gebhart/patrepeval huggingface dataset:
Antitumor efficacy of CD137 ligation is maximized by the use of a CD137 single-chain Fv–expressing whole-cell tumor vaccine compared with CD137-specific monoclonal antibody infusion (2006)

Abstract Tumor-destructive immune responses can be generated by engaging CD137 (4-1BB) via infusing a monoclonal antibody specific for CD137 or vaccinating with a single-chain Fv (scFv) CD137-expressing whole-cell tumor vaccine. We assessed whether such a vaccine can induce tumor rejection in the neu-transgenic (neu-Tg) mouse breast cancer model and compared the antitumor efficacy of vaccination with the infusion of a CD137-specific antibody. Mammary carcinoma cells (MMC) from a neu-Tg mouse were transfected to stably express surface scFv derived from the anti-CD137 rat hybridoma 1D8 or 3H3. The anti-CD137 scFv-expressing cells were rejected when transplanted into neu-Tg mice by a mechanism that involved both CD4+ and CD8+ T cells, and vaccination with such cells delayed the outgrowth of MMC cells transplanted 3 days previously. T cells from neu-Tg mice that had been vaccinated proliferated and produced IFN-γ when stimulated by MMC but not by antigen-negative variant breast cancer cells that did not express the neu tumor antigen. In addition, antibodies binding to the MMC but not to antigen-negative variant cells were detected in sera from some but not all of the immunized mice. Complete regression of s.c. transplanted MMC tumors was observed in mice repeatedly immunized against MMC-1D8 starting on the day the MMC cells were transplanted. In contrast, repeated administration of either of two different anti-CD137 monoclonal antibodies did not induce complete tumor regression, although tumor growth was delayed. [Mol Cancer Ther 2006;5(1):149–55]
Clinical and pathological impact of VHL, PBRM1, BAP1, SETD2, KDM6A, and JARID1c in clear cell renal cell carcinoma (2013)

VHL is mutated in the majority of patients with clear cell renal cell carcinoma (ccRCC), with conflicting clinical relevance. Recent studies have identified recurrent mutations in histone modifying and chromatin remodeling genes, including BAP1, PBRM1, SETD2, KDM6A, and JARID1c. Current evidence suggests that BAP1 mutations are associated with aggressive disease. The clinical significance of the remaining genes is unknown. In this study, targeted sequencing of VHL and JARID1c (entire genes) and coding regions of BAP1, PBRM1, SETD2, and KDM6A was performed on 132 ccRCCs and matched normal tissues. Associations between mutations and clinical and pathological outcomes were interrogated. Inactivation of VHL (coding mutation or promoter methylation) was seen in 75% of ccRCCs. Somatic noncoding VHL alterations were identified in 29% of ccRCCs and may be associated with improved overall survival. BAP1 (11%), PBRM1 (33%), SETD2 (16%), JARID1c (4%), and KDM6A (3%) mutations were identified. BAP1-mutated tumors were associated with metastatic disease at presentation (P = 0.023), advanced clinical stage (P = 0.042) and a trend towards shorter recurrence free survival (P = 0.059) when compared with tumors exclusively mutated for PBRM1. Our results support those of recent publications pointing towards a role for BAP1 and PBRM1 mutations in risk stratifying ccRCCs. Further investigation of noncoding alterations in VHL is warranted.
Nature of smectic ordering at a solid–liquid-crystal interface and its influence on layer growth (1991)

It is found that the layer normal of a chiral smectic-A liquid crystal is tilted away from an easy axis created by a unidirectional rubbing. The alignment angle of the tilted layer normal with respect to the easy axis approaches about 18\ifmmode^\circ\else\textdegree\fi{}, which is substantially larger than what has been previously observed. This larger deviation cannot be described in terms of the surface electronic effect, and an alternative mechanism is proposed on the basis of molecular chirality and the degree of smectic ordering at the surface.
A versatile A2+ B3approach to hyperbranched polyacenaphthenequinones (2014)

