gebhart/patrepeval huggingface dataset:
HER2-mediated enhancement of Ebola virus entry (2020)

Multiple cell surface molecules including TAM receptors (TYRO3, AXL, and MERTK), a family of tyrosine kinase receptors, can serve as attachment receptors for Ebola virus (EBOV) entry into cells. The interaction of these receptors with EBOV particles is believed to trigger the initial internalization events that lead to macropinocytosis. However, the details of how these interactions lead to EBOV internalization have yet to be elucidated. Here, we screened receptor tyrosine kinase (RTK) inhibitors for anti-EBOV activity by using our previously established biologically contained Ebola virus that lacks the VP30 gene (EBOVΔVP30) and identified several RTKs, including human epidermal growth factor receptor 2 (HER2), as potential targets of anti-EBOV inhibitors and as novel host factors that have a role in EBOV infection. Of these identified RTKs, it was only HER2 whose knockdown by siRNAs impaired EBOVΔVP30-induced AKT1 phosphorylation, an event that is required for AKT1 activation and subsequent macropinocytosis. Stable expression of HER2 resulted in constitutive activation of AKT1, resulting in the enhancement of EBOVΔVP30 growth, EBOV GP-mediated entry, and macropinocytosis. Moreover, we found that HER2 interacts with the TAM receptors, and in particular forms a complex with TYRO3 and EBOVΔVP30 particles on the cell surface. Interestingly, HER2 was required for EBOVΔVP30-induced TYRO3 and AKT1 activation, but the other TAM receptors (TYRO3 and MERTK) were not essential for EBOVΔVP30-induced HER2 and AKT1 activation. Our findings demonstrate that HER2 plays an important role in EBOV entry and provide novel insights for the development of therapeutics against the virus.
Non‐Gaussian Linear Mixing Models for Hyperspectral Images (2012)

Modeling of hyperspectral data with non‐Gaussian distributions is gaining popularity in recent years. Such modeling mostly concentrates on attempts to describe a distribution, or its tails, of all image spectra. In this paper, we recognize that the presence of major materials in the image scene is likely to exhibit nonrandomness and only the remaining variability due to noise, or other factors, would exhibit random behavior. Hence, we assume a linear mixing model with a structured background, and we investigate various distributional models for the error term in that model. We propose one model based on the multivariate t ‐distribution and another one based on independent components following an exponential power distribution. The former model does not perform well in the context of the two images investigated in this paper, one AVIRIS and one HyMap image. On the other hand, the latter model works reasonably well with the AVIRIS image and very well with the HyMap image. This paper provides the tools that researchers can use for verifying a given model to be used with a given image.
Evidence that appearance of thymulin in plasma follows lymphoid chimerism and precedes development of immunity in patients with lethal combined immunodeficiency transplanted with T cell-depleted haploidentical marrow. (1990)

Thymulin, a peptide secreted by human thymic epithelial cells, circulates in peripheral blood. Levels of plasma thymulin (FTS-Zn) activity were analyzed in 21 patients with lethal combined immunodeficiency disorders who were treated with transplantation of HLA-haplotype-mismatched parental bone marrow depleted of T cells by differential agglutination with soybean agglutinin and E-rosetting (SBA-E-BMT). Among these 21 infants, 15 were patients with severe combined immunodeficiency (SCID) and 6 had combined immunodeficiency (CID) with Omenn's syndrome or CID with T cell predominance (CIDTP). In contrast to normal infants who possess high levels of plasma thymulin activity, 20 of the 21 patients demonstrated undetectable or low plasma thymulin levels for their age at admission prior to transplantation. Following SBA-E-BMT, however, thymulin became detectable in the plasma of 17 of 18 evaluable patients and reached normal or near-normal levels between 21 and 125 days posttransplant. In patients in whom the timing of engraftment could be established by emergence of donor lymphocytes, thymulin appeared in the plasma at approximately the same time as lymphoid chimerism was detected, and in all patients who were engrafted and immunologically reconstituted, the increment in thymulin levels preceded development of immune functions. These studies support the concept that normal marrow-derived cells in the graft can provide a stimulus necessary for induction of thymic epithelial secretory function in patients with thymic dysplasia. Further, immunologic reconstitution in these patients was not seen following SBA-E-BMT unless and until recovery of thymus function had been observed.
Noninvasive longitudinal quantification of β‐cell mass with [ 111 In]‐labeled exendin‐4 (2019)

