gebhart/patrepeval huggingface dataset:
Design and Development of Molecular Imaging Probes (2010)

Molecular imaging, the visualization, characterization and measurement of biological processes at the cellular, subcellular level, or even molecular level in living subjects, has rapidly gained importance in the dawning era of personalized medicine. Molecular imaging takes advantage of the traditional diagnostic imaging techniques and introduces molecular imaging probes to determine the expression of indicative molecular markers at different stages of diseases and disorders. As a key component of molecular imaging, molecular imaging probe must be able to specifically reach the target of interest in vivo while retaining long enough to be detected. A desirable molecular imaging probe with clinical translation potential is expected to have unique characteristics. Therefore, design and development of molecular imaging probe is frequently a challenging endeavor for medicinal chemists. This review summarizes the general principles of molecular imaging probe design and some fundamental strategies of molecular imaging probe development with a number of illustrative examples.
Multi-Layer Interleave-Division Multiple Access for 3GPP Long Term Evolution (2007)

A multi-layer Interleave-division multiple access (IDMA) based system proposal is presented in order to enhance the universal terrestrial radio access (UTRA) uplink. Compatibility and co-existence with the current UTRA FDD mode are of primary importance. Although focus is on UTRA long term evolution and related research activities initiated by the 3rd generation partnership project (3GPP), multi-layer IDMA may be applied to enhance other direct-sequence code- division multiple access (DS-CDMA) systems, or may serve as an innovative air interface for future systems. As a novel feature, non-uniform power allocation on chip level is introduced.
Probing Chiral Selective Reactions Using a Revised Kataura Plot for the Interpretation of Single-Walled Carbon Nanotube Spectroscopy (2003)

Raman spectroscopy on surfactant-dispersed, aqueous suspensions of single-walled carbon nanotubes is used to verify the energies of interband transitions and validate the spectral assignments of semiconducting and metallic nanotubes determined by spectrofluorimetry for the former and Raman excitation profiles for the latter. The results are compiled into an experimentally based mapping of transition versus nanotube diameter to revise those previously employed using single-electron theoretical treatments. Because this mapping provides the transitions associated with a precise chiral wrapping of a particular nanotube, it allows the monitoring of reaction pathways that are selective to the nanotube chirality vector. This is demonstrated using a model electron-transfer reaction of 4-chlorobenzenediazonium shown to be selective for metallic over semiconducting carbon nanotubes via charge-transfer stabilization of complexes at the surfaces of the former.
Serum levels of interleukin 6, a potent myeloma cell growth factor, as a reflect of disease severity in plasma cell dyscrasias. (1989)

Using a specific and very sensitive (1 pg = 1 U) bioassay, we investigated the presence of IL-6, a potent myeloma cell growth factor, in the sera of 131 subjects with plasma cell dyscrasias. 22 had monoclonal gammopathy of undetermined significance (MGUS), 13 had smoldering myeloma (SMM), 85 had overt multiple myeloma (MM), and 11 had plasma cell leukemia (PCL). Significant serum IL-6 levels were detected in only 3% of the MGUS/SMM group, but in 35% of the overt MM group and 100% of the PCL group. During overt MM, IL-6 was detected in 37% of the patients at diagnosis, 13% of those with stable MM, and 60% of those with fulminating disease. These data demonstrate that serum levels of IL-6, a potent myeloma cell growth factor in vitro, correlate with disease severity in plasma cell dyscrasias. Serial studies performed in 3 patients and correlative studies with labeling index in vivo in 25 patients have confirmed this concept. Taken together, this suggests that this cytokine is probably involved in vivo during the progressive phase of MM. Thus, anti-IL-6 or anti-IL-6 receptor antibodies could be useful as therapeutic agents at this stage of the disease.
[Use of preparation VM 26 (epipodophyllotoxin) for treating lymphomas in children and adults]. (1981)

A coordinated clinical trial (phase II) of preparation VM-26 supplied by Sandos (Switzerland) was carried out at 5 clinics in a total of 61 patients with lymphoma. Two regimens of VM-26 administration were employed: (1) 5-day courses of 30 mg/m2 iv with 7-14 day intervals, or (2) two injections of 50 mg/m2 a week, within 4-6 weeks, depending on drug tolerance Out of 15 children with Hodgkin's disease, 50% of cases showed complete or partial remission. Out of 27 adults with Hodgkin's disease, response was registered in 69.9 and a pronounced effect--in 1 26.1%. Out of 14 patients with lymphosarcomas, response was observed in 78.5 and a pronounced effect--in 57.2%. Toxic effect was not the cause of treatment suspension in most cases.
Adding reagent to droplets with controlled rupture of encapsulated double emulsions (2013)

