Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of prolonged exposure to low dose metformin in thyroid cancer cell lines

Background: Thyroid cancer is generally associated with an excellent prognosis, but there is significant long-term morbidity with standard treatment. Some sub-types however have a poor prognosis. Metformin, an oral anti-diabetic drug is shown to have anti-cancer effects in several types of cancer (breast, lung and ovarian cancer). The proposed mechanisms include activation of the Adenosine Mono-phosphate-activated Protein Kinase (AMPK) pathway and inhibition of the mTOR pathway (which promotes growth and proliferation). By inhibiting hepatic gluconeogenesis and increasing glucose uptake by muscles, metformin decreases blood glucose and circulating Insulin levels. Aims: Explore the effect of metformin on the growth and proliferation of thyroid cancer cell lines. Methods: The effects of metformin on thyroid cancer cell lines (FTC-133, K1E7, RO82-W-1, 8305C and TT) and normal thyroid follicular cells (Nthy-ori 3-1) were investigated using the MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay for cell proliferation; clonogenic assays; FACS analysis for apoptosis and cell cycle, H2A.X phosphorylation (γH2AX) assay for DNA repair and scratch assay for cell migration. Results: Metformin inhibited cell proliferation and colony formation at 0.03 mM and above and inhibited cell migration at 0.3 mM. At concentrations of 0.1 mM and above metformin increased the percentage of apoptotic cells and induced cell cycle arrest in G0/G1 phase at minimum concentration of 0.3 mM. Unlike previous reports, no effect on DNA repair response was demonstrated. Conclusion: Metformin suppressed growth of all thyroid cancer cell lines, at concentrations considered to be within in the therapeutic range for diabetic patients on metformin (<0.3 mM).
CONVERSION OF EXPOSED ASPARTYL AND GLUTAMYL RESIDUES IN PROTEINS TO ASPARAGINYL AND GLUTAMINYL RESIDUES

I. The feasibility of converting exposed carboxyl groups in proteins to carboxamido groups using I-ethyl-3-dimethylaminopropylcarbodiimide (EDC) as a condensing agent was demonstrated. 2. The effectiveness of ammonia as a nucleophile in the EDC-mediated condensation with carboxyl groups in proteins was determined. In 5.5 M NH4C1 at pH 4.75, 11.5, 14.7, 9 . o, 5.o and 5.1 carboxyl groups are converted to carboxamido groups in chymotrypsinogen A, a-chymotrypsin (EC 3-4.4-5), lysozyme (EC 3.2.1.17) , ribonuclease (EC 2.7.7.16 ) and trypsin (EC 3.4.4.4), respectively. 3. The number of carboxamido groups found was determined from the amount of extra ammonia appearing in acid-hydrolyzed protein which was reacted with EDC and NH4C1. In one case, tile number of fland ~-carboxamido groups formed was also determined enzymically by digesting treated protein with proleolytic enzymes and then enzymically assaying the digest for free asparagine and glutamine. Both acid hydrolysis and enzymatic assays gave essentially the same value for the yield of carboxamido groups. 4. 5.5 M NH~C1, I M glycine methylester, and I M glycinamide were all equally effective in modifying carboxyl groups. Since previous studies showed that the glycine derivatives quanti tat ively modify exposed carboxyl groups in proteins, it was concluded that NH4C1 may be used to quanti tat ively convert exposed carboxyl groups in proteins to carboxamido groups. Now that it is possible to convert aspartyl and glutamyl residues in proteins to asparaginyl and glutaminyl residues, it should be possible to establish with greater certainty the role of carboxyl groups in the function and structure of proteins.
γ-Cyclodextrin–folate complex-functionalized quantum dots for tumor-targeting and site-specific labeling

