gebhart/patrepeval huggingface dataset:
RNA Tertiary Folding Monitored by Fluorescence of Covalently Attached Pyrene (1999)

The pathways by which large RNAs adopt tertiary structure are just beginning to be explored, and new methods that reveal RNA folding are highly desirable. Here we report an assay for RNA tertiary folding in which the fluorescence of a covalently incorporated chromophore is monitored. Folding of the 160-nucleotide Tetrahymena group I intron P4-P6 domain was used as a test system. Guided by the P4-P6 X-ray crystal structure, we chose a nucleotide (U107) for which derivatization at the 2'-position should not perturb the folded conformation. A 15-mer RNA oligonucleotide with a 2'-amino substitution at U107 was derivatized with a pyrene chromophore on a variable-length tether, and then ligated to the remainder of P4-P6, providing a site-specifically pyrene-labeled P4-P6 derivative. Upon titration of the pyrene-derivatized P4-P6 with Mg(2+), the equilibrium fluorescence intensity reversibly increased several-fold, as expected if the probe's chemical microenvironment changes as the RNA to which it is attached folds. The concentration and specificity of divalent ions required to induce the fluorescence change (Mg(2+) approximately Ca(2+) > Sr(2+)) correlated well with biochemical folding assays that involve nondenaturing gel electrophoresis. Furthermore, mutations in P4-P6 remote from the chromophore that shifted the Mg(2+) folding requirement on nondenaturing gels also affected in a predictable way the Mg(2+) requirement for the fluorescence increase. Initial stopped-flow studies with millisecond time resolution suggest that this fluorescence method will be useful for following the kinetics of P4-P6 tertiary folding. We conclude that a single site-specifically tethered chromophore can report the formation of global structure of a large RNA molecule, allowing one to monitor both the equilibrium progress and the real-time kinetics of RNA tertiary folding.
The immunocytochemical location of two membrane-associated placental tissue proteins in human and cynomolgus monkey placentae. (1984)

Using the PAP technique, the location of two new membrane-associated placental tissue proteins, MP1 and PP4 was studied in the placenta, its membranes, decidua and umbilical cord of human and cynomolgus monkeys. The results were the same throughout pregnancy. MP1 was located in the syncytiotrophoblast and trophoblastic cells of the reflected chorion. Other placental tissue components (cytotrophoblast, amnion, decidua, and umbilical cord) were negative. At present, MP1 appears to be specific for trophoblast. PP4 was located in the syncytiotrophoblast. Furthermore clear positive staining for PP4 was found in the villous cytotrophoblast, reflected and basal chorion, amnion, umbilical cord and decidua. In addition, PP4 was positive in some granulocyte-like blood cells in the intervillous space. Immunocytochemically, the most positive staining for both proteins was observed in the membrane of villous syncytiotrophoblastic cells. The findings in the placenta of cynomolgus monkeys were similar to those in women. The monkey could, thus, serve as a model for the investigation of these new membrane-associated placental tissue proteins.
Nondestructive, longitudinal measurement of collagen scaffold degradation using computed tomography and gold nanoparticles (2019)

Biodegradable materials, such as collagen scaffolds, are used extensively in clinical medicine for tissue regeneration and/or as an implantable drug delivery vehicle. However, available methods to study biomaterial degradation are typically invasive, destructive, and/or non-volumetric. Therefore, the objective of this study was to investigate a new method for nondestructive, longitudinal, and volumetric measurement of collagen scaffold degradation. Gold nanoparticles (Au NPs) were covalently conjugated to collagen fibrils during scaffold preparation to enable contrast-enhanced imaging of collagen scaffolds. The X-ray attenuation of as-prepared scaffolds increased linearly with increased Au NP concentration such that ≥60 mM Au NPs provided sufficient contrast to measure scaffold degradation. Collagen scaffold degradation kinetics were measured to increase during in vitro enzymatic degradation in media with an increased concentration of collagenase. The scaffold degradation kinetics measured by micro-CT exhibited lower variability compared with gravimetric measurement and were validated by measurement of the release of Au NPs from the same samples by optical spectroscopy. Thus, Au NPs and CT synergistically enabled nondestructive, longitudinal, and volumetric measurement of collagen scaffold degradation.
Carbohydrate nanoparticle‐mediated colloidal assembly for prolonged efficacy of bacteriocin against food pathogen (2011)

