gebhart/patrepeval huggingface dataset:
Comparison of antigen expression of human renal cancers in vivo and in vitro (1984)

Tissue culture lines have become widely utilized in the study of human cancer. Legitimate questions arise as to the degree of similarity between the in vitro cells and their in vivo counterparts. The author has used eleven monoclonal antibodies (mAbs) of defined specificities to compare antigen (Ag) expression of human renal cancers in vivo and in vitro. Nine of the eleven Ags defined by these mAbs have been previously immunochemically characterized. These mAbs were generated by immunizing mice with human cancer cell lines. Nephrectomy specimens from six patients with adenocarcinoma were available for study as both frozen sections (in vivo) and tissue culture lines (in vitro). Frozen sections were typed by an indirect immunoperoxidase assay while established cell lines were typed by an anti-mouse immunoglobulin rosette assay. Antigens were scored either positive (+) or negative (-). Results revealed three patterns of antigenic expression: (1) consistent expression in vivo and in vitro (gp160, gp115, gp120r, gp120nr, GD3, B2.6, HLA-DR); (2) in vivo (-):in vitro (+) (AJ2, gp40, gp130); and (3) in vivo (+):in vitro (-) (S25). These results suggest that while most antigens (Ags) are consistently expressed or repressed when cells adapt to tissue culture, some Ags, e.g., AJ2, gp40 and gp130, appear to be induced and others, e.g., S25, are suppressed in their new milieu. Moreover, expression of these 11 Ags did not change with up to 40 passages in tissue culture. The demonstrated similarities between in vivo and in vitro cells coupled with the logistic advantages offered by cell lines makes an in vitro system a worthwhile approach to the study of human cancer. However, the fact that differences exist between the two systems underscores the need to extend interesting in vitro findings to the in vivo system prior to making á priori extrapolations or assumptions.
PMMA synthesis for applications in radiologic techniques (2021)

This project goal is to synthesize PMMA polymeric films loaded with grains of MgB4O7:Ce,Li crystal. Regarding the steps involved, suspension polymerization of methyl methacrylate (MMA), the precursor monomer, was carried out and resulted in the PMMA polymeric microparticles (Figure 1). Suspension polymerization is simple, fast and of high conversion [4]. Besides, this polymerization process allows the addition of MgB4O7:Ce,Li that will be present in the final PMMA polymeric film. The obtained polymeric films will be characterized by Thermogravimetric analysis (TGA) for determining Tg – transition glass temperature – value; Differential scanning calorimetry (DSC) under nitrogen atmosphere to investigate thermal transitions; Gel permeation chromatography (GPC) for molar masses determination; Fourier transform infrared spectroscopy (FTIR) for the chemical characterization. During this project, polymeric films will be produced with different thicknesses and different percentages and grain sizes of MgB4O7:Ce,Li. Natural boron will be used in this crystal synthesis.
Nanoscale Localized Surface Plasmon Resonance Biosensors (2007)

This chapter contains sections titled: Overview Methods Nanofabrication of Materials for LSPR Spectroscopy and Sensing Film Over Nanowells Solution-Phase NSL-Fabricated Nanotriangles Silver Nanocubes Biosensing Outlook Acknowledgments References
Mechanism of Glucose Isomerization Using a Solid Lewis Acid Catalyst in Water (2010)

Other way round: 1H and 13C NMR spectroscopy on isotopically labeled glucose reveals that in the presence of tin-containing zeolite Sn-Beta, the isomerization reaction of glucose in water proceeds by way of an intramolecular hydride shift (see scheme) rather than proton transfer. This is the first mechanistic demonstration of Sn-Beta acting as a Lewis acid in a purely aqueous environment. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Wireless Scheduling with Partial Channel State Information: Large Deviations and Optimality (2014)