Quantum dots (QDs) encapsulated with high affinity ligands, specifically binding organic ligands, such as antibodies, peptides or small molecules, have been used in intracellular imaging and targeting. In this work, a series of folate-receptor targeted QDs, in which tumor-targeting folic acid (FA) was conjugated to the surface of QDs through cell-penetrated γ-cyclodextrin (γ-CD), was synthesized. The QDs showed good optical properties and biocompatibility, such as strong optical emission, long luminescent lifetime, appropriate size (4–5 nm in diameter), and lower toxicity. In particular, the γ-CD–FA-coated CdSe–ZnSe QDs presented lower cytotoxicity to these cells at higher IC50 concentrations of above 200 μg mL−1 for 48 h. Folate-receptor overexpressed FR(+) and folate-receptor deficient FR(−) cells were incubated with folate-receptor targeted γ-CD–FA-coated QDs and non-targeted L-Cys-β-CD-coated QDs in vitro. It was found that folate-receptor targeted QDs could more effectively recognize cancer cells with folate receptor (FR) over-expression compared to non-targeted QDs by flow cytometry and confocal laser scanning microscopy (CLSM). Confirming the specificity of folate-receptor targeted QDs, binding and internalization were inhibited by free folate, and hardly any uptake was found in FR(+) cells. Inside the cells, the γ-CD–FA-functionalized QDs are mostly distributed within lysosomes. These properties not only offer insights into the mechanism of the functionalized QDs delivery but also will guide the design and development of nanoparticle probes for intracellular imaging and targeting applications.
A case study in test management

Testing is an essential but often under-utilized area of software engineering. A variety of software testing techniques have been developed to effectively identify bugs in source code, yet these techniques are not always fully employed in practice. There are numerous reasons for this, including the difficulty in mastering the complexity of managing all of the test cases for large-scale projects. Test case management involves organizing testing artifacts (e.g., requirements traceability data, test cases, and expected results) in a systematic manner. To be successful, test case management requires a high degree of discipline to accommodate the large volume of artifacts under consideration. This paper presents the results of a case study in centralizing test artifacts in an industrial setting to aid better test management. Several of the challenges in adopting this approach are discussed. In response to these challenges, recommendations on how to better leverage test case management are offered.
Comparison of Power Versus Manual Injection in Bolus Shape and Image Quality on Contrast-Enhanced Magnetic Resonance Angiography: An Experimental Study in a Swine Model

Objective The aim of this study was to compare power versus manual injection in bolus shape and image quality on contrast-enhanced magnetic resonance angiography (CE-MRA). Materials and Methods Three types of CE-MRA (head-neck 3-dimensional [3D] MRA with a test-bolus technique, thoracic-abdominal 3D MRA with a bolus-tracking technique, and thoracic-abdominal time-resolved 4-dimensional [4D] MRA) were performed after power and manual injection of gadobutrol (0.1 mmol/kg) at 2 mL/s in 12 pigs (6 sets of power and manual injections for each type of CE-MRA). For the quantitative analysis, the signal-to-noise ratio was measured on ascending aorta, descending aorta, brachiocephalic trunk, common carotid artery, and external carotid artery on the 6 sets of head-neck 3D MRA, and on ascending aorta, descending aorta, brachiocephalic trunk, abdominal aorta, celiac trunk, and renal artery on the 6 sets of thoracic-abdominal 3D MRA. Bolus shapes were evaluated on the 6 sets each of test-bolus scans and 4D MRA. For the qualitative analysis, arterial enhancement, superimposition of nontargeted enhancement, and overall image quality were evaluated on 3D MRA. Visibility of bolus transition was assessed on 4D MRA. Intraindividual comparison between power and manual injection was made by paired t test, Wilcoxon rank sum test, and analysis of variance by ranks. Results Signal-to-noise ratio on 3D MRA was statistically higher with power injection than with manual injection (P < 0.001). Bolus shapes (test-bolus, 4D MRA) were represented by a characteristic standard bolus curve (sharp first-pass peak followed by a gentle recirculation peak) in all the 12 scans with power injection, but only in 1 of the 12 scans with manual injection. Standard deviations of time-to-peak enhancement were smaller in power injection than in manual injection. Qualitatively, although both injection methods achieved diagnostic quality on 3D MRA, power injection exhibited significantly higher image quality than manual injection (P = 0.001) due to significantly higher arterial enhancement (P = 0.031) and less superimposition of nontargeted enhancement (P = 0.001). Visibility of bolus transition on 4D MRA was significantly better with power injection than with manual injection (P = 0.031). Conclusions Compared with manual injection, power injection provides more standardized bolus shapes and higher image quality due to higher arterial enhancement and less superimposition of nontargeted vessels.
Clinical activity of rituximab in gastric marginal zone non-Hodgkin's lymphoma resistant to or not eligible for anti-Helicobacter pylori therapy.

