gebhart/patrepeval huggingface dataset:
Primary User Localization and Its Error Analysis in 5G Cognitive Radio Networks (2019)

It is crucial to estimate the location of primary users (PUs) for the development of cognitive radio networks (CRNs). Great efforts have been made in the past to develop localization algorithms with better accuracy but low computation. In CRNs, PUs do not cooperate with secondary users (SUs), which makes the localization task challenging. Due to this feature, received signal strength (RSS)-based PU localization techniques, such as centroid localization (CL) and multidimensional scaling (MDS), are the best candidates. However, most of the CL- and MDS-based PU localization methods consider omnidirectional wireless communication. Therefore, in this paper we propose a PU localization method which uses the RSS values at different sectors of the SU antenna, where a scoring strategy is applied to all the sectors to estimate the PU location. Two different scoring functions are proposed. Numerical results show that the proposed localization method is robust to PU locations and channel conditions. The proposed method is validated in terms of various network parameters, such as the number of SUs, beamwidth of the SU sectors, size of the grid, and placement of the PUs. Results show that increasing the number of SUs improve the localization accuracy due to an increased number of measurements. However, the localization accuracy degrades with an increase in the beamwidth of the SU sector because the faraway grid points also participate in the localization. The results are also compared with the conventional CL for PU localization. Compared with conventional CL, it offers a significant improvement in the performance.
Reversible Inhibition of Murine Cytomegalovirus Replication by Gamma Interferon (IFN-γ) in Primary Macrophages Involves a Primed Type I IFN-Signaling Subnetwork for Full Establishment of an Immediate-Early Antiviral State (2011)

Activated macrophages play a central role in controlling inflammatory responses to infection and are tightly regulated to rapidly mount responses to infectious challenge. Type I interferon (alpha/beta interferon [IFN-α/β]) and type II interferon (IFN-γ) play a crucial role in activating macrophages and subsequently restricting viral infections. Both types of IFNs signal through related but distinct signaling pathways, inducing a vast number of interferon-stimulated genes that are overlapping but distinguishable. The exact mechanism by which IFNs, particularly IFN-γ, inhibit DNA viruses such as cytomegalovirus (CMV) is still not fully understood. Here, we investigate the antiviral state developed in macrophages upon reversible inhibition of murine CMV by IFN-γ. On the basis of molecular profiling of the reversible inhibition, we identify a significant contribution of a restricted type I IFN subnetwork linked with IFN-γ activation. Genetic knockout of the type I-signaling pathway, in the context of IFN-γ stimulation, revealed an essential requirement for a primed type I-signaling process in developing a full refractory state in macrophages. A minimal transient induction of IFN-β upon macrophage activation with IFN-γ is also detectable. In dose and kinetic viral replication inhibition experiments with IFN-γ, the establishment of an antiviral effect is demonstrated to occur within the first hours of infection. We show that the inhibitory mechanisms at these very early times involve a blockade of the viral major immediate-early promoter activity. Altogether our results show that a primed type I IFN subnetwork contributes to an immediate-early antiviral state induced by type II IFN activation of macrophages, with a potential further amplification loop contributed by transient induction of IFN-β.
Separation of intermediates in the refolding of reduced erabutoxin b by analytical isoelectric focusing in layers of polyacrylamide gel (1982)

Isoelectric focusing in a thin layer of polyacrylamide gel is shown to be a suitable method for the resolution of intermediates trapped during the refolding process of reduced cystine-containing proteins. The method has been applied to the well-characterized snake neurotoxin erabutoxin b. An explanation is offered for the relatively low rate of refolding of this polypeptide.
Developing architectural platforms: a disciplined approach (2002)

The Mescal project brings a formalized, disciplined methodology to the design of programmable platform-based systems, enabling the exploration of a wide array of architectures and a correct-by-construction path to implementation.
Formal modeling with SysML (2012)

