gebhart/patrepeval huggingface dataset:
Coactivator SRC-2–dependent metabolic reprogramming mediates prostate cancer survival and metastasis (2015)

Metabolic pathway reprogramming is a hallmark of cancer cell growth and survival and supports the anabolic and energetic demands of these rapidly dividing cells. The underlying regulators of the tumor metabolic program are not completely understood; however, these factors have potential as cancer therapy targets. Here, we determined that upregulation of the oncogenic transcriptional coregulator steroid receptor coactivator 2 (SRC-2), also known as NCOA2, drives glutamine-dependent de novo lipogenesis, which supports tumor cell survival and eventual metastasis. SRC-2 was highly elevated in a variety of tumors, especially in prostate cancer, in which SRC-2 was amplified and overexpressed in 37% of the metastatic tumors evaluated. In prostate cancer cells, SRC-2 stimulated reductive carboxylation of α-ketoglutarate to generate citrate via retrograde TCA cycling, promoting lipogenesis and reprogramming of glutamine metabolism. Glutamine-mediated nutrient signaling activated SRC-2 via mTORC1-dependent phosphorylation, which then triggered downstream transcriptional responses by coactivating SREBP-1, which subsequently enhanced lipogenic enzyme expression. Metabolic profiling of human prostate tumors identified a massive increase in the SRC-2-driven metabolic signature in metastatic tumors compared with that seen in localized tumors, further implicating SRC-2 as a prominent metabolic coordinator of cancer metastasis. Moreover, SRC-2 inhibition in murine models severely attenuated the survival, growth, and metastasis of prostate cancer. Together, these results suggest that the SRC-2 pathway has potential as a therapeutic target for prostate cancer.
Quality by Design in the Secondary Drying Step of a Freeze-Drying Process (2012)

This paper is focused on the secondary drying step of a freeze-drying process, where the bound water is desorbed from the (partially) dried product, with the goal to achieve the target value of residual moisture in the final product. Mathematical modeling is used to get a deep understanding of the process, i.e., to study the effect of the operating variables (mainly the temperature of the heating shelf and the duration of the operation) on the state of the product (temperature and residual moisture). An innovative tool is used to provide an effective support to get quality by design: it is based on the measurement of the desorption rate, through the test of pressure rise, and on a mathematical model of the process. It allows us to monitor in-line the process, as well as to determine the kinetic parameters of water desorption and their dependence on the operating conditions. The mathematical model of the process is used to calculate the design space of the secondary drying process, i.e., to identify those operating conditions that allow the fulfillment of product quality requirements, and then to minimize the duration of the secondary drying. The case study used to test the proposed methodology is the drying of 5% w/w aqueous solutions of sucrose: a linear dependence of the desorption rate on the residual moisture is evidenced by the experimental investigation, and the Arrhenius equation appears to adequately describe the dependence of the kinetic constant on the temperature, with a frequency factor equal to 277 s−1, and an activation energy equal to 37,714 J mol−1. The model is then used to calculate the design space, as well as to optimize the operating conditions; in case the target value of residual moisture is 2%, the duration of secondary drying can be decreased from 16 h in case of constant shelf temperature to 7.35 h in case the recipe is optimized.
A human antibody selective for transthyretin amyloid removes cardiac amyloid through phagocytic immune cells (2021)

Transthyretin amyloid (ATTR) cardiomyopathy is a debilitating disease leading to heart failure and death. It is characterized by the deposition of extracellular ATTR fibrils in the myocardium. Reducing myocardial ATTR load is a therapeutic goal anticipated to translate into restored cardiac function and improved patient survival. For this purpose, we developed the selective anti-ATTR antibody NI301A, a recombinant human monoclonal immunoglobulin G1. NI301A was cloned following comprehensive analyses of memory B cell repertoires derived from healthy elderly subjects. NI301A binds selectively with high affinity to the disease-associated ATTR aggregates of either wild-type or variant ATTR related to sporadic or hereditary disease, respectively. It does not bind physiological transthyretin. NI301A removes ATTR deposits ex vivo from patient-derived myocardium by macrophages, as well as in vivo from mice grafted with patient-derived ATTR fibrils in a dose- and time-dependent fashion. The biological activity of ATTR removal involves antibody-mediated activation of phagocytic immune cells including macrophages. These data support the evaluation of safety and tolerability of NI301A in an ongoing phase 1 clinical trial in patients with ATTR cardiomyopathy.
Aminoquinoline–Rhodium(II) Conjugates as Src-Family SH3 Ligands (2019)

