. 81% of the eyes showed one of the cicatricial stages of RLF, III to V, and 45% showed the grade V of the disease. 11% of the eyes showed corneal opacities, 44% a flat or absent anterior chamber, 11% had intraocular pressure of ≥ 30 mmHg and 21% showed lenticular opacities.
Copy number variation of GATA4 and NKX2‐5 in Chinese fetuses with congenital heart disease

Congenital heart disease (CHD) is one of the most common birth defects in newborns. The etiology of CHD has remained largely unknown, but it is assumed to result from the combined effects of genetic and environmental factors. Recent investigations have detected potentially pathogenic copy number variations (CNV) in a proportion of patients with CHD. The present case–control study evaluated whether CNV in the GATA4 and NKX2‐5 genes contribute to the pathogenesis of CHD in Chinese fetuses (n = 117), by comparing them with non‐CHD control subjects (n = 100).
Alzheimer'S Disease, Dementia, Mild Cognitive Impairment and the Menopause: A ‘Window of Opportunity’?

Alzheimer's disease (AD) is not an inevitable consequence of aging and may be modified by both adverse and protective factors. The pathological changes of AD commence in midlife and AD has a long preclinical phase that may be diagnosed by biomarkers in the cerebrospinal fluid and by brain MRI. New clinical criteria for the diagnosis of AD dementia and AD mild cognitive impairment (MCI) have been proposed. MCI and dementia are frequently the result of AD and cerebrovascular disease combined. Over the age of 85 years, MCI and dementia are more common in women than in men. Women with a surgical premature menopause have an increased risk of MCI and AD. Menopausal hormone therapy from the menopause to the age of 60 years, when any risks of menopausal hormone therapy are extremely small, may provide a ‘window of opportunity’ to reduce the risk of MCI and AD in later life. Many measures may help to prevent, delay or minimize AD in both women and men and should be actively encouraged.
Increased Expression of Tenascin in Pheochromocytomas Correlates With Malignancy

Tenascin is a significant extracellular matrix glycoprotein, which is upregulated in various neoplasias and pathologic processes. Pheochromocytomas are rare tumors of the sympathoadrenal system, whose malignancy is almost impossible to predict. There are no histologic or chemical markers available that would define the malignant behavior of these tumors, except the discovery of metastases. In our search for new markers, we investigated the immunohistochemical expression of tenascin in a large number of pheochromocytomas and paragangliomas. Seven tumors were metastasized and were thus considered malignant. Normal adrenal medulla was tenascin negative. A striking difference was seen between malignant and benign pheochromocytomas. All malignant pheochromocytomas expressed stromal tenascin strongly or moderately, whereas most benign pheochromocytomas (28 of 37, 70%) showed no or only weak immunopositivity. The staining was strong or moderate also in 13 of 28 (46%) of the tumors that showed histologically suspicious features, here called borderline tumors. Paragangliomas showed a more heterogeneous staining pattern, and no significant difference was found between benign and malignant paragangliomas. To our knowledge, this is the first study to demonstrate the expression of tenascin in pheochromocytomas and particularly the enhanced expression in malignant pheochromocytomas. We therefore suggest that tenascin may be associated with the malignant transformation and metastasis of pheochromocytomas. It is also a potential marker predicting more aggressive behavior in pheochromocytomas.
Global Gene Expression Profiling of Bovine Immature B Cells using Serial Analysis of Gene Expression

The Peyer's patches of the small intestine are important sites of antigen processing. The follicles of the Peyer's patches receive the antigen transported by the M cells at the mucosal surface and then play a major role in development of both protective humoral and mucosal immune responses. Serial analysis of gene expression (SAGE) was employed to derive the global gene expression profile of B lymphocytes isolated from the IPPF. Analysis of the SAGE data revealed the identity of genes and the level to which they are expressed by IPPF B lymphocytes. This analysis indicated that they were metabolically active and that the transcripts encoding proteins necessary for a response to antigen presentation were expressed. These transcripts included the B cell receptor components CD76a and b (Ig-alpha and Ig-beta) and accessory c-Src family kinases Lyn and Blk. Furthermore, many of the positive and negative regulators, and accessory proteins that are necessary for B cell antigen receptor signaling were identified. Also present were transcripts encoding interleukins and their cognate receptors. Overall, this SAGE analysis yielded a global picture of gene expression in IPPF B lymphocytes and provides a starting point for the comparison of gene expression in further functional studies.
The end of the net as we know it? Deep packet inspection and internet governance

