Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of the anti-citrullinated protein antibody repertoire prior to the onset of rheumatoid arthritis.

OBJECTIVE To examine how anti-citrullinated protein antibody (ACPA) epitope spreading takes place prior to the onset of clinical rheumatoid arthritis (RA), and to analyze the pattern of autoantigen reactivity at the beginning of the immune response. METHODS Multiple consecutive serum samples from 79 RA patients who had donated blood before disease onset were available for analysis. Fifty-three patients tested positive for ACPAs prior to the onset of clinical RA. For these patients, a median of 6 (interquartile range 4-9) sequential pre-RA serum samples obtained 1-2 years apart were tested. Reactivity to 5 distinct citrullinated peptides was measured by enzyme-linked immunosorbent assay. Two peptides were derived from fibrinogen, 1 from vimentin, 1 from α-enolase, and 1 from filaggrin. RESULTS In 25 of 53 ACPA-positive patients, seroconversion from ACPA absence to ACPA presence was observed. In 72% of these patients, the immune response started with reactivity to 1 peptide, without preference for a particular peptide. The number of peptides recognized increased over time, without a dominant epitope-spreading pattern. ACPAs appeared in low levels several years prior to the diagnosis of RA. Antibody titers increased markedly ∼2-4 years before diagnosis. CONCLUSION Our findings indicate that ACPA epitope spreading occurs over several years prior to the onset of clinical RA. The initial autoimmune response is mostly directed toward only 1 autoantigen, but this is not always the same antigen. The marked increase in ACPA titers a few years prior to the diagnosis of RA suggests a second stage in disease development, which might be due to a variety of factors.
Purification of Glycogen Phosphorylase from Bovine Brain and Immunocytochemical Examination of Rat Glial Primary Cultures Using Monoclonal Antibodies Raised Against This Enzyme

Abstract: The physiological function in brain of glycogen and the enzyme catalyzing the rate‐limiting step in glycogenolysis, glycogen phosphorylase (EC 2.4.1.1), is unknown. As a first step toward elucidating such a function, we have purified bovine brain glycogen phosphorylase isozyme BB 1,700‐fold to a specific activity of 24 units/mg protein. When analyzed by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and subsequent silver staining, a single major protein band corresponding to an apparent molecular mass of 97 kDa was observed. Mouse monoclonal antibodies raised against the enzyme were purified and shown to be monospecific as indicated by immunoblotting. Immunocytochemical examination of astroglia‐rich primary cultures of rat brain cells revealed a colocalization of glycogen phosphorylase with the astroglial marker glial fibrillary acidic protein in many cells. The staining for the enzyme appeared at two levels of intensity. There were other cells in the culture showing no specific staining under the experimental conditions employed. Neurons in neuron‐rich primary cultures did not show positive staining. The data suggest that glycogen phosphorylase may be predominantly an astroglial enzyme and that astroglia cells play an important role in the energy metabolism of the brain.
Agricultural Awareness Days: Integrating Agricultural Partnerships and STEM Education

In the United States there is a need to educate young children in science, technology, and agriculture. Through collaboration with many agricultural groups, the Southern Piedmont Agricultural Research and Education Center has set up a program that works with 3rd grade students and teachers to reinforce the science that has been taught in the classroom in a hands-on environment. This program has grown in size and scope over the years that it has been in place, but the partnerships that come together from Extension, Virginia Tech, USDA, and many others is what makes this program such a success.
Selective targeting of radiation-resistant tumor-initiating cells