A series of hyperbranched polyacenaphthenequinones has been prepared by superelectrophilic aromatic substitution of (substituted) acenaphthenequinone and 1,3,5-tris-(4-phenoxybenzoyl)benzene via a facile A2 + B3 approach. Because of the strongly increased reactivity of the second A functionality, gelation was efficiently avoided during the polymerization. The structure of the resulting polymer was characterized by NMR spectroscopy and gel permeation chromatography. Further modification of the hyperbranched polyacenaphthenequinone was explored both on the acenaphthenequinone and aromatic moieties. Moreover, the polymer modified through sulfonation was investigated as a water-soluble acid catalyst for the degradation of biomass resources. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014, 52, 2596-2603
Amplitude- and phase-resolved nano-spectral imaging of phonon polaritons in hexagonal boron nitride (2015)

Phonon polaritons are quasiparticles resulting from strong coupling of photons with optical phonons. Excitation and control of these quasiparticles in 2D materials offer the opportunity to confine and transport light at the nanoscale. Here, we image the phonon polariton (PhP) spectral response in thin hexagonal boron nitride (hBN) crystals as a representative 2D material using amplitude- and phase-resolved near-field interferometry with broadband mid-IR synchrotron radiation. The large spectral bandwidth enables the simultaneous measurement of both out-of-plane (780 cm-1) and in-plane (1370 cm-1) hBN phonon modes. In contrast to the strong and dispersive in-plane mode, the out-of-plane mode PhP response is weak. Measurements of the PhP wavelength reveal a proportional dependence on sample thickness for thin hBN flakes, which can be understood by a general model describing two-dimensional polariton excitation in ultrathin materials.
Asphaltene Onset Pressure Uncertainty and Other Asphaltene Issues in Field Development Planning (2017)

Abstract Deepwater fields, such as those encountered in the Gulf of Mexico (GoM), often exhibit reservoir tar deposits and asphaltene instability (Dumont et al, 2012, Mullins et al, 2016). This instability may manifest itself within the reservoir in the form of out of equilibrium asphaltene gradients and tar deposits. These tar deposits can present drilling hazards which are a major nuisance for drilling operations, and can force operators to drill multiple sidetracks or bypass wells. This of course leads to increase well spend and rig time usage. For instance, the last two years showed that approximately 5% of the wells drilled in the GoM encountered severe drilling issues related to asphaltenes/tar deposits. Even more critical and concerning, is that asphaltene instability can have major implications for field developments, stretching expenditure risks beyond a single well to that of an entire field. From a flow assurance point of view, comingling incompatible oil produced from different zones or reservoirs can precipitate, and worse, deposit asphaltenes in the production path even when the unmixed oils are individually stable. Thus for reservoir management and field development plan, tar deposits can seal off aquifer support and have a detrimental impact on the productivity index of the field. During field development planning, it is essential to know the Asphaltene Onset Pressure (AOP) of the produced oils at reservoir conditions and its change with pressure and temperature along the wellpath. In addition, for unstable oils, AOP gradients variations across the field should be evaluated as AOP can vary largely as a result of Reservoir Fluid Geodynamics (RFG) processes occurring within the reservoir. For instance, fluid mixing due to a secondary charge into a reservoir after trap filling increases the AOP of the resulting oil. In addition, the non-homogeneity of AOP can then be mislabeled as AOP laboratory uncertainty. As AOP field variability can impact all aspects of the journey of the oil to surface, (well placement, completion, recovery factor, injection for pressure support, surface facility, and subsea equipment) and because no model exist to predict AOP gradients, the measurement and the evaluation of these AOP gradients, coupled with simple chemistry understanding are key inputs to a successful field development plan. This paper discuss AOP gradients within a reservoir, their impact on Field Development Plan (FDP), their origin, and proposes a methodology to characterize them.
A frequent PNPLA3 variant predicts disease course in PSC patients with dominant bile duct strictures (2012)