The goal of this study was to demonstrate the ability of carbohydrate nanoparticle-stabilized emulsion to prolong the efficacy of bacteriocin against food pathogens. An amphiphilic, negatively charged carbohydrate nanoparticle, phytoglycogen octenyl succinate (PG-OS), was used to form oil-in-water emulsion for delivering bacteriocin nisin against the food pathogen Listeria monocytogenes. Dynamic light scattering test showed that in emulsion all PG-OS nanoparticles were adsorbed at the surface of oil droplets. Zeta-potential analysis indicated an effective adsorption of positively charged nisin molecules at the surface of PG-OS interfacial layer. Nisin depletion model showed that, during 50 days of storage, the anti-listerial activity of nisin-containing PG-OS-stabilized emulsion was substantially greater than that of nisin solution. In contrast, the emulsion stabilized with a neutral, small-molecule surfactant (Tween 20) or negatively charged, hyperbranched carbohydrate polymer (modified starch) was either ineffective or less effective than the nanoparticle-stabilized emulsion to retain nisin activity during storage.
Strong Optical Confinement between Nonperiodic Flat Dielectric Gratings (2011)

We present a novel design of optical microcavity where the optical energy resides primarily in free space and therefore is readily accessible to foreign objects such as atoms, molecules, mechanical resonators, etc. We describe the physics of these resonators and propose a design method based on stochastic optimization. Cavity designs with diffraction-limited mode volumes and quality factors in the range of 10(4)-10(6) are presented. With a purely planar geometry, the cavity can be easily integrated on-chip by using conventional micro- and nanofabrication processes.
Kaposi's Sarcoma-Associated Herpesvirus-Encoded Oncogenes and Oncogenesis (1998)

Molecular biologic studies of Kaposi's sarcoma-associated herpesvirus (KSHV) have identified a number of potential viral oncogenes that may contribute to KSHV-related neoplasia including a D-type cyclin, an IL-6-like cytokine, and a novel member of the interferon regulatory factor family. KSHV is functionally related to other DNA tumor viruses by encoding specific proteins to inhibit pRb, pro-apoptotic, and interferon-signaling tumor suppressor pathways. The virus appears to employ molecular piracy of cellular regulatory genes as a mechanism to avoid cellular antiviral responses. The transparency of the KSHV genome allows ready identification of the cellular regulatory pathways which may be involved in transformation by KSHV. This provides strong support to the notion that some tumor suppressor pathways serve the dual function of being antiviral pathways to induce cell cycle arrest, apoptosis, and enhanced cell-mediated immunity in response to virus infection. Neoplasia may result from specific viral strategies to overcome these host defense pathways.
Determination of Arsenic and Selenium in Whole Fish by Continuous-Flow Hydride Generation Atomic Absorption Spectrophotometry (1989)

A combined wet chemical and dry ash digestion and use of a continuous-flow hydride generator coupled with a flame-heated quartz cell enabled the simple, precise, and highly automated atomic absorption determination of arsenic and selenium in tissues of whole fish. Percent relative standard deviation averaged 4% for each element; method detection limits (micrograms/g dry wt) were about 0.06 for arsenic and 0.04 for selenium. Digestion of samples proceeded with little operator attention and without perchloric acid. Analysis for arsenic as As(V) simplified sample preparation but care had to be exercised to avoid interferences from high concentrations of selenium.
ChemInform Abstract: Selective Deprotection of Methylene Acetal and MOM Ether in the Presence of Ketal‐Type Protective Groups: Remarkable Effect of TBSOTf. (2013)