Tumor-initiating cells (TICs) have been shown both experimentally and clinically to be resistant to radiation and chemotherapy, potentially resulting in residual disease that can lead to recurrence. In this study, we demonstrate that TICs isolated from p53 null mouse mammary tumors repair DNA damage following in vivo ionizing radiation more efficiently than the bulk of the tumor cells. Down-regulation of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) was observed both in fluorescence activated cell sorting (FACS)-isolated TICs as compared to non-TICs and in TIC-enriched mammospheres as compared to primary tumor cells depleted of TICs. This effect was accompanied by increased Akt signaling, as well as by the direct activation of the canonical Wnt/β-catenin signaling pathway specifically within the TIC subpopulation by phosphorylation of β-catenin on serine 552. Using limiting dilution transplantation performed on p53 null tumor cells transduced with Wnt reporter lentivirus, we demonstrated that FACS sorting of cells expressing TOP-eGFP resulted in a marked enrichment for TICs. Furthermore, FACS analysis demonstrated that cells with active Wnt signaling overlapped with the TIC subpopulation characterized previously using cell surface markers. Finally, pharmacological inhibition of the Akt pathway in both mammospheres and syngeneic mice bearing tumors was shown to inhibit canonical Wnt signaling as well as the repair of DNA damage selectively in TICs, sensitizing them to ionizing radiation treatment. Thus, these results suggest that pretreatment with Akt inhibitors before ionizing radiation treatment may be of potential therapeutic benefit to patients.
The anomalous-stemmed species of Heteropterys subsect. Aptychia (Malpighiaceae)

Species of the anomalous-stemmed complex ofHeteropterys are revised after intensive fieldwork in eastern Brazil.Heteropterys patens (=H. anomala) is redefined, and three new species are described (H. admirabilis, H. imperata, andH. nordestina). In addition, this treatment provides brief synonymy, lectotypifications, illustrations, and comments for those four species, and a key to all taxa of the complex. ResumenEspécies do complexo de ramos anômalos deHeteropterys são revisadas com base em coleções atualmente disponíveis e em intensivo trabalho de campo realizado no leste do Brasil.Heteropterys patens (=H. anomala) é redefinida e três novas espécies são descritas (H. admirabilis, H. imperata, eH. nordestina). Em adição, esse tratamento providencia breves sinônimos, lectotipificações, ilustrações e comentários para essas quatro espécies e uma chave analítica para todos os taxa do complexo.
Cellular Factors Binding to a Novel cis-Acting Element Mediate Steroid Hormone Responsiveness of Mouse Mammary Tumor Virus Promoter (*)

Steroid hormone receptors regulate mouse mammary tumor virus (MMTV) gene expression by binding to hormone response DNA elements present in the long terminal repeat. Tissue-specific expression of MMTV is unlikely to be regulated by steroid hormone-receptor complex alone, and mammary cell-specific factors might play a role in the hormone-induced transcriptional activation. In this report we have investigated the function of a novel cis-acting element designated Kil (−204 to −188) which is located adjacent to the distal glucocorticoid response element, in steroid hormone-induced transcription of MMTV. Electrophoretic mobility shift assays indicate that cellular factors bind to the Kil element, and dexamethasone stimulation results in alterations in the binding pattern of proteins in this region. By transient transfection assays using wild type and deletion mutants of the Kil element, we show that this novel cis-acting element is necessary for hormone-induced transcription of MMTV and functions in mammary tumor cells but not in NIH/3T3 cells. Mutagenesis of the Kil sequence suggests that the entire Kil element functioning as one unit is necessary for hormone-induced transcription of MMTV. When placed in the context of heterologous promoters, neither Kil element nor glucocorticoid response element is able to induce significant hormone-induced transcription of MMTV. The presence of both the DNA elements in tandem results in optimal induction of transcription in the presence of steroid hormones. Our results also indicate that the Kil element functions in human breast carcinoma cell lines such as T47D and MCF-7. These results suggest that Kil element in combination with distal glucocorticoid response element functions as a mammary cell-specific enhancer to regulate MMTV transcription.
Establishment of an Osteoid Preosteocyte‐like Cell MLO‐A5 That Spontaneously Mineralizes in Culture