We consider a server serving a time-slotted queued system of multiple packet-based flows, with exogenous packet arrivals and time-varying service rates. At each time, the server can observe instantaneous service rates for only a subset of flows (from within a fixed collection of observable subsets) before scheduling a flow in the subset for service. We are interested in queue-length aware scheduling to keep the queues short, and develop scheduling algorithms that use only partial service rate information from subsets of channels to minimize the likelihood of queue overflow in the system. Specifically, we present a new joint subset-sampling and scheduling algorithm called Max-Exp that uses only the current queue lengths to pick a subset of flows, and subsequently schedules a flow using the Exponential rule. When the collection of observable subsets is disjoint, we show that Max-Exp achieves the best exponential decay rate, among all scheduling algorithms using partial information, of the tail of the longest queue in the system. Towards this, we employ novel analytical techniques for studying the performance of scheduling algorithms using partial state, which may be of independent interest. These include new sample-path large deviations results for processes obtained by non-random, predictable sampling of sequences of independent and identically distributed random variables. A consequence of these results is that scheduling with partial state information yields a rate function significantly different from scheduling with full channel information. In the special case when the observable subsets are singleton flows, i.e., when there is effectively no a priori channel-state information, Max-Exp reduces to simply serving the flow with the longest queue; thus, our results show that to always serve the longest queue in the absence of any channel-state information is large-deviations optimal.
Intranasal fusion inhibitory lipopeptide prevents direct-contact SARS-CoV-2 transmission in ferrets (2021)

Containment of the COVID-19 pandemic requires reducing viral transmission. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is initiated by membrane fusion between the viral and host cell membranes, which is mediated by the viral spike protein. We have designed lipopeptide fusion inhibitors that block this critical first step of infection and, on the basis of in vitro efficacy and in vivo biodistribution, selected a dimeric form for evaluation in an animal model. Daily intranasal administration to ferrets completely prevented SARS-CoV-2 direct-contact transmission during 24-hour cohousing with infected animals, under stringent conditions that resulted in infection of 100% of untreated animals. These lipopeptides are highly stable and thus may readily translate into safe and effective intranasal prophylaxis to reduce transmission of SARS-CoV-2.
Super Learner Analysis of Electronic Adherence Data Improves Viral Prediction and May Provide Strategies for Selective HIV RNA Monitoring (2020)

Regular HIV RNA testing for all HIV positive patients on antiretroviral therapy (ART) is expensive and has low yield since most tests are undetectable. Selective testing of those at higher risk of failure may improve efficiency. We investigated whether a novel analysis of adherence data could correctly classify virological failure and potentially inform a selective testing strategy.
Polymer-Based Electrooptical (2004)

An integrated circular-polarization modulator (CPM) is designed and fabricated with electrooptic (EO) poly- meric materials employing contact poling. Tilted-poling is employed to activate the conversion between TE and TM modes, while the tensor nature of the poled polymeric materials is used to generate the phase-difference modulation. With appropriate voltage control, the outputs at the 45 -tilted linear, left-hand-cir- cular (LHC), 45 -tilted linear, and right-hand-circular (RHC) polarization states are achieved. The extinction ratios at the linearly polarized states are larger than 25 dB. Index Terms—Electrooptic modulation, integrated optics, optical planar waveguide, optical polarization, optical polymers.
Overall survival in a trial of orally administered CCR2 inhibitor CCX872 in locally advanced/metastatic pancreatic cancer: Correlation with blood monocyte counts. (2018)