Advances in network equipment now allow internet service providers to monitor the content of data packets in real-time and make decisions about how to handle them. If deployed widely this technology, known as deep packet inspection (DPI), has the potential to alter basic assumptions that have underpinned internet governance to date. The article explores the way internet governance is responding to deep packet inspection and the political struggles around it. Avoiding the extremes of technological determinism and social constructivism, it integrates theoretical approaches from the sociology of technology and actor-centered institutionalism into a new framework for technology-aware policy analysis.
Implications of Dengue Outbreaks for Blood Supply, Australia

Dengue outbreaks have increased in size and frequency in Australia, and transfusion-transmitted dengue poses a risk to transfusion safety. Using whole blood samples collected during the large 2008–2009 dengue epidemic, we estimated the risk for a dengue-infectious blood donation as ≈1 in 7,146 (range 2,218–50,021).
The Disulfide Folding Pathway of Human Epidermal Growth Factor (*)

Human epidermal growth factor (EGF) contains three disulfides and 53 amino acids. Reduced/denatured EGF refolds spontaneously in vitro to acquire its native structure. The mechanism of this folding process has been elucidated by structural analysis of both acid and iodoacetate trapped intermediates. The results reveal that the folding is accompanied by a sequential flow of unfolded EGF (0-disulfide) through three groups of folding intermediates, namely 1-disulfide, 2-disulfide, and 3-disulfide (scrambled) EGF isomers, to reach the native structure. Equilibrium occurs among isomers of each class of disulfide species, and the composition of intermediates appears to be highly heterogeneous. Together, at least 27 fractions of folding intermediates have been identified, but there exist only limited numbers of well populated species which constitute more than 80% of the total intermediates found during EGF folding. Six species of such well populated intermediates have been isolated, which included two 1-S-S, two 2-S-S, and two 3-S-S scrambled species. Their disulfide structures have been identified here. Both 1-S-S isomers are found to contain non-native disulfides. One of the 2-S-S species consists of two non-native disulfides and the other admits two native disulfides. Among the six disulfides of the two scrambled species, only one is native. Together, native disulfides constitute 25% of the total disulfides found in these six well populated intermediates. These results contrast sharply to those observed with bovine pancreatic trypsin inhibitor, which has shown that well populated folding intermediates consist of exclusively native disulfides (Weissman, J. S., and Kim, P. S. (1991) Science 253, 1386-1393). We propose that well populated folding intermediates, regardless of whether they contain native or non-native disulfides, do not necessarily represent the productive species and specify the folding pathway. Furthermore, conditions influencing the efficiency of EGF folding have been investigated. It is demonstrated here that under optimized compositions of redox agents, including the use of cysteine/cystine and protein disulfide isomerase, the in vitro folding of EGF could be achieved quantitatively within 1 min.
Requirement of poly(ADP-ribose) polymerase in recovery from DNA damage in mice and in cells.

Poly(ADP-ribose) polymerase [PARP; NAD+ ADP-ribosyltransferase; NAD+: poly(adenosine-diphosphate-D-ribosyl)-acceptor ADP-D-ribosyltransferase, EC 2.4. 2.30] is a zinc-finger DNA-binding protein that detects specifically DNA strand breaks generated by genotoxic agents. To determine its biological function, we have inactivated both alleles by gene targeting in mice. Treatment of PARP-/- mice either by the alkylating agent N-methyl-N-nitrosourea (MNU) or by gamma-irradiation revealed an extreme sensitivity and a high genomic instability to both agents. Following whole body gamma-irradiation (8 Gy) mutant mice died rapidly from acute radiation toxicity to the small intestine. Mice-derived PARP-/- cells displayed a high sensitivity to MNU exposure: a G2/M arrest in mouse embryonic fibroblasts and a rapid apoptotic response and a p53 accumulation were observed in splenocytes. Altogether these results demonstrate that PARP is a survival factor playing an essential and positive role during DNA damage recovery.
Light intensity modulates the regulatory network of the shade avoidance response in Arabidopsis