High-affinity, selective ligands are sought for a variety of biomolecules but are particularly difficult to generate in the protein-protein interaction space. Rhodium(II) conjugates provide a structure-based approach to improved affinity and specificity for targeting protein-protein interactions such as SH3 domains. In this study of small-molecule-rhodium conjugates, we report a potent ligand <b>4b</b> (<i>K</i> <sub><i>d</i></sub> of 27 nM) for the Lyn SH3 domain, based on an aminoquinoline fragment. The results demonstrate robust affinity gains possible from even modest small-molecule leads through cooperative inorganic-organic binding, based on specific histidine interactions. A docking study sheds light on the structural basis of binding and supports a previously proposed binding model.
Diagnostic markers of urothelial cancer based on DNA methylation analysis (2013)

Based on these preliminary findings, diagnostic markers based on differential DNA methylation at specific loci can be useful for non-invasive and reliable detection of UC and epigenetic field defect.
GNSS Code Multipath Mitigation by Cascading Measurement Monitoring Techniques (2018)

Various measurement monitoring techniques are investigated to mitigate the effect of global navigation satellite systems (GNSS) code multipath through error correction, stochastic weighting of measurements and detection and exclusion (or de-weighting) of affected measurements. Following a comprehensive review of each approach, the paper focuses on detection/exclusion and detection/de-weighting techniques where several single and dual-frequency monitoring metrics are employed in a combination with time-averaging and the <i>M of N</i> detection strategy. A new Geometry-Free (GF) detection metric is proposed given its capability to be combined with a preceding Code-Minus-Carrier (CMC)-based error correction to reduce the number of excluded or de-weighted measurements and thus preserve the measurement geometry. Three geometry-based algorithms, namely measurement subset testing, consecutive exclusion and iterative change of measurement weights are investigated to address multipath scenarios with multiple simultaneously affected measurements. Experimental results are provided using GPS L1, L2C and L5 data collected in multipath environments for static and kinematic scenarios. For GPS L1, the proposed combined method shows more than 38% improvement over a conventional Carrier-to-Noise-density ratio (C/N₀)-based Least-Squares (LS) solution in all but deep urban canyons. Lower performance was observed for L2C and L5 frequencies with a limited number of satellites in view.
Polyurethane–polyacrylate interpenetrating polymer networks. II (1975)

Abstract Two component topologically interpenetrating polymer networks of the SIN type (simultaneous interpenetrating networks) composed of a melamine‐cured polyacrylate and three different polyether‐based polyurethanes were prepared. The linear polymers and prepolymers were combined in solution, together with the necessary crosslinking agents and catalysts, films were cast and subsequently chain extended and crosslinked in situ . In all cases, maxima in tensile strength significantly higher than the tensile strengths of the component networks occurred at 50% polyurethane : 50% polyacrylate. This was explained by an increase in crosslink density resulting from interpenetration. One of the interpenetrating polymer networks showed only one glass transition temperature ( T g ) (measured calorimetrically) intermediate in temperature to the T g 's of the components and as sharp as the component T g 's. This is indicative of phase mixing and indicates at least partial chain entanglement (interpenetration). Some enhancement of other physical properties was also noted.
Human phosphodiesterase 4D7 (PDE4D7) expression is increased in TMPRSS2-ERG-positive primary prostate cancer and independently adds to a reduced risk of post-surgical disease progression (2015)

We further characterise and add physiological relevance to PDE4D7 as a novel marker that is associated with the development and progression of prostate tumours. We propose that the assessment of PDE4D7 levels may provide a novel, independent predictor of post-surgical disease progression.
Oxygen Saturation in Optic Nerve Head Structures by Hyperspectral Image Analysis (2007)

Percent oxygen saturation was determined from hyperspectral images of the ONH tissue and retinal vessels overlying the ONH at normal and elevated IOP. Pressure elevation was shown to reduce blood oxygen saturation in vessels and ONH structures, with the smallest reduction in the ONH observed in the temporal cup. IOP-induced saturation changes were visualized in color maps using an algorithm that follows saturation-dependent changes in the blood spectrum and blood volume differences across tissue. Reduced arterial saturation at high IOP may have resulted from a flow-dependent mechanism.
Automatically finding and recommending resources to support knowledge workers' activities (2008)