Often designated as a UML profile for system modeling, SysML brings some changes that enhance the possibilities of describing systems specificities, but raise new criticisms on the language interpretation. In the last SysML standard document, the new concepts are presented in an informal manner and the revised ones are often described in a way that makes difficult the appreciation of the changes. The internal block diagram, which replaces the UML composite structure diagram, is of interest regarding the innovative concepts it introduces in the old notation. We propose, in this paper, to formalize the semantics related to both of its structure and behavior. To conduct the formalization in an efficient manner, we go towards a semantic domain that fits the diagram characteristics. Hierarchical Colored Petri Nets constitute an appropriate choice. The formalization is validated by model checking. A case study, based on a system that meets the specific features SysML has been intended to model, illustrates the approach throughout the paper.
Meniscal Treatment Options (2012)

The importance of the meniscus is well established and damage to this structure, followed by its loss, results in the development of radiographic changes. One recent systematic review indicated that, as Fairbank reported after open meniscectomy,1 osteoarthritic changes are present at 8 to 16 years after arthroscopic partial meniscectomy; however, clinical symptoms are not significant.2,3 Another systematic review points out that while meniscus removal has a lower reoperation rate than meniscal repair, meniscal repair is associated with better long-term outcomes.4 Consequently, a link between meniscal loss and diminished knee function seems reasonable and the commonly held belief that every effort should be made to repair a torn meniscus seems appropriate. Several approaches to arthroscopic meniscal repair have developed. These can be described as outside-in, inside-out, and all-inside. As the articles in this issue make abundantly clear, regardless of the technique chosen the key to meniscal repair healing is a good blood supply, the absence of meniscal degeneration, and a stable knee (intact or concurrently reconstructed ACL). Several investigators are exploring the potential for the enhancement of meniscal healing using biologic techniques,5 allografts,6 or synthetic meniscal replacement.7,8 The current literature confirms several clinically significant observations. Medial meniscus repair is more likely to fail than lateral meniscus repair, presumably because of the better blood supply associated with the lateral meniscus and the different mechanical stresses between compartments. Also, meniscal repairs performed at the time of anterior cruciate ligament reconstruction have lower failure rates than repairs done without a reconstruction. Yet, evidence exists that not all meniscal tears need repair and that some (especially the lateral meniscus) can heal or at least remain asymptomatic long term. In reviewing the literature of meniscal repair techniques, it is clear that level 1 or 2 data are lacking to support many of these conclusions. Outcome measures vary between published studies, and the continuing introduction of new “improved” repair devices makes the collection of a significant number of cases with long-term results using 1 repair technique problematic. This issue of Sports Medicine and Arthroscopy Review tackles the subject of what to do with the meniscus and gives a glimpse of future treatment options. This includes leaving the torn meniscus in situ without debridement, meniscectomy (whether this should or should not be done), and the various techniques for meniscal repair. Meniscal replacement with either an allograft or a synthetic implant is addressed, and the current state of biologic enhancement is reviewed. Finally, surgeons often focus on specific surgical techniques and overlook postoperative care. A thoughtful discussion of the area of postoperative management after meniscal repair is presented. F. Alan BarberMD, FACS Eric D. Bava, MD Plano Orthopedic Sports Medicine and Spine Center, Plano, Texas
Perlecan Binds to the β‐Amyloid Proteins (Aβ) of Alzheimer's Disease, Accelerates Aβ Fibril Formation, and Maintains Aβ Fibril Stability (1997)