PURPOSE Preliminary results using rituximab in extranodal marginal zone (MALT) non-Hodgkin's lymphoma (NHL) patients seem to indicate a relevant clinical activity. Aim of the present study is to investigate the efficacy of conventional weekly treatment using rituximab in gastric MALT NHL patients resistant/refractory or not suitable for eradication treatment, and to evaluate the relevance of the t(11; 18)(q21; q21) translocation and its possible role as a predictive criteria of response. PATIENTS AND METHODS Twenty-seven patients presenting with gastric MALT NHL at any stage, relapsed/refractory to initial treatment or not suitable for eradication were treated with rituximab in a weekly conventional schedule and evaluated for response and relapse. Flourescence in situ hybridization (FISH) analysis for the presence of 18q21 translocation was performed in 21 patients and was evaluated with clinical outcome. RESULTS Among the 26 evaluated patients, 20 (77%) achieved an objective response. Twelve patients (46%) had a pathological and clinical complete remission, and eight (31%) had a partial response. With a median follow-up of 33 months, only two patients relapsed at 26 and 14 months, respectively. No correlation was founded between FISH analysis and response or relapse. CONCLUSION Our experience seems to confirm the clinical activity of rituximab in gastric MALT NHL patients resistant/refractory to antibiotics treatment or not presenting with clinical evidence of Helicobacter pylori infection. The t(11; 18)(q21; q21) translocation seems not to be a predictive marker to response or to subsequent relapse.
University of Pennsylvania ScholarlyCommons Center for Human Modeling and Simulation Department of Computer & Information Science June 1994 Model-based Analysis of Cardiac Motion from Tagged MRI Data

We develop a new method for analyzing the motion of the left ventricle (LV) of a heart from tagged MRI data. Our technique is based on the development of a new class of physics-based deformable models whose parameters are functions allowing the definition of new parameterized primitives and parameterized deformations. These parameter functions improve the accuracy of shape description through the use of a few intuitive parameters such as functional twisting. Furthermore, these parameters require no complex postprocessing in order to be used by a physician. Using a physics-based approach, we convert these geometric models into deformable models that deform due to forces exerted from the datapoints and conform to the given dataset. We present experiments involving the extraction of shape and motion of the LV from MRISPAMM data based on a few parameter functions. Furthermore, by plotting the variations over time of the extracted model parameters from normal and abnormal heart data we are able to characterize quantitatively their differences. Comments Copyright 1994 IEEE. Reprinted from Proceedings of the IEEE Seventh Symposium Computer-Based Medical Systems, July 1994 pages 40-45. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of the University of Pennsylvania's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to pubs-permissions@ieee.org. By choosing to view this document, you agree to all provisions of the copyright laws protecting it. This conference paper is available at ScholarlyCommons: http://repository.upenn. edu/hms/105 Model-based Analysis of Cardiac Motion from Tagged MRI Data Jinah Park’, Dimitri Metaxas’, Alistair Young2 and Leon Axel2 ‘Department of Computer & Information Science University of Pennsylvania Philadelphia PA 19 104-6389 *Department of Radiology University of Pennsylvania Philadelphia PA 19104
Multiple harmonics control of single-phase PWM rectifiers

This paper proposes a multi-resonant control (MRSC) scheme for PWM rectifiers to eliminate selective current harmonics distortion. Phase compensation enables MRSC to include more resonant components to yield better power quality current. Experiment results of a single-phase PWM rectifier are provided to demonstrate the effectiveness of proposed MRSC method.
Screening for Insulitis in Adult Autoantibody-Positive Organ Donors