Background and aims: Primary sclerosing cholangitis (PSC) is caused by chronic inflammation of the bile ducts and can progress to end-stage liver disease. The rs738409 variant (I148M) of the PNPLA3 gene is associated with alcoholic and non-alcoholic liver disease and we evaluated its impact on the disease course of PSC.
Evaluation of rinse material and process for EUV lithography (2015)

Extreme ultraviolet lithography (EUVL) is the most promising option for future manufacturing of IC devices at sub-10nm node. However, resist pattern collapse is one concern for high volume manufacturing. To mitigate resist pattern collapse, rinse material is applied for EUVL. However at narrow pitches, it was found that some rinse materials caused pattern bridging and critical dimension (CD) shift. In this study, we suggest a model of resist deformation by surfactant penetration to resist pattern. Moreover, we focused on affinity between resist and surfactant which is main components in rinse material to clarify the pattern bridging and CD-shift issue by inducing surfactant penetration to resist pattern. To define the affinity between each material, Solubility Parameter (SP) value and Difference of Solubility Parameter value (DSP) of each material was calculated. The relation between surfactant penetration and DSP of each material was investigated. To clarify the relation, stress test was applied to enhance pattern deformation. As a result, it can be said that there is good correlation between surfactant penetration and SP value. Using these studies, rinse material design with low affinity surfactant for resist was able to achieve no CD-shift and less pattern bridging defect number.
Clinicopathologic report of ocular involvement in ALS patients with C9orf72 mutation (2014)

Our objective was to present clinicopathologic evidence of anterior visual pathway involvement in patients with amyotrophic lateral sclerosis (ALS) secondary to a C9orf72 mutation. Two related patients from an extended pedigree with ALS and GGGGCC hexanucleotide repeat expansion in the C9orf72 gene (C9-ALS) underwent neuro-ophthalmologic examination. Following death and tissue donation of the younger ALS patient, histopathologic examination of the retina, optic nerve and central nervous system (CNS) was performed. Ophthalmologic examination revealed contrast sensitivity impairment in the younger C9-ALS patient. Immunohistochemistry performed on this patient's donor tissue demonstrated p62-positive, pTDP43-negative perinuclear inclusions in the inner nuclear layer of the retina and CNS. Further colocalization with GLT-1 and recoverin suggested that the majority of retinal p62-positive inclusions are found within cone bipolar cells as well as some amacrine and horizontal cells. In conclusion, this is the first report that identifies disease-specific pathologic inclusions in the anterior visual pathway of a patient with a C9orf72 mutation. Cone bipolar cell involvement within the inner nuclear layer of the retina may explain the observed subtle visual function deficiencies in this patient. Further clinical and histopathologic studies are needed to fully characterize a larger population of C9-ALS patients and explore these findings in other forms of ALS.
AutoScale: Learning to Scale for Crowd Counting and Localization (2019)

Recent works on crowd counting mainly leverage CNNs to count by regressing density maps, and have achieved great progress. In the density map, each person is represented by a Gaussian blob, and the final count is obtained from the integration of the whole map. However, it is difficult to accurately predict the density map on dense regions. A major issue is that the density map on dense regions usually accumulates density values from a number of nearby Gaussian blobs, yielding different large density values on a small set of pixels. This makes the density map present variant patterns with significant pattern shifts and brings a long-tailed distribution of pixel-wise density values. We propose a simple and effective Learning to Scale (L2S) module, which automatically scales dense regions into reasonable closeness levels (reflecting image-plane distance between neighboring people). L2S directly normalizes the closeness in different patches such that it dynamically separates the overlapped blobs, decomposes the accumulated values in the ground-truth density map, and thus alleviates the pattern shifts and long-tailed distribution of density values. This helps the model to better learn the density map. We also explore the effectiveness of L2S in localizing people by finding the local minima of the quantized distance (w.r.t. person location map). To the best of our knowledge, such a localization method is also novel in localization-based crowd counting. We further introduce a customized dynamic cross-entropy loss, significantly improving the localization-based model optimization. Extensive experiments demonstrate that the proposed framework termed AutoScale improves upon some state-of-the-art methods in both regression and localization benchmarks on three crowded datasets and achieves very competitive performance on two sparse datasets.
A Contextual Investigation of Location in the Home Using Bluetooth Low Energy Beacons (2017)