Perlecan is a specific heparan sulfate proteoglycan that accumulates in the fibrillar beta-amyloid (A beta) deposits of Alzheimer's disease. Perlecan purified from the Engelbreth-Holm-Swarm tumor was used to define perlecan's interactions with A beta and its effects on A beta fibril formation. Using a solid-phase binding immunoassay, freshly solubilized full-length A beta peptides bound immobilized perlecan at two sites, representing both high-affinity [K(D) = approximately 5.8 x 10(-11) M for A beta (1-40); K(D) = approximately 6.5 x 10(-12) M for A beta (1-42)] and lower-affinity [K(D) = 3.5 x 10(-8) M for A beta (1-40); K(D) = 4.3 x 10(-8) M for A beta (1-42)] interactions. An increase in the binding capacity of A beta (1-40) to perlecan correlated with an increase in A beta amyloid fibril formation during a 1-week incubation period. The high-capacity binding of A beta (1-40) to perlecan was similarly observed using perlecan heparan sulfate glycosaminoglycans and was completely abolished by heparin, but not by chondroitin-4-sulfate. Using a thioflavin T fluorometry assay, perlecan accelerated the rate of A beta (1-40) amyloid fibril formation, causing a significant increase in A beta fibril assembly over a 2-week incubation period at 1 h (2.8-fold increase), 1 day (3.6-fold increase), and 3 days (2.8-fold increase) in comparison with A beta (1-40) alone. Perlecan also initially accelerated the formation of A beta (1-42) fibrils within 1 h and maintained significantly higher levels of A beta (1-42) thioflavin T fluorescence throughout a 2-week experimental period in comparison with A beta (1-42) alone, suggesting perlecan's ability to maintain amyloid fibril stability. Perlecan's effects on A beta (1-40) fibril formation and maintenance of A beta (1-42) fibril stability occurred in a dose-dependent manner and was also mediated primarily by perlecan's glycosaminoglycan chains. Perlecan was the most effective enhancer and accelerator of A beta fibril formation when compared directly with other amyloid plaque components, including apolipoprotein E, alpha1-antichymotrypsin, P component, C1q, and C3. This study, therefore, demonstrates that perlecan not only binds to the predominant isoforms of A beta, but also accelerates A beta fibril formation and stabilizes amyloid fibrils once formed, confirming pivotal roles for perlecan in the pathogenesis of A beta amyloidosis in Alzheimer's disease.
Semi‐interpenetrating polymer network cryogels based on poly(ethylene glycol) diacrylate and collagen as potential off‐the‐shelf platforms for cancer cell research (2021)

In the present work, we investigated the potential of novel semi-interpenetrating polymer network (semi-IPN) cryogels, obtained through ultraviolet exposure of aqueous mixtures of poly(ethylene glycol) diacrylate and type I collagen, as tunable off-the-shelf platforms for 3D cancer cell research. We synthesized semi-IPN cryogels with variable collagen amounts (0.1% and 1% w/v) and assessed the effect of collagen on key cryogel properties for cell culture, for example, porosity, degradation rate and mechanical stiffness. Then, we investigated the ability of the cryogels to sustain the long-term growth of two pancreatic ductal adenocarcinoma (PDAC) cell populations, the parenchymal Panc1 cells and their derived cancer stem cells. Results revealed that both cell lines efficiently infiltrated, attached and expanded in the cryogels over a period of 14 days. However, only when grown in the cryogels with the highest collagen concentration, both cell lines reproduced their characteristic growth pattern previously observed in collagen-enriched organotypic cultures, biomimetic of the highly fibrotic PDAC stroma. Cellular preembedding in Matrigel, that is, the classical approach to develop/grow organoids, interfered with an efficient intra-scaffold migration and growth. Although preliminary, these findings highlight the potential of the proposed cryogels as reproducible and tunable cancer cell research platforms.
Land use change and soil fertility assessment in the vicinity of Zagreb landfill (2018)

The aim of this study was to give quantification of the present land use, land use change and assessment of agricultural soil in the area surrounding Jakuševec landfill in Zagreb, Croatia. A map of land use types of approximately 2 km zone around the landfill was created, based on photointerpretation during 2012 and according to Corine Land Cover 2000, 2006 and 2012 database. For soil fertility evaluation, soil was sampled at four locations at a distance of up to 300 m around the landfill. Spatial analysis revealed thirteen land use categories of total size around 3,161 ha. These categories were divided into three larger groups based on land use types (water: 5%, agricultural land: 50% and city: 45% of the total analysed area). Mixed agriculture is very important in this urban area regardless of the closeness of the waste landfill, because it relies on fertile soil and vicinity of large market of the capital city. The main land use changes included increase in industrial or commercial units and transport infrastructure, and decrease of agricultural land.
187 Stereotactic Radiotherapy (SRT) is Associated with Improved Rates of Hearing Preservation for Patients with Vestibular Schwannoma (2012)