Currently, quantifying β‐cell mass (BCM) requires harvesting the pancreas. In this study, we investigated a potential noninvasive method to quantify BCM changes longitudinally using [Lys 12 ( 111 In‐BnDTPA‐Ahx)] exendin‐4 ([ 111 In]‐Ex4) and single‐photon emission computed tomography (SPECT). We used autoradiography and transgenic mice expressing green fluorescent protein under the control of mouse insulin 1 gene promotor to evaluate the specificity of [ 111 In]‐Ex4 toward β cells. Using nonobese diabetic (NOD) mice, we injected [ 111 In]‐Ex4 (3.0 MBq) intravenously and performed SPECT 30 min later, repeating this at a 2‐wk interval. After the second scan, we harvested the pancreas and calculated BCM from immunohistochemically stained pancreatic sections. Specific accumulation of [ 111 In]‐Ex4 in β cells was confirmed by autoradiography, with a significant correlation ( r = 0.94) between the fluorescent and radioactive signal intensities. The radioactive signal from the pancreas in the second SPECT scan significantly correlated ( r = 0.89) with BCM calculated from the immunostained pancreatic sections. We developed a regression formula to estimate BCM from the radioactive signals from the pancreas in SPECT scans. BCM can be quantified longitudinally and noninvasively by SPECT imaging with [ 111 In]‐Ex4. This technique successfully demonstrated longitudinal changes in BCM in NOD mice before and after onset of hyperglycemia.—Fujita, N., Fujimoto, H., Hamamatsu, K., Murakami, T., Kimura, H., Toyoda, K., Saji, H., Inagaki, N. Noninvasive longitudinal quantification of β‐cell mass with [ 111 In]‐labeled exendin‐4. FASEB J. 33, 11836‐11844 (2019). www.fasebj.org
InfoNCE Loss Provably Learns Cluster-Preserving Representations (2023)

The goal of contrasting learning is to learn a representation that preserves underlying clusters by keeping samples with similar content, e.g. the ``dogness'' of a dog, close to each other in the space generated by the representation. A common and successful approach for tackling this unsupervised learning problem is minimizing the InfoNCE loss associated with the training samples, where each sample is associated with their augmentations (positive samples such as rotation, crop) and a batch of negative samples (unrelated samples). To the best of our knowledge, it was unanswered if the representation learned by minimizing the InfoNCE loss preserves the underlying data clusters, as it only promotes learning a representation that is faithful to augmentations, i.e., an image and its augmentations have the same representation. Our main result is to show that the representation learned by InfoNCE with a finite number of negative samples is also consistent with respect to clusters in the data, under the condition that the augmentation sets within clusters may be non-overlapping but are close and intertwined, relative to the complexity of the learning function class.
Diketopyrrolopyrrole-based semiconducting polymer bearing thermocleavable side chains (2012)

The synthesis of a diketopyrrolopyrrole (DPP)-based semiconducting polymer bearing thermocleavable side chains is described. This polymer can be converted into a native semiconductive polymer by thermal annealing at 200 °C. The resulting side chain-free polymer showed a good p-type semiconductor performance in organic thin film transistors.
Phase I/II double-blinded randomized study to determine the tolerability and efficacy of two different doses of lenalidomide (Len) in biochemically relapsed prostate cancer (BRPC) (M0) patients (pts). (2010)