The mechanisms controlling the initiation of mineralization of bone matrix are not clear. To examine this process, we established a cell line called MLO‐A5 that mineralizes in sheets, not nodules, within 3 days of culture in the presence of β‐glycerophosphate (β‐GP) and ascorbic acid and within 7 days in the absence of β‐GP and ascorbic acid. The mineral formed in both cases was shown to be bonelike apatite by Fourier transformed infrared (FTIR) spectroscopy. Mineral‐to‐matrix ratios (min/matrix) calculated from the FTIR data, which are related directly to ash weight, were approximately 0.4 in the absence of β‐GP and ascorbic acid and approximately 1.2 in the presence of β‐GP and ascorbic acid. By comparison, these ratios in fetal rat calvarial cells without β‐GP equal 0 and with β‐GP 1.9. This cell line and three others (MLO‐A2, −D1, and −D6) were isolated from the long bones of transgenic mice expressing the large T‐antigen driven by the osteocalcin promoter, the same mice from which the osteocyte‐like cell line MLO‐Y4 was isolated. (1) The cell lines were selected based on a dendritic or stellate morphology. MLO‐A5 cells express high alkaline phosphatase, collagen type 1, parathyroid hormone/parathyroid hormone‐related peptide (PTH/PTHrP) receptor, bone sialoprotein (BSP), and osteocalcin (767 ng/106 cells compared with <1–2.2 ng/106 cell for primary mouse osteoblasts and five osteoblast cell lines). The single unique feature of the MLO‐A5 cells compared with the other three nonmineralizing cell lines is the high expression of messenger RNA (mRNA) for BSP. These cell lines may represent stages of osteocyte differentiation and the MLO‐A5 cells represent the postosteoblast, preosteocyte responsible for triggering mineralization of osteoid.
Kinetic analysis of pausing and fidelity of human immunodeficiency virus type 1 reverse transcription.

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase catalyzes DNA synthesis from RNA and DNA templates by a sequential mechanism. This enzyme is neither processive nor distributive but has a rather intermediate behavior; at any template position, there is a certain probability that the replica strand will be extended, which we define as extensibility. The extensibility depends on the substrate concentration, i.e. on the concentration of the cognate (and to a smaller extent of the noncognate) deoxynucleoside triphosphates, in a typical Michaelis-Menten mode. The extensibility varies from position to position in a sequence-dependent manner, being particularly low at certain sites, accordingly called pause sites. The rate and fidelity of successive incorporation of nucleotides were measured and then compared with numerical integrations of the pertinent rate equations, which were composed to describe a suitable reaction mechanism and parameterized starting starting with rate constants reported in the literature. We found that agreement between stimulation and experiment requires two-step binding of enzyme to the template-primer. In an initial second-order step, an "outer" binary complex is rapidly formed; this is followed by a slower conformational change into an "inner" complex. During multiple rounds of nucleotide incorporation, the complex remains in the inner form; the rate-determining step for enzyme release is the reversion from the inner to the outer complex, with a standard rate constant of 0.2s-1. This rate constant may be significantly increased at pause sites. In order to match the experimental results, the standard rate constants had to be modified for pause sites. At low concentrations or in the absence of the cognate nucleotide, the site-specific misinsertion frequency, a function of the nucleotide pool is bias and of the efficiency to discriminate against a noncognate nucleotide, can be determined from the dependence of extensibility on concentration of cognate and noncognate substrates. The error frequency was found to be somewhat smaller than the misinsertion frequency, because mismatches are extended less efficiently than matched pairs.
Facial diagnosis of mild and variant CdLS: Insights from a dysmorphologist survey

Cornelia de Lange syndrome (CdLS) is a dominant disorder with classic severe forms and milder atypical variants. Central to making the diagnosis is identification of diagnostic facial features. With the recognition that patients with SMC1A and SMC3 mutations have milder, atypical features, we surveyed 65 dysmorphologists using facial photographs from 32 CdLS patients with the goals of (1) Illustrating examples of milder patients with SMC1A mutations and (2) Obtaining objective data to determine which facial features were useful and misleading in making a diagnosis of CdLS. Clinicians were surveyed whether the patient had CdLS or another diagnosis, the certainty of response and the clinical features used to support each response. Using only facial photographs, an average of 24 cases (75%) were accurately diagnosed per clinician. Correct diagnoses were made in 90% of classic CdLS and 87% of non‐CdLS cases, however, only 54% of mild or variant CdLS were correctly diagnosed by respondents. We confirmed that CdLS is most accurately diagnosed in childhood and the diagnosis becomes increasingly difficult with age. This survey demonstrated that emphasis is placed on the eyebrows, nasal features, prominent upper lip and micrognathia. In addition, the presence of fuller, atypical eyebrows, a prominent nasal bridge and significant prognathism with age dissuaded survey takers from arriving at a diagnosis of CdLS in individuals with mild NIPBL and SMC1A mutations. This work underscores the difficulty in diagnosing patients with mild and variant CdLS and serves to objectively classify both useful and misleading features in the diagnosis of CdLS. © 2010 Wiley‐Liss, Inc.
Proactive Recruitment of Frontoparietal and Salience Networks for Voluntary Decisions