Abstract A novel procedure for the highly selective deprotection of methylene acetals and Mom‐groups in the presence of ketal‐type protective groups is developed utilizing a combination of Tbs‐O‐Tf and 2,2′‐bipyridyl.
Parasitic bipolar gain reduction and the optimization of 0.25-μm partially depleted SOI MOSFETs (1999)

An in-depth analysis of the role of parasitic bipolar gain reduction in 0.25-/spl mu/m partially depleted SOI MOSFETs is presented, considering both dc characteristics as well as circuit operation. The effect of channel doping, silicide proximity, and germanium implantation on the lateral bipolar gain are characterized for optimal performance and manufacturability. Channel doping has the expected impact on bipolar gain. Silicide proximity is shown also to have a large impact. Germanium implantation into the source/drain regions reduces the lateral bipolar gain due to the introduction of defects that act as recombination centers in the source, reducing emitter efficiency. Further, germanium implantation serves to finely control the silicidation process, leading to good manufacturing control of the lateral silicide encroachment. Analysis of MOSFET dc I-V characteristics shows that threshold voltages for SOI have to be set only 30-50 mV higher for comparable dc off current to bulk CMOS. Finally, the impact of bipolar gain on floating-body-induced hysteretic effects and on alpha-particle-induced SRAM soft error rates are described.
What Questions Are on the Minds of STEM Undergraduate Students and How Can They Be Addressed? (2021)

Addressing common student questions in introductory STEM courses early in the term is one way that instructors can ensure that their students have all been presented with information about how to succeed in their courses. However, categorizing student questions and identifying evidence-based resources to address student questions takes time, and instructors may not be able to easily collect and respond to student questions at the beginning of every course. To help faculty effectively anticipate and respond to student questions, we 1) administered surveys in multiple STEM courses to identify common student questions, 2) conducted a qualitative analysis to determine categories of student questions (e.g., what are best practices for studying, how can in- and out-of- course time be effectively used), and 3) collaboratively identified advice on how course instructors can answer these questions. Here, we share tips, evidence-based strategies, and resources from faculty that instructors can use to develop their own responses for students. We hope that educators can use these common student questions as a starting point to proactively address questions throughout the course and that the compiled resources will allow instructors to easily find materials that can be considered for their own courses.
Correlation coefficient control for a frequency reconfigurable dual-band compact MIMO antenna destined for LTE (2014)

In this contribution, we are proposing a compact design for an implementation of a two element MIMO antenna destined for LTE smart phones. The antennas are collocated at one end of the PCB to minimize antenna volume. Each element is dual-band and frequency reconfigurable using tunable capacitors. The MIMO performance is investigated in two different channel models through efficiency, branch power imbalance and envelope correlation. The proposed antennas have acceptable levels of isolation between them, even in the low-bands, while having a good efficiency. Furthermore, the correlation coefficient is controlled by manipulating the ground currents between the antennas using a tunable capacitor. Nonetheless, using this mechanism to control the coupling between the antennas, the total efficiency is affected.
Reflectance microscopy techniques for 3D imaging of the alveolar structure (2010)

Lung disease involving the alveoli and distal bronchioles are poorly understood and most commonly studied indirectly via lung function tests. Available imaging tools for the non-destructive assessment of the alveolar structure include X-ray computed tomography, intra-vital fluorescence microscopy and Optical Coherence Tomography, which are either limited by long acquisition time, inadequate resolution and contrast, or shallow imaging depth.