4554 Background: Preliminary data suggest that Len, an immunomodulatory agent and angiogenesis inhibitor, is active in prostate cancer. Aims: Evaluate the safety and efficacy of 6 months (mo) administration of 5 or 25 mg/day of Len. Methods: 60 noncastrate BRPC pts were stratified (PSADT, surgery/RT, prior ADT, Gleason) and randomized to oral Len at 5 (n=26) or 25 mg/day (n=34) given 3/4 weeks for 6 mo or until PSA progression (> 25% over baseline), clinical/radiographic progression or dose-limiting toxicity (tox). Disease status was evaluated at the end of every 6 mo cycle with scans and PSAs (collected/2 mo, assayed at 6 mo) and tox monthly. The proportion of pts with disease progression or dose limiting tox at 6 mo was compared between arms by chi-square test. Regression of the log PSA on the time of PSA measurement for each pt before and on study, was used to calculate pre and on study PSA slopes. The change in slope, on study slope minus pre study slope, was estimated for each pt and the mean changes for the two dose groups compared using a t-test. Results: Pre study parameters were balanced between arms. The occurrence of grade 3/4 tox was 11.5% with 5 mg and 29.4% with 25 mg, p=0.1, most commonly neutropenia (5 pts, all on 25 mg), venous thromboembolism (2 in each group), fatigue (2), skin rash (2). Mean (range) steady state Len plasma concentration (ng/ml) was 12.67 (6.1-19.2) versus 65.14 (24.3-106.0), p=0.01, for 5mg and 25mg respectively. Mean (range) follow up (mo) is 28.3±10.4 (12-41). A significant decrease in PSA slope favored the 25 mg (-0.172 vs. -0.033, p = 0.005) (Table). 50% and 44% of pts on 5 mg and 25 mg respectively, had PSA/scans progression at 6 mo. Currently 9 patients are still on study, 6 on 25 mg and 3 on 5 mg. Conclusions: Long-term Len treatment has acceptable tox, results in dose-dependent changes in PSA slope, and potentially delays progression of BRPC (M0). Randomized studies evaluating conventional disease endpoints should be performed. 5 mg 25 mg p value Mean (95% CI) pre-study PSA slope 0.16 (0.11 to 0.21) 0.18 (0.13 to 0.23) 0.55 Mean (95% CI) pre/post PSA slope −0.033 (−0.11 to 0.04) −0.172 (−0.24 to −0.11) 0.005 No significant financial relationships to disclose.
Computation-centric memory models (1998)

We present a computation-centric theory of memory models.
Tuning the structure and the mechanical properties of epoxy–silica sol–gel hybrid materials (2016)

A new epoxy–silica porous material prepared <italic>via</italic> one-pot sol–gel process. Mechanical properties can be continuously tuned by modifying reactant proportions.
Transferring Liquid Metal to form a Hybrid Solid Electrolyte via a Wettability‐Tuning Technology for Lithium‐Metal Anodes (2022)

Integrating solid-state electrolyte (SSE) into Li-metal anodes has demonstrated great promise to unleash the high energy density of rechargeable Li-metal batteries. However, fabricating a highly cyclable SSE/Li-metal anode remains a major challenge because the densification of the SSE is usually incompatible with the reactive Li metal. Here, a liquid-metal-derived hybrid solid electrolyte (HSE) is proposed, and a facile transfer technology to construct an artificial HSE on the Li metal is reported. By tuning the wettability of the transfer substrates, electron- and ion-conductive liquid metal is sandwiched between electron-insulating and ion-conductive LiF and oxides to form the HSE. The transfer technology renders the HSE continuous, dense, and uniform. The HSE, having high ion transport, electron shut-off, and mechanical strength, makes the composite anode deliver excellent cyclability for over 4000 h at 0.5 mA cm<sup>-2</sup> and 1 mAh cm<sup>-2</sup> in a symmetrical cell. When pairing with LiFePO<sub>4</sub> and sulfur cathodes, the HSE-coated Li metal dramatically enhances the performance of full cells. Therefore, this work demonstrates that tuning the interfacial wetting properties provides an alternate approach to build a robust solid electrolyte, which enables highly efficient Li-metal anodes.
Equilibration-Based Preconcentrating Minicolumn Sensors for Trace Level Monitoring of Radionuclides and Metal Ions in Water without Consumable Reagents (2006)