INTRODUCTION: Vestibular schwannoma (VS) is a skull base tumor most commonly in the CP angle. Hearing loss commonly occurs in varying degrees as a result of VS and can have a significant and lasting impact on quality of life. In this study, we compare the long term clinical outcomes of patients with VS treated with either SRS or SRT. METHODS: A retrospective analysis of 197 patients receiving SRS or SRT for VS between 1996 and 2010 at the UCLA Medical Center was performed. The inclusion criteria: 1) diagnosis of VS without other intracranial tumors, 2) SRS or SRT performed at UCLA Ronald Reagan Medical Center. Patients without clinical follow up data and those with neurofibromatosis were excluded from this analysis. RESULTS: In this analysis, 32% of the patients received SRS while 68% received SRT. The average age at completion of SRS or SRT was 55 years old (range: 23-83). The median dose for SRS was 12Gy, and the average dose for SRT was 180cGy to the 90% IDL over 30 fractions. Patients had an average radiological and clinical follow-up of greater than 3 years. SRT demonstrated a trend towards a higher rate of tumor control following treatment relative to SRS, this difference though was not statistically significant (96% vs 80%, P = 0.067). Conversely, in patients with functional hearing prior to treatment, SRT was associated with significantly improved functional hearing preservation compared to SRS (97% vs 60%, respectively, P = 0.045). CONCLUSION: Our data indicates excellent tumor control with long term follow up for both SRS and SRT. This analysis suggests that SRT may be associated with improved rates of hearing preservation when compared to SRS. Further investigation is required to further characterize the optimal use of SRS and SRT for treatment of VS.
Structural Features of the DNA Hairpin d(ATCCTA-GTTA-TAGGAT): Formation of a G-A Base Pair in the Loop (1997)

The three-dimensional structure of the hairpin formed by d(ATCCTA-GTTA-TAGGAT) has been determined by means of two-dimensional NMR studies, distance geometry and molecular dynamics calculations. The first and the last residues of the tetraloop of this hairpin form a sheared G-A base pair on top of the six Watson-Crick base pairs in the stem. The glycosidic torsion angles of the guanine and adenine residues in the G-A base pair reside in the anti and high- anti domain ( approximately -60 degrees ) respectively. Several dihedral angles in the loop adopt non-standard values to accommodate this base pair. The first and second residue in the loop are stacked in a more or less normal helical fashion; the fourth loop residue also stacks upon the stem, while the third residue is directed away from the loop region. The loop structure can be classified as a so-called type-I loop, in which the bases at the 5'-end of the loop stack in a continuous fashion. In this situation, loop stability is unlikely to depend heavily on the nature of the unpaired bases in the loop. Moreover, the present study indicates that the influence of the polarity of a closing A.T pair is much less significant than that of a closing C.G base pair.
Regenerative capacity of the corneal transition zone for endothelial cell therapy (2020)

The corneal endothelium located on the posterior corneal surface is responsible for regulating stromal hydration. This is contributed by a monolayer of corneal endothelial cells (CECs), which are metabolically active in a continuous fluid-coupled efflux of ions from the corneal stroma into the aqueous humor, preventing stromal over-hydration and preserving the orderly arrangement of stromal collagen fibrils, which is essential for corneal transparency. Mature CECs do not have regenerative capacity and cell loss due to aging and diseases results in irreversible stromal edema and a loss of corneal clarity. The current gold standard of treatment for this worldwide blindness caused by corneal endothelial failure is the corneal transplantation using cadaveric donor corneas. The top indication is Fuchs corneal endothelial dystrophy/degeneration, which represents 39% of all corneal transplants performed. However, the global shortage of transplantable donor corneas has restricted the treatment outcomes, hence instigating a need to research for alternative therapies. One such avenue is the CEC regeneration from endothelial progenitors, which have been identified in the peripheral endothelium and the adjacent transition zone. This review examines the evidence supporting the existence of endothelial progenitors in the posterior limbus and summarizes the existing knowledge on the microanatomy of the transitional zone. We give an overview of the isolation and ex vivo propagation of human endothelial progenitors in the transition zone, and their growth and differentiation capacity to the corneal endothelium. Transplanting these bioengineered constructs into in vivo models of corneal endothelial degeneration will prove the efficacy and viability, and the long-term maintenance of functional endothelium. This will develop a novel regenerative therapy for the management of corneal endothelial diseases.
Supplementary Data from Three Epigenetic Biomarkers, &lt;i&gt;GDF15&lt;/i&gt;, &lt;i&gt;TMEFF2&lt;/i&gt;, and &lt;i&gt;VIM&lt;/i&gt;, Accurately Predict Bladder Cancer from DNA-Based Analyses of Urine Samples (2023)