92 Background: The CCL2-CCR2 signaling axis may facilitate migration of myeloid derived suppressor cells to pancreatic cancer resulting in an immune suppressive tumor microenvironment. CCR2 inhibition in patients with non-metastatic pancreatic cancer was previously reported to decrease tumor-infiltrating macrophages/Treg cells and increase effector T cells (Nywening et al, 2016). Here, a CCR2 specific antagonist CCX872 was used in combination with FOLFIRINOX to treat subjects with locally advanced or metastatic, non-resectable pancreatic cancer in a multi-center study. Methods: Fifty subjects (ECOG score ≤ 2) were enrolled, receiving FOLFIRINOX (fluorouracil [5-FU], leucovorin, irinotecan, oxaliplatin) once every two weeks (maximum 12 cycles) plus 150 mg CCX872 QD or BID for 12 weeks. Subjects showing at least stable disease at the end of the 12-week treatment period were eligible to CCX872 treatment until disease progression. In this ongoing study, all subjects are followed for overall survival (OS). Blood samples were taken at baseline and at intervals throughout the active treatment period for hematologic and flow cytometric analysis of circulating immune cell populations. Results: The all-subjects OS at 18 months is 29%. This compares favorably with previously published data: i.e., OS of only 18.6% at 18 months for FOLFIRINOX regimen alone (Conroy et al, 2011). Peripheral blood monocyte counts at baseline inversely correlate with OS (p = 0.0071, Hazard ratio = 1.169) with CCX872 and FOLFIRINOX combination therapy. Overall, circulating monocytes, inflammatory monocytes and monocytic myeloid derived suppressor cells were reduced by treatment. Conclusions: CCX872-B plus FOLFIRINOX resulted in an OS of 29% at 18 months with no safety issues. Better OS was associated with lower peripheral blood monocyte counts at baseline. Clinical trial information: NCT02345408.
Development and implementation of the SUM breast cancer cell line functional genomics knowledge base (2020)

Several years ago, the SUM panel of human breast cancer cell lines was developed, and these cell lines have been distributed to hundreds of labs worldwide. Our lab and others have developed extensive omics data sets from these cells. More recently, we performed genome-scale shRNA essentiality screens on the entire SUM line panel, as well as on MCF10A cells, MCF-7 cells, and MCF-7LTED cells. These gene essentiality data sets allowed us to perform orthogonal analyses that functionalize the otherwise descriptive genomic data obtained from traditional genomics platforms. To make these omics data sets available to users of the SUM lines, and to allow users to mine these data sets, we developed the SUM Breast Cancer Cell Line Knowledge Base. This knowledge base provides information on the derivation of each cell line, provides protocols for the proper maintenance of the cells, and provides a series of data mining tools that allow rapid identification of the oncogene signatures for each line, the enrichment of KEGG pathways with screen hit and gene expression data, an analysis of protein and phospho-protein expression for the cell lines, as well as a gene search tool and a functional-druggable signature tool. Recently, we expanded our database to include genomic data for an additional 27 commonly used breast cancer cell lines. Thus, the SLKBase provides users with deep insights into the biology of human breast cancer cell lines that can be used to develop strategies for the reverse engineering of individual breast cancer cell lines.
Single‐Molecule Approach to DNA Minor‐Groove Association Dynamics (2012)

Getting in the groove: Fluorescence correlation spectroscopy reveals that the dynamics of the association process of the bisbenzamidine minor-groove binder BBA-OG (blue with green star, see scheme) to dsDNA is not controlled by diffusion, but by the insertion of the binder into the groove at the specific site (red), as shown by the rate constants for each step of the binding event. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Special Issue on Fiber-Optics. Research and Development of Optical Fiber Sensors for Monitoring Parameters in High Voltage Electric Power Apparatus. (1994)

This paper describes a review concerning research and development of optical fiber sensors for high voltage electric power apparatus. Firstly, advantages of optical fiber sensing technique for monitoring parameters in high voltage power apparatus are explained. Then several examples of research and of developed devices are introduced in the field of current measurement, voltage measurement, corona discharge detection, and methods for cllection of signals from multiple sensors.
A phase 3 randomised study of enzalutamide plus leuprolide and enzalutamide monotherapy in high-risk non-metastatic hormone-sensitive prostate cancer with rising PSA after local therapy: EMBARK study design (2021)

NCT02319837.
Downlink and Uplink Decoupling in Two-Tier Heterogeneous Networks with Multi-Antenna Base Stations (2017)