We present a method to add reagent to microfluidic droplets by enveloping them as a double emulsions in reagent-filled droplets and then rupturing them with an electric field. When the double emulsions rupture, they release their contents into the enveloping droplets, ensuring mixing with reagent while limiting cross-droplet contamination.
Paramagnetic Ultrasmall Gadolinium Oxide Nanoparticles as Advanced T1 MRI Contrast Agent: Account for Large Longitudinal Relaxivity, Optimal Particle Diameter, and In Vivo T1 MR Images (2009)

Paramagnetic ultrasmall gadolinium oxide (Gd(2)O(3)) nanoparticles with particle diameters (d) of approximately 1 nm were synthesized by using three kinds of Gd(III) ion precursors and by refluxing each of them in tripropylene glycol under an O(2) flow. A large longitudinal relaxivity (r(1)) of water proton of 9.9 s(-1) mM(-1) was estimated. As a result, high contrast in vivo T(1) MR images of the brain tumor of a rat were observed. This large r(1) is discussed in terms of the huge surface to volume ratio (S/V) of the ultrasmall gadolinium oxide nanoparticles coupled with the cooperative induction of surface Gd(III) ions for the longitudinal relaxation of a water proton. It is found from the d dependence of r(1) that the optimal range of d for the maximal r(1), which may be used as an advanced T(1) MRI contrast agent, is 1-2.5 nm.
PPP Authentication Protocols (1992)

The Point-to-Point Protocol (PPP) [1] provides a standard method of encapsulating Network Layer protocol information over point-to-point links.PPP also defines an extensible Link Control Protocol, which allows negotiation of an Authentication Protocol for authenticating its peer before allowing Network Layer protocols to transmit over the link.This document defines two protocols for Authentication: the Password Authentication Protocol and the Challenge-Handshake Authentication Protocol.
Epigenetic alteration at the DLK1-GTL2 imprinted domain in human neoplasia: analysis of neuroblastoma, phaeochromocytoma and Wilms' tumour (2005)

Epigenetic alterations in the 11p15.5 imprinted gene cluster are frequent in human cancers and are associated with disordered imprinting of insulin-like growth factor (IGF)2 and H19. Recently, an imprinted gene cluster at 14q32 has been defined and includes two closely linked but reciprocally imprinted genes, DLK1 and GTL2, that have similarities to IGF2 and H19, respectively. Both GTL2 and H19 are maternally expressed RNAs with no protein product and display paternal allele promoter region methylation, and DLK1 and IGF2 are both paternally expressed. To determine whether methylation alterations within the 14q32 imprinted domain occur in human tumorigenesis, we investigated the status of the GTL2 promoter differentially methylated region (DMR) in 20 neuroblastoma tumours, 20 phaeochromocytomas and, 40 Wilms' tumours. Hypermethylation of the GTL2 promoter DMR was detected in 25% of neuroblastomas, 10% of phaeochromocytoma and 2.5% of Wilms' tumours. Tumours with GTL2 promoter DMR hypermethylation also demonstrated hypermethylation at an upstream intergenic DMR thought to represent a germline imprinting control element. Analysis of neuroblastoma cell lines revealed that GTL2 DMR hypermethylation was associated with transcriptional repression of GTL2. These epigenetic findings are similar to those reported in Wilms' tumours in which H19 repression and DMR hypermethylation is associated with loss of imprinting (LOI, biallelic expression) of IGF2. However, a neuroblastoma cell line with hypermethylation of the GTL2 promoter and intergenic DMR did not show LOI of DLK1 and although treatment with a demethylating agent restored GTL2 expression and reduced DLK1 expression. As described for IGF2/H19, epigenetic changes at DLK1/GTL2 occur in human cancers. However, these changes are not associated with DLK1 LOI highlighting differences in the imprinting control mechanisms operating in the IGF2-H19 and DLK1-GTL2 domains. GTL2 promoter and intergenic DMR hypermethylation is associated with the loss of GTL2 expression and this may contribute to tumorigenesis in a subset of human cancers.
The structural basis of R-spondin recognition by LGR5 and RNF43 (2013)