&lt;p&gt;Supplementary Figures S1-S4 and Supplementary Tables S1-S7.&lt;/p&gt;
Novel System for 3D Facial Caricaturing Friendly to Users (2003)

ユーザインタフェースとして顔メディアを用いる可能性が示唆され, 顔の認識・生成技術が注目されている. 顔に対する人の印象を造形する手法として似顔絵, とりわけ立体で構成される似顔絵が意味を持ち始めている. 我々は3 次元空間上の顔特徴を抽出して似顔絵化する技術について提案してきたが, 生成結果には局所的な, あるいは, 全体的に顔の形が不自然にくずれる現象が見られた.平均顔と入力顔の差ベクトルを入力顔の個人性特徴とする基本手法において, 本論文では平均顔生成で標本平均を算出するだけでなく, 特徴点列における値のばらつきも平均顔に付随する情報とすることで, 新しい似顔絵生成手法を提案し, また実験的に考察を行った. 結果として, 似顔絵モデルにあわせて, 視覚感性的な顔らしさから逸脱することなく誇張をする, スマートな似顔絵生成システム実現の可能性を示した.
ChemInform Abstract: Organic Diradicals and Polyradicals: From Spin Coupling to Magnetism? (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The RRE of human immunodeficiency virus type 1 contributes to cell-type-specific viral tropism (1993)

As part of a general program investigating the mechanism of the Rev axis of human immunodeficiency virus type 1 (HIV-1) autoregulation, a series of proviral HIV-1 mutants which differ from the parental HXB2 strain at selected positions within the RRE were constructed. All of the mutations were designed to perturb the RRE by introducing local helix disruptions without altering the coding potential of the overlapping envelope open reading frame. Viral replication in various cell types was monitored by a cell supernatant reverse transcriptase assay and Northern (RNA blot) analysis. All proviral RRE mutants displayed at least some impairment in replication. However, the relative impairment varied drastically among the various cell types tested. This suggests that the RRE may contribute to cell-type-specific viral tropism.
Antibody Recognition of a Flexible Epitope at the DNA Binding Site of the Human Papillomavirus Transcriptional Regulator E2 (2006)

We have obtained a monoclonal antibody (ED15) against the C-terminal DNA-binding domain of the high-risk human papillomavirus strain-16 E2 protein that strongly interferes with its DNA-binding activity. We here characterize the recognition mechanism of this antibody and find that the ED15-E2 interaction has a strong electrostatic component, which correlates with the high proportion of acidic residues found in the antibody combining site. Further circular dichroism experiments in the presence of phosphate show that, in addition to electrostatic screening of key potential interactions, ionic strength affects the conformation of the epitope. In addition, the interaction is strongly modulated by pH, which correlates with the local flexibility of the epitope rather than the presence of pH sensitive residues at the interface. Noticeably, this finding is well correlated with the strong entropic component of the interaction. Site directed mutagenesis indicates that the ED15 epitope involves at least part of the DNA-binding helix of E2, explaining the mAb inhibitory activity. At physiological salt concentrations, the equilibrium dissociation constant of the E2-ED15 interaction is 10(-7) M and the association rate is 10(4) M-1 s-1, at least 1 order of magnitude slower than those generally reported in the most extensively described "nonflexible" antibody-protein interactions, indicating the presence of a slow conformational rearrangement on the antigen as the rate-limiting step. The crucial role of antigen flexibility in antibody-protein recognition is discussed.
Comparative proteomic analysis of different bilateral adrenocortical hyperplasia (2020)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)