In order to improve the uplink performance of future cellular networks, the idea to decouple the downlink (DL) and uplink (UL) association has recently been shown to provide significant gain in terms of both coverage and rate performance. However, all the work is limited to SISO network. Therefore, to study the gain provided by the DL and UL decoupling in multi-antenna base stations (BSs) setup, we study a two tier heterogeneous network consisting of multi-antenna BSs, and single antenna user equipments (UEs). We use maximal ratio combining (MRC) as a linear receiver at the BSs and using tools from stochastic geometry, we derive tractable expressions for both signal to interference ratio (SIR) coverage probability and rate coverage probability. We observe that as the disparity in the beamforming gain of both tiers increases, the gain in term of SIR coverage probability provided by the decoupled association over non-decoupled association decreases. We further observe that when there is asymmetry in the number of antennas of both tier, then we need further biasing towards femto-tier on the top of decoupled association to balance the load and get optimal rate coverage probability.
3D-Überwachung des OP-Saals - stören sich PMD-Kameras, Trackingsysteme und Spielkonsolenzubehör? (2011)

Fur verschiedene heutige und kunftige Aufgaben im Operationssaal konnen 3D-Kameras nutzliche Erganzungen darstellen oder neue Moglichkeiten eroffnen. Neben klassischen Time-of-Flight Kameras erfreut sich derzeit vor allem die Microsoft Kinect wachsender Beliebtheit – trotz ihrer Vermarktung als Spielkonsolenzubehor. Da die Mehrzahl der 3DKameras ebenso wie markerbasierte Trackingsysteme mit aktiver Aussendung von Licht im Infrarotbereich arbeitet, besteht die Gefahr, dass diese sich bei simultaner Verwendung ohne aufwendige Synchronisierung gegenseitig storen. Anhand dreier Kameramodelle und eines Trackingsystems wird dieser Sachverhalt untersucht und aufgezeigt, welche Kombinationen ohne entsprechende Mechanismen keine nennenswerten Beeinflussungen aufweisen und zwischen welchen Komponenten eine Synchronisierung notwendig ist. Schlusselworte: 3D-Kamera, Kinect, Uberwachungssystem, Operationssaal, Evaluation
S-Nitrosylation Signaling in Cell Biology (2003)

S-Nitrosylated proteins form when a cysteine thiol reacts with nitric oxide (NO) in the presence of an electron acceptor to form an S-NO bond. Under physiological conditions, this posttranslational modification affects the function a wide array of cell proteins, ranging from ion channels to nuclear regulatory proteins. Recent evidence suggests that 1) S-nitrosylated proteins can be synthesized by exposure of specific redox-active motifs to NO, through transnitrosation/transfer reactions, or through metalloprotein-catalyzed reactions; 2) S-nitrosothiols can be sequestered in membranes, lipophilic protein folds, or in vesicles to preserve their activity; and 3) S-nitrosothiols can be degraded by a number of enzymes systems. These recent insights regarding the bioactivities, molecular signaling pathways, and metabolism of endogenous S-nitrosothiols have suggested several new therapies for disease ranging from cystic fibrosis to pulmonary hypertension.
Graphene Decorated with PtAu Alloy Nanoparticles: Facile Synthesis and Promising Application for Formic Acid Oxidation (2011)

PtAu/graphene nanocomposites with high activity toward formic acid oxidation were synthesized in the presence of poly(diallyldimethylammonium chloride), which not only acted as “nanoreactors” for the preparation of PtAu alloy NPs but also facilitated the uniform loading of PtAu NPs on graphene nanosheets.
Resonance-aware methodology for system level power distribution network co-design (2009)

Power delivery network (PDN) design continues to be a major challenge because it demands a good portion of available silicon, package, and board routing resources. In this paper, we outline a frequency and time domain co-design flow that uses frequency domain results to construct time domain input vectors, resulting in a resonance aware time domain analyses flow that can highlight low and mid frequency behaviors dominated by board and package components and parasitics.
Electro-refractive photonic device (2023)