Antibodies against islet cell antigens are used as predictive markers of type 1 diabetes, but it is unknown whether they reflect an ongoing autoimmune process in islet tissue. We investigated whether organs from adult donors that are positive for autoantibodies (aAbs) against islet cell antigens exhibit insulitis and/or a reduced β-cell mass. Serum from 1,507 organ donors (age 25–60 years) was analyzed for islet cell antibodies (ICAs), glutamate decarboxylase aAbs (GADAs), insulinoma-associated protein 2 aAbs (IA-2As), and insulin aAbs. Tissue from the 62 aAb+ donors (4.1%) and from matched controls was examined for the presence of insulitis and for the relative area of insulin+ cells. Insulitis was detected in two cases; it was found in 3 and 9% of the islets and consisted of CD3+/CD8+ T-cells and CD68+ macrophages; in one case, it was associated with insulin+ cells that expressed the proliferation marker Ki67. Both subjects belonged to the subgroup of three donors with positivity for ICA, GADA, and IA-2-Ab and for the susceptible HLA-DQ genotype. Comparison of relative β-cell area in aAb+ and aAb− donors did not show a significant difference. Insulitis was found in two of the three cases that presented at least three aAbs but in none of the other 59 antibody+ subjects or 62 matched controls. It was only detected in <10% of the islets, some of which presented signs of β-cell proliferation. No decrease in β-cell mass was detected in cases with insulitis or in the group of antibody+ subjects.
VICO: a tool for supporting visual comparisons of different pine-beetle management approaches

In this paper a visual tool for comparing different mountain pine-beetle management approaches is presented. This comparison tool gives the users the possibility of viewing their information, but more importantly it provides the ability to visually see the similarities and the differences between two simulations. This tool can help users to make decisions regarding their future actions against beetle attacks. The technique used is based on colour indexing combined with the mapping of the strategies into colour histograms. The system is entitled VICO from the phrase Visual Comparison.
Flexibility of Networks: a new measure for network design space analysis?

Flexibility is often claimed as a competitive advantage when proposing new network designs. However, most proposals provide only qualitative arguments for their improved support of flexibility. Quantitative arguments vary a lot among different proposals. A general understanding for flexibility is not yet clearly defined, leaving it to the reader to draw the right conclusions based on background information. The term flexibility is commonly defined as the ability to adapt to changes. For networks, flexibility would refer to the ability to adapt the available network resources, such as flows or topology, to changes of design requirements, e.g., shorter latency budgets or different traffic distributions. Recent concepts such as Software Defined Networking, Network Virtualization and Network Function Virtualization have emerged claiming to provide more flexibility in networks. Nevertheless, a deeper understanding of what flexibility means and how it could be quantified to compare different network designs remains open. In this paper, we ask whether flexibility can be a new measure for network design space analysis. As it is quite challenging to formulate a flexibility measure that covers all network aspects, we propose an initial set of flexibility aspects to start grounding guidelines. Our initial selection is backed up by an analysis of Software Defined Networking, Network Virtualization and Network Function Virtualization for their support of the selected flexibility aspects. Our research methodology is based on a systematic approach that leads to network design guidelines with respect to flexibility.
Summarizing Event Opinions for News Reports

Opinions on the news reports are very useful for people to understand an event, while the vast availability of such opinions becomes overwhelming to people when there is too much to digest. In this paper, we present an approach on summarizing event opinions for news reports. Firstly, we search relevant reports by submitting event-describing keywords, and for each report, we extract main textual content and separate subjective opinions from objective facts. Secondly, we propose a subjectivity detection approach to identify the opinion sentences. Thirdly, in order to summarize opinions, we propose a digest approach to list and compare standpoints by classifying opinions into positive/negative camps according to their sentiment polarities. In each camp, besides salient opinions, we also identify and present opinion holders (e.g. people, organizations, and countries), which contribute to a better understanding of their stances and relations. Lastly, we develop a system to display the opinion summarization of the event that is searched. An evaluation on effectiveness shows that it is favored by users.
Traceback of DOS Over Autonomous Systems