R-spondins (RSPOs) enhance Wnt signaling, affect stem cell behavior, bind to leucine-rich repeat-containing G-protein-coupled receptors 4-6, (LGR4-6) and the transmembrane E3 ubiquitin ligases RING finger 43/zinc and RING finger 3 (RNF43/ZNRF3). The structure of RSPO1 bound to both LGR5 and RNF43 ectodomains confirms their physical linkage. RSPO1 is sandwiched by LGR5 and RNF43, with its rod module of the cysteine-rich domain (CRD) contacting LGR5 and a hairpin inserted into RNF43. LGR5 does not contact RNF43 but increases the affinity of RSPO1 to RNF43, supporting LGR5 as an engagement receptor and RNF43 as an effector receptor. Disease mutations map to the RSPO1-RNF43 interface, which promises therapeutic targeting.
Coordinating Multiple Droplets in Planar Array Digital Microfluidic Systems (2005)

In this paper we present an approach to coordinate the motions of droplets in digital microfluidic systems, a new class of lab-on-a-chip systems for biochemical analysis. A digital microfluidic system typically consists of a planar array of cells with electrodes that control the droplets. The primary challenge in using droplet-based systems is that they require the simultaneous coordination of a potentially large number of droplets on the array as the droplets move, mix, and split. In this paper we describe a general-purpose system that uses simple algorithms and yet is versatile. First, we present a semi-automated approach to generate the array layout in terms of components. Next, we discuss simple algorithms to select destination components for the droplets and a decentralized scheme for components to route the droplets on the array. These are then combined into a reconfigurable system that has been simulated in software to perform analyses such as the DNA polymerase chain reaction. The algorithms have been able to successfully coordinate hundreds of droplets simultaneously and perform one or more chemical analyses in parallel. Because it is challenging to analytically characterize the behavior of such systems, simulation methods to detect potential system instability are proposed.
Vascular cell adhesion molecule-1 is expressed in human coronary atherosclerotic plaques. Implications for the mode of progression of advanced coronary atherosclerosis. (1993)

Endothelial attachment is the initial step in leukocyte recruitment into developing atherosclerotic lesions. To determine whether vascular cell adhesion molecule-1 (VCAM-1) expression may play a role in inflammatory cell recruitment into human atherosclerotic lesions, immunohistochemistry was performed with a polyclonal rabbit antisera, raised against recombinant human VCAM-1, on 24 atherosclerotic coronary plaques and 11 control coronary segments with nonatherosclerotic diffuse intimal thickening from 10 patients. Immunophenotyping was performed on adjacent sections to identify smooth muscle cells, macrophages, and endothelial cells. To confirm VCAM-1-expressing cell types, double immunostaining with VCAM-1 antisera and each of the cell-specific markers and in situ hybridization were performed. All atherosclerotic plaques contained some VCAM-1, compared to 45% of control segments. VCAM-1 was found infrequently on endothelial cells at the arterial lumen din both plaques (21%) and in control segments (27%), but was prevalent in areas of neovascularization and inflammatory infiltrate in the base of plaques. Double immunostaining and in situ hybridization confirmed that most VCAM-1 was expressed by subsets of plaque smooth muscle cells and macrophages. The results document the presence of VCAM-1 in human atherosclerosis, demonstrate VCAM-1 expression by human smooth muscle cells in vivo, and suggest that intimal neovasculature may be an important site of inflammatory cell recruitment into advanced coronary lesions.
Association between dental caries and pneumonia in patients with systemic lupus erythematosus. (2006)

Poor oral hygiene and third-grade caries are common in patients with SLE who develop pneumonia.
Pharmacokinetics and Topical Vaginal Effects of Two Tenofovir Gels in Rabbits (2012)