The various technologies presented herein relate to phase shifting light to facilitate any of light switching, modulation, amplification, etc. Structures are presented where a second layer is juxtaposed between a first layer and a third layer with respective doping facilitating formation of p-n junctions at the interface between the first layer and the second layer, and between the second layer and the third layer. Application of a bias causes a carrier concentration change to occur at the p-n junctions which causes a shift in the effective refractive index per incremental change in an applied bias voltage. The effective refractive index enhancement can occur in both reverse bias and forward bias. The structure can be incorporated into a waveguide, an optical resonator, a vertical junction device, a horizontal junction device, a Mach-Zehnder interferometer, a tuneable optical filter, etc.
Polarization-gradient-assisted subrecoil cooling: Quantum calculations in one dimension (1994)

We present a fully quantum-mechanical analysis of laser cooling of an angular momentum ${\mathit{J}}_{\mathit{g}}$=1 to ${\mathit{J}}_{\mathit{e}}$=1 transition in a laser configuration consisting of two counterpropagating linearly polarized laser beams. The essential feature of this configuration is the coexistence of velocity-selective coherent population trapping (VSCPT) and polarization-gradient cooling. The role of polarization-gradient cooling is to provide (i) for short interaction times ``precooling'' of the initial momentum distribution and (ii) in the long-time limit ``confinement of velocities.'' This eventually leads to a larger number of atoms being captured in the dark state when compared with the schme of Aspect et al. [Phys. Rev. Lett. 61, 826 (1988)]. We find that the optimum parameter values for polarization-gradient cooling and VSCPT are in a completely different parameter regime: polarization-gradient cooling works best off resonance and for low intensities, while VSCPT works best on resonance. We can combine the advantages of polarization-gradient cooling and VSCPT in a scheme where we cycle in time between the optimum cooling parameters for both cooling mechanisms.
Spondylocheirodysplastic Ehlers-Danlos syndrome (SCD-EDS) and the mutant zinc transporter ZIP13 (2014)

The zinc transporter protein ZIP13 plays crucial roles in bone, tooth, and connective tissue development, and its dysfunction is responsible for the spondylocheirodysplastic form of Ehlers-Danlos syndrome (SCD-EDS, OMIM 612350). We recently reported that the pathogenic mutations in ZIP13 reduce its functional protein level by accelerating the protein degradation via the VCP-linked ubiquitin proteasome pathway, resulting in the disturbance of intracellular zinc homeostasis that appears to contribute to SCD-EDS pathogenesis. Finally, we implicate that possible therapeutic approaches for SCD-EDS would be based on regulating the degradation of the pathogenic mutant ZIP13 proteins.
Optical Coherence Technology of the Retina (2002)

Although the question of why the pupil is black had attracted the attention of writers dating back to the time of Ancient Rome, it was not until 1851 that Herman Ludwig von Helmholtz unlocked the door to the back of the eye by inventing the Augenspiegel, or ophthalmoscope. Von Helm-holtz’s groundbreaking invention enabled examination of both normal and diseased eyes. It also allowed drawings to be made of the fundus. The first images of the retina were useful to physicians for communicating both normal and unusual findings to their colleagues.
Reducing Capsule Based on Electron Programming: Versatile Synthesizer for Size‐Controlled Ultra‐Small Metal Clusters (2016)

Controlled reducing capsules with a specific number of reducing electrons were achieved by appropriately placed BH<sub>3</sub> units in the dendritic polyphenylazomethines (DPAs). Using the 1:1 coordination fashion on their basic branches with radius affinity gradient, the 4th generation DPA (DPAG4) possessing four BH<sub>3</sub> units in the central positions was prepared as a template synthesizer for size-controlled ultra-small metal clusters. This was well-demonstrated by reduction of Ag, Pt, and other metal ions resulting in monodispersed ultra-small clusters.