Denial of service (DoS) is a significant security threat in open networks such as the Internet. The existing limitations of the Internet protocols and the common availability tools make a DoS attack both effective and easy to launch. There are many different forms of DoS attack and the attack size could be amplified from a single attacker to a distributed attack such as a distributed denial of service (DDoS). IP traceback is one important tool proposed as part of DoS mitigation and a number of traceback techniques have been proposed including probabilistic packet marking (PPM). PPM is a promising technique that can be used to trace the complete path back from a victim to the attacker by encoding of each router's 32-bit IP address in at least one packet of a traffic flow. However, in a network with multiple hops through a number of autonomous systems (AS), as is common with most Internet services, it may be undesirable for every router to contribute to packet marking or for an AS to reveal its internal routing structure. This paper proposes two new efficient autonomous system (AS) traceback techniques to identify the AS of the attacker by probabilistically marking the packets. Traceback on the AS level has a number of advantages including a reduction in the number of bits to be encoded and a reduction in the number of routers that need to participate in the marking. Our results show a better performance comparing to PPM and other techniques.
The effect of reperfusion on neuroprotection using an inhibitor of poly(ADP-ribose) polymerase.

The activation of poly(ADP-ribose) polymerase (PARP) by free radical-damaged DNA plays a pivotal role in mediating ischemia-reperfusion injury. The purpose of the present study was to examine the neuroprotective effects of a PARP inhibitor, 3-aminobenzamide (3-ABA), which was administered either prior to or following reperfusion, to determine the importance of PARP inhibition prior to reperfusion. 3-ABA was injected i.p. either 15 min before or 15 min following reperfusion in a transient focal ischemia model in the rat. Treatment prior to the reperfusion led to a significant decrease in the volume of damaged tissue at 24 h (118.7 +/- 18.8 mm3, mean +/- s.d., p < 0.01), compared with the control (176.1 +/- 22.8 mm3). However, treatment after the reperfusion failed to produce a reduction in the damaged volume (171.9 +/- 27.6 mm3). These findings suggest that PARP activation sufficient to produce cellular damage occurs immediately after the reperfusion following cerebral ischemia.
Novel Markers for Diagnosis and Prognosis of Oral Intraepithelial Neoplasia

Squamous carcinoma of the oral cavity is a slow multi-steps process, based on progressive accumulation of genetic events leading to the selection of clonal populations of transformed epithelial cells (HaC Gale et al 2006). In their evolution, most cases of OILs are self-limiting and reversible, whereas some persist and may progress to SCC in spite of careful follow-up and treatment (KambicˇG Crissman et al, 1993).
Fractals for secondary key retrieval

In this paper we propose the use of fractals and especially the Hilbert curve, in order to design good distance-preserving mappings. Such mappings improve the performance of secondary-key- and spatial- access methods, where multi-dimensional points have to be stored on an 1-dimensional medium (e.g., disk). Good clustering reduces the number of disk accesses on retrieval, improving the response time. Our experiments on range queries and nearest neighbor queries showed that the proposed Hilbert curve achieves better clustering than older methods (“bit-shuffling”, or Peano curve), for every situation we tried.
The New Stigma of Relocated Public Housing Residents: Challenges to Social Identity in Mixed–Income Developments

Public housing residents have long experienced stigma as members of an urban “underclass. ” One policy response is the creation of mixed–income developments; by deconcentrating poverty and integrating residents into communities in which their residences are indistinguishable from neighbors, such efforts might reduce stigma associated with residency in traditional public housing. Through in–depth interviews with 35 relocated public housing residents and 184 field observations at three mixed–income developments in Chicago, we find this is not the case. Stigma associated with living in public housing is ameliorated, yet residents report that their experience of stigma has intensified in other ways. The negative response of higher–income residents, along with stringent screening and rule enforcement, amplifies the sense of difference many residents feel in these contexts. We demonstrate that this new form of stigma has generated a range of coping responses as relocated public housing residents seek to maintain eligibility while buttressing their social identity.