There is evidence that neural patterns are predictive of voluntary decisions, but findings come from paradigms that have typically required participants to make arbitrary choices decisions in highly abstract experimental tasks. It remains to be seen whether proactive neural activity reflects upcoming choices for individuals performing decisions in more complex, dynamic, scenarios. In this functional Magnetic Resonance Imaging (fMRI) study, we investigated proactive neural activity for voluntary decisions compared with instructed decisions in a virtual environment, which more closely mimicked a real-world decision. Using partial least squares (PLS) analysis, we found that the frontoparietal and salience networks were associated with voluntary choice selection from a time at which decisions were abstract and preceded external stimuli. Using multi-voxel pattern analysis (MVPA), we showed that participants’ choices, which were decodable from motor and visual cortices, could be predicted with lower accuracy for voluntary decisions than for instructed decisions. This corresponded to eye-tracking data showing that participants made a greater number of fixations to alternative options during voluntary choices, which might have resulted in less stable choice representations. These findings suggest that voluntary decisions engage proactive choice selection, and that upcoming choices are encoded in neural representations even while individuals continue to consider their options in the environment.
Prostaglandin D2 Synthase Inhibits the Exaggerated Growth Phenotype of Spontaneously Hypertensive Rat Vascular Smooth Muscle Cells*

Lipocalin-type prostaglandin D2 synthase (L-PGDS) has recently been linked to a variety of pathophysiological cardiovascular conditions including hypertension and diabetes. In this study, we report on the 50% increase in L-PGDS protein expression observed in vascular smooth muscle cells (VSMC) isolated from spontaneously hypertensive rats (SHR). L-PGDS expression also increased 50% upon the differentiation of normotensive control cells (WKY, from Wistar-Kyoto rats). In addition, we demonstrate differential effects of L-PGDS treatment on cell proliferation and apoptosis in VSMCs isolated from SHR versus WKY controls. L-PGDS (50 μg/ml) was able to significantly inhibit VSMC proliferation and DNA synthesis and induce the apoptotic genes bax, bcl-x, and ei24 in SHR but had no effect on WKY cells. Hyperglycemic conditions also had opposite effects, in which increased glucose concentrations (20 mm) resulted in decreased L-PGDS expression in control cells but actually stimulated L-PGDS expression in SHR. Furthermore, we examined the effect of L-PGDS incubation on insulin-stimulated Akt, glycogen synthase kinase-3β (GSK-3β), and ERK phosphorylation. Unexpectedly, we found that when WKY cells were pretreated with L-PGDS, insulin could actually induce apoptosis and failed to stimulate Akt/GSK-3β phosphorylation. Insulin-stimulated ERK phosphorylation was unaffected by L-PGDS pretreatment in both cell lines. We propose that L-PGDS is involved in the balance of VSMC proliferation and apoptosis and in the increased expression observed in the hypertensive state is an attempt to maintain a proper equilibrium between the two processes via the induction of apoptosis and inhibition of cell proliferation.
Arabic/English word translation disambiguation approach based on naive Bayesian classifier

We present a word sense disambiguation approach with application in machine translation from Arabic to English. The approach consists of two main steps: First, a natural language processing method that deals with the rich morphology of Arabic language and second, the translation including word sense disambiguation. The main innovative features of this approach are the adaptation of the Naive Bayesian approach with new features to consider the Arabic language properties and the exploitation of a large parallel corpus to find the correct sense based on its cohesion with words in the training corpus. We expect that the resulting system will overcome the problem of the absence of the vowel signs, which is the main reason for the translation ambiguity between Arabic and other languages.
Elevated C-reactive protein associates with early-stage carotid atherosclerosis in young subjects with type 1 diabetes.