Location sensing is a key enabling technology for Ubicomp to support contextual interaction. However, the laboratories where calibrated testing of location technologies is done are very different to the domestic situations where ‘context’ is a problematic social construct. This study reports measurements of Bluetooth beacons, informed by laboratory studies, but done in diverse domestic settings. The design of these surveys has been motivated by the natural environment implied in the Bluetooth beacon standards relating the technical environment of the beacon to the function of spaces within the home. This research method can be considered as a situated, ‘ethnographic’ technical response to the study of physical infrastructure that arises through social processes. The results offer insights for the future design of ‘seamful’ approaches to indoor location sensing, and to the ways that context might be constructed and interpreted in a seamful manner.
Fully functional 0.5-/spl mu/m 64-kbit embedded SBT FeRAM using a new low temperature SBT deposition technique (1999)

0.5 /spl mu/m design rule embedded 64 kbit SBT (SrBi/sub 2/(Ta,Nb)/sub 2/O/sub 9/) FeRAMs (ferroelectric RAM) are fabricated using a new low temperature SBT deposition technique. The developed deposition technique has successfully lowered SBT crystallization temperature from 800/spl deg/C to 700/spl deg/C, resulting in co-fabrication of FeRAM and fine CMOS logic devices with W plugs. The fabricated devices are proven to be fully functional.
Experimental Pleural Effusion as a Manifestation of Delayed Hypersensitivity to Tuberculin PPD (1968)

Summary Evidence is presented that pleural effusions in guinea pigs may be induced by hypersensitivity to PPD in the absence of infection with tuberculous organisms. Transfer of this reaction with cells from immunized animals indicates a predominant role of the delayed type of hypersensitivity, and documents an additional physiologic effect of this form of hypersensitivity reaction in vivo. Differences found in the protein concentrations of these effusions are compatible with differences in control of macromolecular movement in effusions induced by this hypersensitivity reaction, when compared with effusions resulting from nonspecific chemical injury. Studies utilizing in vitro incubations of lungs from sensitized donors indicate a role of soluble mediators released during the hypersensitivity reaction in the induction of pleural effusions, and thus suggest the importance of such mediators in in vivo manifestations of delayed hypersensitivity.
Vulnerable plaque intervention: State of the art (2008)

Progressive atherosclerotic disease is responsible for many of the late adverse clinical events that detract from the high procedural and clinical success of percutaneous coronary intervention. Despite recent advances in catheter based technology for the treatment of obstructive coronary artery disease, the greater risk to the patient over time may in fact come from the significant rate of acute coronary events triggered by nonculprit and/or nonobstructive coronary artery lesions. These areas of vulnerability within the epicardial coronary tree have generated a great deal of interest surrounding the concepts of vulnerable plaque (VP), vulnerable blood and the vulnerable patient. This 'state of the art' review discusses the limitations of coronary angiography alone in providing risk assessment; reviews the underlying biological concepts of VP; discusses evolving noninvasive and invasive imaging technologies for the detection of VP; and finally provides a futuristic look at how the field of interventional cardiology may transcend the traditional angiogram and move toward a more comprehensive treatment approach that benefits the patients' overall coronary health.
Development and Manufacture of a Curtius Rearrangement Using Continuous Flow towards the Large-Scale Manufacture of AZD7648 (2022)

Flow chemistry has been more frequently used in the development and manufacture of pharmaceuticals due to the progression of equipment and the availability of manufacturing facilities. This important tool for manufacture enables chemistries which were previously inefficient, hazardous, or not viable on scale in batch. Described herein is how continuous flow has been used to overcome issues with respect to the handling of hazardous materials in batch. The manufacturing step described is a Curtius reaction using diphenylphosphoryl azide (DPPA) as the azide precursor in the formation of a purinone at high temperatures with inline infrared monitoring.
Brain-wide representations of prior information in mouse decision-making (2023)