In this study, we investigated the potential of two high-resolution reflectance microscopy imaging techniques, Spectrally Encoded Confocal Microscopy (SECM; 1µm (x) x 1µm (y) x 5µm (z) resolution) and Full Field Optical Coherence Microscopy (FFOCM; 1µm (x) x 1µm (y) x 1µm (z) resolution), for imaging alveolar microstructural detail. Two mouse lung samples were imaged with both SECM and FFOCM. The specimens were inflation-fixed using a modified Heitzman fixation technique at 20 cm H2O pressure. They were cut in 500mm thick slices and water immersed for imaging. Images were obtained and analyzed to determine whether or not the resolution and contrast of these techniques are sufficient to visualize the fine structures of the alveolar wall.

Alveolar microstructure could be resolved in three dimensions in images obtained by both technologies. Alveolar septal walls from multiple layers could be clearly identified while sub-cellular structures such as nuclei were also visible in the SECM technique. In conclusion, we have demonstrated that two imaging technologies provide important sub-cellular detail that is required to study alveolar microstructure. Future research to develop these imaging modalities further so that they may be used in vivo is merited.
Hydrogen decoration of radiation damage induced defect structures (2014)

The defect complexes that are formed when protons with energies in the MeV-range were implanted into high-purity silicon were investigated. After implantation, the samples were annealed at 400 °C or 450 °C for times ranging between 15 minutes and 30 hours. The resistivity of the samples was then analyzed by Spreading Resistance Profiling (SRP). The resistivity shows minima where there is a high carrier concentration and it is possible to extract the carrier concentration from the resistivity data. Initially, there is a large peak in the carrier concentration at the implantation depth where most of the hydrogen is concentrated. For longer anneals, this peak widens as the hydrogen diffuses away from the implantation depth. Following the changes in resistivity as a function of annealing time allows us to characterize the diffusion of hydrogen through these samples. Differences in the diffusion were observed depending on whether the silicon was grown by the magnetic Czochralski (m:Cz) method or the Float zone (Fz) method.
RF Power Silicon-On-Glass VDMOSFETs (2004)

Applicability of vertical double-diffused MOSFETs for future base station power amplifiers has been demonstrated by characterizing the first devices fabricated in a substrate transfer silicon-on-glass technology. For a gate length of 0.8 μm and gate width of 350 μm, the measured f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> /f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> is 6/10 GHz, and the breakdown voltage approaches 100 V. The devices feature an output power of 12 dBm at the 1-dB compression point, excellent linearity (IM3/IM5 of -50/ -70 dBc at 10-dB backoff) and high power gain (14 dB) at 2 GHz, and are the first vertical DMOSFETs suitable for 2-GHz power applications. Excellent heat sinking and no significant degradation of the quiescent current due to hot-carrier injection ensure thermal stability and good long-term reliability of the fabricated devices.
ChemInform Abstract: Patterned Self‐Assembled Monolayers: Efficient, Chemically Defined Tools for Cell Biology (2012)

Abstract Review: 43 refs.
Tumor Suppressor Function of the SEMA3B Gene in Human Lung and Renal Cancers (2015)

The SEMA3B gene is located in the 3p21.3 LUCA region, which is frequently affected in different types of cancer. The objective of our study was to expand our knowledge of the SEMA3B gene as a tumor suppressor and the mechanisms of its inactivation. In this study, several experimental approaches were used: tumor growth analyses and apoptosis assays in vitro and in SCID mice, expression and methylation assays and other. With the use of the small cell lung cancer cell line U2020 we confirmed the function of SEMA3B as a tumor suppressor, and showed that the suppression can be realized through the induction of apoptosis and, possibly, associated with the inhibition of angiogenesis. In addition, for the first time, high methylation frequencies have been observed in both intronic (32-39%) and promoter (44-52%) CpG-islands in 38 non-small cell lung carcinomas, including 16 squamous cell carcinomas (SCC) and 22 adenocarcinomas (ADC), and in 83 clear cell renal cell carcinomas (ccRCC). Correlations between the methylation frequencies of the promoter and the intronic CpG-islands of SEMA3B with tumor stage and grade have been revealed for SCC, ADC and ccRCC. The association between the decrease of the SEMA3B mRNA level and hypermethylation of the promoter and the intronic CpG-islands has been estimated in renal primary tumors (P < 0.01). Using qPCR, we observed on the average 10- and 14-fold decrease of the SEMA3B mRNA level in SCC and ADC, respectively, and a 4-fold decrease in ccRCC. The frequency of this effect was high in both lung (92-95%) and renal (84%) tumor samples. Moreover, we showed a clear difference (P < 0.05) of the SEMA3B relative mRNA levels in ADC with and without lymph node metastases. We conclude that aberrant expression and methylation of SEMA3B could be suggested as markers of lung and renal cancer progression.
Supplementary Methods, Figures 1-4, Tables 1-2 from Potent, Selective Inhibitors of Fibroblast Growth Factor Receptor Define Fibroblast Growth Factor Dependence in Preclinical Cancer Models (2023)