OBJECTIVE To evaluate whether low-grade inflammation contributes to early-stage advanced carotid atherosclerosis in young subjects with type 1 diabetes. RESEARCH DESIGN AND METHODS The mean and maximum (max) intima-media thicknesses (IMT) of the carotid artery were assessed using ultrasound B-mode imaging in 55 patients with type 1 diabetes (22 men and 33 women, aged 22.1 +/- 3.6 years (+/- SD), duration of diabetes 14.2 +/- 5.7 years) and 75 age-matched healthy nondiabetic subjects (28 men and 47 women). High-sensitive C-reactive protein (hs-CRP) levels were measured with a latex-enhanced immunonephelometer. RESULTS The patients with type 1 diabetes had significantly higher hs-CRP levels (median 0.35, range 0.05-1.47 mg/l vs. median 0.14, range 0.05-1.44 mg/l; P = 0.001) as well as significantly higher mean IMT and max IMT than the nondiabetic subjects (mean IMT 0.76 +/- 0.09 vs. 0.72 +/- 0.04 mm, P = 0.003; max IMT 0.84 +/- 0.11 vs. 0.77 +/- 0.06 mm, P < 0.0001). Hs-CRP levels were significantly correlated with the mean and max IMT of patients with type 1 diabetes and with the max IMT of nondiabetic patients. Multivariate regression analyses for both diabetic and nondiabetic subjects as a single group showed that hs-CRP levels are independently correlated with the mean IMT and max IMT levels (P = 0.002 and P = 0.023, respectively) as well as with diastolic blood pressure, sex, and duration of diabetes. CONCLUSIONS Our data indicate that hs-CRP levels are elevated in young patients with type 1 diabetes, possibly corresponding with early-stage advanced carotid atherosclerosis.
Changes in miniature end‐plate potentials due to moderate hypertonicity at the frog neuromuscular junction.

The effect of an increase in tonicity on the amplitude and frequency of miniature end‐plate potentials (m.e.p.p.s) following superfusion of 50 mM‐ or 100 mM‐sucrose‐Ringer solution was determined from intracellular recording at end‐plates of the frog cutaneous pectoris muscle, in the absence of drugs and using on‐line statistical analysis. An immediate decrease in mean amplitude of the order of 20% control was associated with a marked increase in mean frequency. A delayed increase in mean amplitude, independent of frequency, followed the initial response in the majority of end‐plates exposed to 100 mM‐sucrose‐Ringer solution. The net gain was of the order of 34% and was attained over 20‐40 min. This was not reversible over at least 20 min. There was an increase in the variability of m.e. p.p. amplitudes associated with the increase of mean amplitude but this was reversible. A moderate increase in tonicity is considered to induce two kinds of presynaptic changes. First, an immediate increase in the probability of release of smaller quantal packets and secondly, an increased loading of transmitter into vesicles within the readily releasable store.
Cardiac dysfunction associated with trastuzumab

The HER2/neu gene is amplified in ∼ 25% of breast cancers, leading to HER2 protein overexpression and shortened overall survival and time to relapse. Trastuzumab is a humanised, monoclonal antibody against HER2, which improves survival for women with metastatic HER2-overexpressing breast cancer and reduces the risk of recurrence in women with early stage HER2-overexpressing breast cancer. Cardiac toxicity was an unexpected finding in the pivotal Phase III trial leading to the approval of trastuzumab, and prospective cardiac monitoring has, therefore, been incorporated into more recent clinical trials of trastuzumab. This article reviews the cardiac toxicity findings in key trastuzumab clinical trials and clinical characteristics of trastuzumab-associated cardiac toxicity.
The improvement of signal-to-noise ratio by solid-state nanopores using a salt gradient

Solid-state nanopore is widely used as detector to analyze individual unlabeled DNA molecules in solutions. The small scale of nanopore(d<;5nm) is of the capability to obtain high signal-to-noise ratio information, but its most drawback is that this kind of nanopore is easily blocked during the molecules thread into the pore. At the same time, it is extremely difficult to be manufactured. Although the large diameter nanopore is not easily blocked and the fabricating cost is less, it is also hard to achieve efficient signal. In this paper, we find a solution which can enhance the signal-to-noise ratio for large scale nanopores-when the cis reservoir concentration is fixed at 1 M KCl, amplitude of the ionic current decrease is significantly enhanced with the trans reservoir concentration changing from 1 M KCl to 0.1 M KCl. So it is efficient to distinguish different kind of molecules and enhance the signal-to-noise ratio, thereby advancing the possibility of analyzing DNA samples using nanopores.