Tenofovir (TFV) 1% gel has proven effective in preclinical and clinical studies in preventing sexual transmission of HIV-1. The impact of changing the current gel formulation to reduce its osmolality was evaluated using pharmacokinetic assessments and local tissue effects in the rabbit. Following vaginal administration of TFV 1% gel and reduced-glycerin TFV 1% gel, TFV was measured in plasma, vaginal tissues, vaginal fluids, and iliac lymph nodes. After a single dose, plasma C(max) and AUC(0-4h) were significantly higher in the TFV 1% gel group compared with the reduced-glycerin TFV 1% gel group. After 14 days of once-daily dosing, differences in these parameters were insignificant. Vaginal fluid concentrations were ∼100 μg/ml following the first dose and up to a mean of about 500 μg/ml after 14 once-daily doses. Mean (and median) cranial TFV tissue concentrations were generally in excess of 100 μg/g following a single dose and 14 once-daily doses of both gels; concentrations in the caudal vaginal tissues were comparatively lower, although in nearly all cases mean values exceeded 10 μg/g. Treatment of tissues with phosphatase to liberate TFV from its diphosphate and monophosphate metabolites increased recovery of TFV by 60-120%. Median TFV concentrations in iliac lymph nodes ranged from 44 ng/g to 196 ng/g; differences between iliac lymph node TFV concentrations following dosing of the two gels were insignificant. There were no differences observed in histological evaluation in the cranial vagina following 14 days of once-daily dosing of either gel. There was an apparent impact of TFV on rabbit vaginal epithelium (increased secretory depletion and increased cellular vacuolization) independent of formulation. These data indicate that the reduced-glycerin TFV 1% gel may be a suitable alternative to TFV 1% gel.
Conducting Polymer Composite Materials for Hydrogen Generation (2010)

A novel conducting polymer/non-conducting polymer composite (PEDOT/PEG), produced by vapor phase polymerization of PEDOT in the presence of PEG, shows stable electrocatalytic reduction of protons to hydrogen with conversion currents and over-potential comparable to platinum. The swelling of the composite by PEG and especially its ability to coordinate protons seems to be essential for the catalytic activity of the composite.
An experiment to test centrifugal confinement for fusion (2001)

The basic idea of centrifugal confinement is to use centrifugal forces from supersonic rotation to augment conventional magnetic confinement. Optimizing this “knob” results in a fusion device that features four advantages: steady state, no disruptions, superior cross-field confinement, and a simpler coil configuration. The idea rests on two prongs: first, centrifugal forces can confine plasmas to desired regions of shaped magnetic fields; second, the accompanying large velocity shear can stabilize even magnetohydrodynamic (MHD) instabilities. A third feature is that the velocity shear also viscously heats the plasma; no auxiliary heating is necessary to reach fusion temperatures. Regarding transport, the velocity shear can also quell microturbulence, leading to fully classical confinement, as there are no neoclassical effects. Classical parallel electron transport then sets the confinement time. These losses are minimized by a large Pastukhov factor resulting from the deep centrifugal potential well: at Mach 4–5, the Lawson criterion is accessible. One key issue is whether velocity shear will be sufficient by itself to stabilize MHD interchanges. Numerical simulations indicate that laminar equilibria can be obtained at Mach numbers of 4–5 but that the progression toward laminarity with increasing Mach number is accompanied by residual convection from the interchanges. The central goal of the Maryland Centrifugal Torus (MCT) [R. F. Ellis et al., Bull. Am. Phys. Soc. 44, 48 (1998)] is to obtain MHD stability from velocity shear. As an assist to accessing laminarity, MCT will incorporate two unique features: plasma elongation and toroidal magnetic field. The former raises velocity shear efficiency, and modest magnetic shear should suppress residual convection.
Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT) (2014)

Given M sequences with N bi-allelic variable sites, an O(NM) algorithm to derive a representation of the data based on positional prefix arrays is given, which is termed the positional Burrows-Wheeler transform (PBWT). On large datasets this compresses with run-length encoding by more than a factor of a hundred smaller than using gzip on the raw data. Using this representation a method is given to find all maximal haplotype matches within the set in O(NM) time rather than O(NM(2)) as expected from naive pairwise comparison, and also a fast algorithm, empirically independent of M given sufficient memory for indexes, to find maximal matches between a new sequence and the set. The discussion includes some proposals about how these approaches could be used for imputation and phasing.
Microsatellite instability in endometrial carcinoma. (1994)