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Magic Pyramid: Accelerating Inference with Early Exiting and Token Pruning (2021)

Pre-training and then fine-tuning large language models is commonly used to achieve state-of-the-art performance in natural language processing (NLP) tasks. However, most pre-trained models suffer from low inference speed. Deploying such large models to applications with latency constraints is challenging. In this work, we focus on accelerating the inference via conditional computations. To achieve this, we propose a novel idea, Magic Pyramid (MP), to reduce both width-wise and depth-wise computation via token pruning and early exiting for Transformer-based models, particularly BERT. The former manages to save the computation via removing non-salient tokens, while the latter can fulfill the computation reduction by terminating the inference early before reaching the final layer, if the exiting condition is met. Our empirical studies demonstrate that compared to previous state of arts, MP is not only able to achieve a speed-adjustable inference but also to surpass token pruning and early exiting by reducing up to 70% giga floating point operations (GFLOPs) with less than 0.5% accuracy drop. Token pruning and early exiting express distinctive preferences to sequences with different lengths. However, MP is capable of achieving an average of 8.06x speedup on two popular text classification tasks, regardless of the sizes of the inputs.
Dense Indoor Sensor Networks: Towards passively sensing human presence with LoRaWAN (2022)

Sensors have become ubiquitous in buildings but are rarely connected to a network, and their potential to analyse the performance, use, and interaction with a building is not yet fully realised. In the coming years, we expect sensors in buildings to become part of the Internet of Things (IoT) and grow in numbers to form a Dense Indoor Sensor Network (DISN) that allows for unprecedented analysis of the performance, use, and interaction with buildings. Multiple technologies vie for leading this transformation. We explore Long Range Wide Area Network (LoRaWAN) as an alternative for creating indoor sensor networks that extends beyond its original long-distance communication purpose. For the present paper, we developed a DISN with 390 sensor nodes and four gateways and empirically evaluated its performance for two years. Our analysis of more than 86 million transmissions revealed that DISNs achieve a much lower distance coverage compared to estimations from previous research indicating that more gateways are required. In addition, the deployment of multiple gateways decreased the loss of transmissions due to environmental and network factors. Given the complexity of our system, we received few colliding concurrent messages, which demonstrates a gap between the projected requirements of LoRaWAN systems and the actual requirements of real-world applications given sufficient gateways. We also contribute to the modelling of transmissions with our comparison of attenuation models derived from multiple methodologies. Across all models, we find that robust coverage in an indoor environment can be maintained by placing a gateway every 30 m and every 5 floors. Finally, we also investigate the application of DISNs for the passive sensing and visualisation of human presence using a Digital Twin (DT) and a Fused Twins (FT) representation in Augmented Reality (AR). A passive sensing approach allows us to gather relevant data on human use of a building while still preserving privacy via the aggregation process. Immersive in situ visualisations in FT allow for new interactions and new forms of participation. We conclude that DISNs are already technologically feasible today and basing them on Low Power Wide Area Network (LPWAN) offers intriguing possibilities to reduce energy consumption, maintenance cost, and bandwidth use while also enabling new forms of human-building interaction.