The neural representations of prior information about the state of the world are poorly understood. To investigate them, we examined brain-wide Neuropixels recordings and widefield calcium imaging collected by the International Brain Laboratory. Mice were trained to indicate the location of a visual grating stimulus, which appeared on the left or right with prior probability alternating between 0.2 and 0.8 in blocks of variable length. We found that mice estimate this prior probability and thereby improve their decision accuracy. Furthermore, we report that this subjective prior is encoded in at least 20% to 30% of brain regions which, remarkably, span all levels of processing, from early sensory areas (LGd, VISp) to motor regions (MOs, MOp, GRN) and high level cortical regions (ACAd, ORBvl). This widespread representation of the prior is consistent with a neural model of Bayesian inference involving loops between areas, as opposed to a model in which the prior is incorporated only in decision-making areas. This study offers the first brain-wide perspective on prior encoding at cellular resolution, underscoring the importance of using large scale recordings on a single standardized task.
DeepRadioID: Real-Time Channel-Resilient Optimization of Deep Learning-based Radio Fingerprinting Algorithms (2019)

Radio fingerprinting provides a reliable and energy-efficient IoT authentication strategy. By mapping inputs onto a very large feature space, deep learning algorithms can be trained to fingerprint large populations of devices operating under any wireless standard. One of the most crucial challenges in radio fingerprinting is to counteract the action of the wireless channel, which decreases fingerprinting accuracy significantly by disrupting hardware impairments. On the other hand, due to their sheer size, deep learning algorithms are hardly re-trainable in real-time. Another aspect that is yet to be investigated is whether an adversary can successfully impersonate another device fingerprint. To address these key issues, this paper proposes DeepRadioID, a system to optimize the accuracy of deep-learning-based radio fingerprinting algorithms without retraining the underlying deep learning model. We extensively evaluate DeepRadioID on a experimental testbed of 20 nominally-identical software-defined radios, as well as on two datasets made up by 500 ADS-B devices and by 500 WiFi devices provided by the DARPA RFMLS program. Experimental results show that DeepRadioID (i) increases fingerprinting accuracy by about 35%, 50% and 58% on the three scenarios considered; (ii) decreases an adversary's accuracy by about 54% when trying to imitate other device fingerprints by using their filters; (iii) achieves 27% improvement over the state of the art on a 100-device dataset.
Load Balancing in Small-Cell Access Point Placement (2023)

We address the uplink small-cell access point (AP) placement problem for optimal throughput, while considering load balancing (LB) among the APs. To consider LB and consequently incorporate fairness in user spectral access, i.e., the frequency of user-to-AP communications, we modify the Lloyd algorithm from vector quantization so that delays incurred by the existence of a large number of users in a cell are accounted for in the AP placement process. Accordingly, we present two methods, the first of which involves the incorporation of weights proportional to the cell occupancy, hence called the Occupancy Weighted Lloyd algorithm (OWLA). The second method adds a new step to the Lloyd algorithm, which involves re-assigning users from higher to lower occupancy cells, and the adoption of a distance threshold to cap the throughput lost in the assignment process. This formulated Lloyd-type algorithm is called the Cell Equalized Lloyd Algorithm-α (CELA-α) where α is a factor that allows for throughput and spectrum access delay trade-off. Extensive simulations show that both CELA-α and OWLA algorithms provide significant gains, in comparison to the standard Lloyd algorithm, in 95%-likely user spectral access. For the α values considered in this paper, CELA-α achieves gains up to 20.83%, while OWLA yields a gain of 12.5%. Both algorithms incur minimal throughput losses of different degrees, and the choice of using one algorithm over the other for AP placement depends on system LB as well as throughput requirements.