A sensor technique is described that captures analyte species on a preconcentrating minicolumn containing a selective solid-phase sorbent. In this approach, the sample is pumped through the column until the sorbent phase is fully equilibrated with the sample concentration, and the exit concentration equals the inlet concentration. On-column detection of the captured analytes using radiometric and spectroscopic methods is demonstrated. In trace level detection applications, this sensor provides a steady-state signal that is proportional to sample analyte concentration and is reversible. The method is demonstrated for the detection of Tc-99 using anion-exchange beads mixed with scintillating beads and light detection, Sr-90 using SuperLig 620 beads mixed with scintillating beads and light detection; and hexavalent chromium detection using anion-exchange beads with spectroscopic detection. Theory has been developed to describe the signal at equilibration and to describe analyte uptake as a function of volume and concentration, using parameters and concepts from frontal chromatography. It is shown that experimental sensor behavior closely matches theoretical predictions and that effective sensors can be prepared using low plate number columns. This sensor modality has many desirable characteristics for in situ sensors for trace level contaminant long-term monitoring where the use of consumable reagents for sensor regeneration would be undesirable. Initial experiments in groundwater matrixes demonstrated the detection of Tc-99 at drinking water level standards (activity of 0.033 Bq/mL) and detection of hexavalent chromium to levels below drinking water standards of 50 ppb.
Demonstration of the Allam Cycle: An Update on the Development Status of a High Efficiency Supercritical Carbon Dioxide Power Process Employing Full Carbon Capture (2017)

The Allam cycle is a novel CO2, oxy-fuel power cycle that utilizes hydrocarbon fuels while inherently capturing approximately 100% of atmospheric emissions, including nearly all CO2 emissions at a cost of electricity that is highly competitive with the best available energy production systems that do not employ CO2 capture. The proprietary system achieves these results through a semi-closed-loop, high-pressure, low-pressure-ratio recuperated Brayton cycle that uses supercritical CO2 as the working fluid, dramatically reducing energy losses compared to steam- and air-based cycles. In conventional cycles, the separation and removal of low concentration combustion derived impurities such as CO2 results in a large additional capital cost and increased parasitic power. As a result, removal in conventional cycles can increase the cost of electricity by 50% to 70% [1]. The compelling economics of the Allam Cycle are driven by high target efficiencies, 59% net for natural gas and 51% net for coal (LHV basis) while inherently capturing nearly 100% CO2 at pipeline pressure with low projected capital and O&M costs. Additionally, for a small reduction in performance the cycle can run substantially water free. The system employs only a single turbine, utilizes a small plant footprint, and requires smaller and fewer components than conventional hydrocarbon fueled systems. The Allam Cycle was first presented at GHGT-11 [2]. Since then, significant progress has been made, including detailed system design, component testing and the construction of a 50 MWth demonstration plant commencing in Q1 2016 and now entering commissioning as of Q4 2016. This paper will review the development status of the Allam Cycle; for the demonstration plant, the construction and commissioning status, schedule, key components, layout, and detailed design; turbine design, manufacturing status; development of a novel dynamic control system and control simulator for the demonstration plant; and other key aspects of the cycle. It will provide an update on the progress of the gasified solid fuel Allam Cycle and then address the overall Allam Cycle commercialization program, benefits and applications, and the expected design of the natural gas 300 MWe commercial NET Power plant projected for 2020.
Erratum: Media selection for anammox‐based polishing filters: Balancing anammox enrichment and retention with filtration function (2022)

The following corrections are noted for the article “Media selection for anammox-based polishing filters: Balancing anammox enrichment and retention with filtration function” Water Environment Research, 94, e10724 (2022): On page 11, the heading “Indications for PdNA or AnAOB filters application” is incorrect. This should be corrected to “Implications for PdNA or AnAOB filters application.” On page 12, the Author Contributions list is incorrect. Below is the complete Author Contribution list. Rahil Fofana: Data curation, formal analysis, and writing–original draft. Bo Peng: Data curation. Huu Huynh: Data curation. Mehran Sajjad: Data curation. Kimberly Jones: Supervision and writing–review & editing. Ahmed Al-Omari: Conceptualization and methodology. Charles Bott: Conceptualization and methodology. Jeseth Delgado Vela: Supervision and writing–review & editing. Sudhir Murthy: Conceptualization and methodology. Bernhard Wett: Conceptualization and methodology. Christine Debarbadillo: Conceptualization and methodology. Haydee De Clippeleir: Conceptualization, funding acquisition, methodology, and supervision. The authors apologize for these errors.
Antigen Shedding May Improve Efficiencies for Delivery of Antibody-Based Anticancer Agents in Solid Tumors (2012)