Microsatellite instability (MI), detected as electrophoretic shifts in allele sizes of microsatellite DNA sequences, has been identified in some colorectal carcinomas. Investigators have previously attributed such microsatellite instability to replication errors (RER). The colorectal carcinomas with RER have been found to arise either sporadically or in association with the hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Because endometrial carcinoma is also commonly associated with HNPCC, we studied 30 cases of endometrial carcinoma to characterize the presence of MI in these neoplasms. Seven cases (23%) showed MI. Four cases showed both Type I (large shifts) and Type II (small shifts) mutation patterns and the remaining three cases showed Type I mutations only. We conclude that MI frequently occurs in endometrial cancers and that this type of genetic alteration may be an important pathogenetic feature of this tumor type.
SUN attribute database: Discovering, annotating, and recognizing scene attributes (2012)

In this paper we present the first large-scale scene attribute database. First, we perform crowd-sourced human studies to find a taxonomy of 102 discriminative attributes. Next, we build the “SUN attribute database” on top of the diverse SUN categorical database. Our attribute database spans more than 700 categories and 14,000 images and has potential for use in high-level scene understanding and fine-grained scene recognition. We use our dataset to train attribute classifiers and evaluate how well these relatively simple classifiers can recognize a variety of attributes related to materials, surface properties, lighting, functions and affordances, and spatial envelope properties.
CD86+/CD206+, Diametrically Polarized Tumor-Associated Macrophages, Predict Hepatocellular Carcinoma Patient Prognosis (2016)

Tumor-associated macrophages (TAMs), the most abundant infiltrating immune cells in tumor microenvironment, have distinct functions in hepatocellular carcinoma (HCC) progression. CD68⁺ TAMs represent multiple polarized immune cells mainly containing CD86⁺ antitumoral M1 macrophages and CD206⁺ protumoral M2 macrophages. TAMs expression and density were assessed by immunohistochemical staining of CD68, CD86, and CD206 in tissue microarrays from 253 HCC patients. Clinicopathologic features and prognostic value of these markers were evaluated. We found that CD68⁺ TAMs were not associated with clinicopathologic characteristics and prognosis in HCC. Low presence of CD86⁺ TAMs and high presence of CD206⁺ TAMs were markedly correlated with aggressive tumor phenotypes, such as multiple tumor number and advanced tumor-node-metastasis (TNM) stage; and were associated with poor overall survival (OS) (p = 0.027 and p = 0.024, respectively) and increased time to recurrence (TTR) (p = 0.037 and p = 0.031, respectively). In addition, combined analysis of CD86 and CD206 provided a better indicator for OS (p = 0.011) and TTR (p = 0.024) in HCC than individual analysis of CD86 and CD206. Moreover, CD86⁺/CD206⁺ TAMs predictive model also had significant prognosis value in α-fetoprotein (AFP)-negative patients (OS: p = 0.002, TTR: p = 0.005). Thus, these results suggest that combined analysis of immune biomarkers CD86 and CD206 could be a promising HCC prognostic biomarker.
Carriage Frequency, Intensity of Carriage, and Strains of Oral Yeast Species Vary in the Progression to Oral Candidiasis in Human Immunodeficiency Virus-Positive Individuals (2002)

Candida samples were taken over a period of 2 years from 54 human immunodeficiency virus (HIV)-positive asymptomatic subjects to evaluate changes in yeast carriage, intensity of carriage, and genotype over time. Overall, we found that HIV-positive patients with CD4(+)-cell counts of between 200 and 400/microl had significantly more yeast colonization than healthy control subjects. Of the 54 patients, 11 developed thrush. We found that intensity of carriage in these 11 patients increased significantly in the progression from asymptomatic yeast carrier to an episode of oral thrush. Also, the most common yeast species isolated was Candida albicans; however, we did see a number of patients harboring multiple species at the same time. Using the C. albicans-specific probe Ca3, we found that 54% (n = 6) of the 11 patients who developed thrush maintained genetically similar strains throughout the study period, with minor genetic variations in all patients except one. Forty-six percent of these patients had either multiple strains throughout the study period (n = 2), strain replacement (n = 1), or species replacement (n = 2). Of the patients who had multiple strains, one (I4) was infected by two different strains of Candida dubliniensis distinguished by a recently developed species-specific probe. These results suggest that commensal strains colonizing HIV-positive individuals can undergo alterations prior to producing an episode of thrush.