Significance Plants sense foliar shade and neighbors who may become competitors for light. Shade-sensitive species elongate in response to both situations to enhance access to unfiltered sunlight, which is known as the shade avoidance response (SAR). During neighbor detection, plants have access to plenty of light (energy resources), whereas in true shade, light resources are scarce. Our analysis of the molecular mechanisms underlying SAR under these contrasting conditions shows that light intensity balances the production and sensitivity of the growth hormone auxin. In foliar shade, the production of auxin is reduced, whereas the downstream sensitivity to the auxin signal is enhanced. This hints at a resource-aware signaling where the strength of the hormonal signal is tuned to the available resources. Plants such as Arabidopsis thaliana respond to foliar shade and neighbors who may become competitors for light resources by elongation growth to secure access to unfiltered sunlight. Challenges faced during this shade avoidance response (SAR) are different under a light-absorbing canopy and during neighbor detection where light remains abundant. In both situations, elongation growth depends on auxin and transcription factors of the phytochrome interacting factor (PIF) class. Using a computational modeling approach to study the SAR regulatory network, we identify and experimentally validate a previously unidentified role for long hypocotyl in far red 1, a negative regulator of the PIFs. Moreover, we find that during neighbor detection, growth is promoted primarily by the production of auxin. In contrast, in true shade, the system operates with less auxin but with an increased sensitivity to the hormonal signal. Our data suggest that this latter signal is less robust, which may reflect a cost-to-robustness tradeoff, a system trait long recognized by engineers and forming the basis of information theory.
Efficient use of a small genome to generate antigenic diversity in tick-borne ehrlichial pathogens

Ehrlichiae are responsible for important tick-transmitted diseases, including anaplasmosis, the most prevalent tick-borne infection of livestock worldwide, and the emerging human diseases monocytic and granulocytic ehrlichiosis. Antigenic variation of major surface proteins is a key feature of these pathogens that allows persistence in the mammalian host, a requisite for subsequent tick transmission. In Anaplasma marginale pseudogenes for two antigenically variable gene families, msp2 and msp3, appear in concert. These pseudogenes can be recombined into the functional expression site to generate new antigenic variants. Coordinated control of the recombination of these genes would allow these two gene families to act synergistically to evade the host immune response.
Incidence and risk factors for the development of chronic atrophic gastritis: Five year follow‐up of a population‐based cohort study

Chronic atrophic gastritis (CAG) is a well‐established precursor of intestinal gastric cancer. However, data on incidence of CAG are rare, especially from population‐based studies. The aim of this analysis was to estimate the incidence of CAG in a large population‐based study among older adults from Germany and to identify major risk factors associated with its development. In the baseline and 5‐year follow‐up examinations of the ESTHER study, serological measurements of pepsinogen (PG) I and II and Helicobacter pylori antibodies were performed in 5,229 women and men, aged 50–74 years at baseline. Information on additional potential risk factors was obtained by questionnaire. CAG was defined by PGI < 70 ng/mL and PGI/PGII < 3. In total, there were 58 (1.1%) incident CAG cases. CAG incidence increased with increasing age from 0.5% in age group 50–54 years to 2.1% in age group 70–74 years. Seropositivity with H. pylori was strongly associated with CAG incidence, with adjusted odds ratios of 5.0 [95% confidence interval (CI): 1.6–15.8] and 11.3 (95% CI: 4.2–30.0) for participants with cytotoxin associated gene A (cagA) negative and cagA positive H. pylori infection at both baseline and follow‐up compared to those without H. pylori infection, respectively. Gender, education, smoking, alcohol consumption and family history of gastric cancer were not significantly associated with CAG incidence. Incidence of CAG is rather low in the German population. Older age and infection with H. pylori are key risk factors for the development of CAG.
Efficient 2D approximation for Layout-dependent Relaxation of Etch Stop Liner Stress due to Contact Holes

Stress engineering to enhance device performance has become widespread. One way is to apply an etch stop liner with intrinsic stress, which causes stress and thus changed mobility in the channel of the device. Etching contact holes reduces this stress. Investigating the dependence of the channel stress on the position of the contact holes is a genuine 3D problem. Here we describe a method to determine the width-averaged channel stress by a much more efficient 2D simulation