Recombinant immunotoxins (RIT) are targeted anticancer agents that are composed of a targeting antibody fragment and a protein toxin fragment. SS1P is a RIT that targets mesothelin on the surface of cancer cells and is being evaluated in patients with mesothelioma. Mesothelin, like many other target antigens, is shed from the cell surface. However, whether antigen shedding positively or negatively affects the delivery of RIT remains unknown. In this study, we used experimental data with SS1P to develop a mathematical model that describes the relationship between tumor volume changes and the dose level of the administered RIT, while accounting for the potential effects of antigen shedding.
The Collision Cross Sections of Iodide Salt Cluster Ions in Air via Differential Mobility Analysis-Mass Spectrometry (2013)

To date, most collision cross section (CCS) predictions have invoked gas molecule impingement-reemission rules in which specular and elastic scattering of spherical gas molecules from rigid polyatomic surfaces are assumed. Although such predictions have been shown to agree well with CCSs measured in helium bath gas, a number of studies reveal that these predictions do not agree with CCSs for ions in diatomic gases, namely, air and molecular nitrogen. To further examine the validity of specular-elastic versus diffuse-inelastic scattering models, we measured the CCSs of positively charged metal iodide cluster ions of the form [MI]n[M(+)]z, where M = Na, K, Rb, or Cs, n = 1 - 25, and z = 1 - 2. Measurements were made in air via differential mobility analysis mass spectrometry (DMA-MS). The CCSs measured are compared with specular-elastic as well as diffuse-inelastic scattering model predictions with candidate ion structures determined from density functional theory. It is found that predictions from diffuse-inelastic collision models agree well (within 5%) with measurements from sodium iodide cluster ions, while specular-elastic collision model predictions are in better agreement with cesium iodide cluster ion measurements. The agreement with diffuse-inelastic and specular-elastic predictions decreases and increases, respectively, with increasing cation mass. However, even when diffuse-inelastic cluster ion predictions disagree with measurements, the disagreement is of a near-constant factor for all ions, indicating that a simple linear rescaling collapses predictions to measurements. Conversely, rescaling cannot be used to collapse specular-elastic predictions to measurements; hence, although the precise impingement reemission rules remain ambiguous, they are not specular-elastic.
Radiation from and force acting on a point charge moving through a cylindrical hole in a conducting medium (1986)

The radiation from and the force acting on a point charge, moving with relativistic velocity through a cylindrical hole in a conducting medium, is determined. It is shown that a Cerenkov effect occurs if the conductivity of the medium is sufficiently small. Explicit results are given for the time dependence of the field demonstrating the existence of a Cerenkov cone. The dragging force on the moving particle due to radiation losses is examined in detail. The proposed method also applies to dispersive media.
Single Laser Shot Photoinduced Phase Transition of Rubidium Manganese Hexacyanoferrate Investigated by X‐ray Diffraction (2019)

We have studied by X‐ray diffraction the phase transition of microcrystals of rubidium manganese hexacyanoferrate, for which combined electron transfer and structural reorganization are responsible for a change of magnetic properties. The Rb 0.94 Mn[Fe(CN) 6 ] 0.98 · 2.5H 2 O system undergoes a phase transition between the tetragonal phase Fe II (S = 0)–CN–Mn III (S = 2) and the cubic Fe III (S = 1/2)–CN–Mn II (S = 5/2) phases. The thermal equilibrium phase transition shows a broad regime of bistability, responsible for the appearance of a thermal hysteresis in the approximate 185–300 K temperature range. We used a deposited film to study by X‐ray diffraction the switching from the tetragonal phase to the cubic phase, induced inside the thermal hysteresis by a single laser shot of tuneable power. Compared to previous measurements using local probes, our results show that the ns laser pulse induces a stable long‐range ordered cubic phase when conversion is partial or complete.
The Coming of the Cataclysm (1997)

Abstract This chapter examines the stages in the development of the Cultural Revolution in China. The first stage was set in May 1966 in Beijing where Mao Zedong was working behind the scenes. It was Kang Sheng's wife Cao Yiou who persuaded Peking University teachers to denounce university administrators, which started a series of demonstrations. This was followed by the public appearance of Mao in July 1966, his meeting with leftist leaders, and his decision in the eleventh Plenum to rule without restraint. A crucial tactical element in Mao's game plan was the differential treatment of Liu Shaoqi and Deng Xiaoping.