Knowledge workers perform many different activities daily. Each activity defines a distinct work context with different information needs. In this paper we leverage users' activity representations, stored in an activity management system, to automatically recommend resources to support knowledge workers in their current activity. We developed a collaborative activity predictor to both predict the current work activity and measure a resource's relevance to a specific activity. Relevant resources are then displayed in a contextual side bar on the desktop. We describe the system, our new activity-centric search algorithm, and experimental results based on the data from 50 real users.
CCD Focal Plane Convolver (Smart Eyeball) (1985)

The CCD focal plane convolver is a smart optical sensor capable of off-loading the massive number of multiplies and additions required for extracting many of the spatial primatives required in optical pattern recognition; most spatial and temperal convolutions can be extracted at extremely rapid rates and in parallel.
Non-intrusive Multiple Zone Distributed Acoustic Sensor Flow Metering (2015)

Abstract The Distributed Acoustic Sensor (DAS) used here (Parker et al., 2012), allows both the amplitude and the phase of acoustic signals to be continuously recorded along a length of optical fiber. In this paper, non-intrusive flow metering based on the use of this sensor is performed for different pipe sizes and flow conditions. By wrapping a continuous length of fiber helically around the exterior pipe, the system measures the dynamic radial strain (hoop strain) along a pipe with a spatial resolution on the order of millimeters and a time resolution on the order of tenths of milliseconds. As a result, this implementation of the sensing system output makes it possible to visualize the generation and convection of eddies by using a waterfall plot of distance versus time. By analyzing the recorded data using a frequency-space transformation (f-k plot), it is possible to determine precisely both the speed of eddies, as well as the speed of sound. This paper will present experimental results from single- and multi-phase tests to demonstrate the applicability of the technology to the monitoring of fluid velocity and the determination of flow composition. It will be seen that the system, which can be installed unobtrusively, is straightforward to apply for several types of commonly encountered flow regimes. Further, this paper will also consider several practical aspects regarding the installation and use of such a system in the oilfield. Finally, it will be shown how multiple monitoring zones can be incorporated using a single optical fiber. It will be seen that this system is non-intrusive and can be retrofitted to existing pipes to monitor the flow simultaneously at multiple locations for accurate flow profiling and characterization.
Geminiviral vectors based on bean yellow dwarf virus for production of vaccine antigens and monoclonal antibodies in plants (2011)

Expression of recombinant vaccine antigens and monoclonal antibodies using plant viral vectors has developed extensively during the past several years. The approach benefits from high yields of recombinant protein obtained within days after transient delivery of viral vectors to leaves of Nicotiana benthamiana, a tobacco relative. Modified viral genomes of both RNA and DNA viruses have been created. Geminiviruses such as bean yellow dwarf virus (BeYDV) have a small, single stranded DNA genome that replicates in the nucleus of an infected plant cell, using the cellular DNA synthesis apparatus and a virus-encoded replication initiator protein (Rep). BeYDV-derived expression vectors contain deletions of the viral genes encoding coat and movement proteins and insertion of an expression cassette for a protein of interest. Delivery of the geminiviral vector to leaf cells via Agrobacterium-mediated delivery produces very high levels of recombinant DNA that can act as a transcription template, yielding high levels of mRNA for the protein of interest. Several vaccine antigens, including Norwalk virus capsid protein and hepatitis B core antigen, were expressed using the BeYDV vector at levels up to 1 mg per g of leaf mass. BeYDV replicons can be stacked in the same vector molecule by linking them in tandem, which enables production of multi-subunit proteins like monoclonal antibody (mAb) heavy and light chains. The protective mAb 6D8 against Ebola virus was produced at 0.5 mg per g of leaf mass. Multi-replicon vectors could be conveniently used to produce protein complexes, e.g. virus-like particles that require two or more subunits.
IL‐34 deficiency impairs FOXP3<sup>+</sup> Treg function in a model of autoimmune colitis and decreases immune tolerance homeostasis (2022)

-Absence of expression of IL-34 in Il34<sup>-/-</sup> rats and mice leads to an unstable immune phenotype, with a production of multiple auto-antibodies and exacerbated immune pathology under inflammatory conditions. -Il34<sup>-/-</sup> CD4<sup>+</sup> Tregs are unable to protect Il2rg<sup>-/-</sup> rats from colitis induced by transfer of pathogenic cells. -IL-34 treatment delayed EAE in mice, as well as acute GVHD and human skin allograft rejection in immune-humanized immunodeficient NSG mice.
Comparison of virtual and real electric powered wheelchair driving using a position sensing joystick and an isometric joystick (2002)

There are limited interface options for electric powered wheelchairs, which results in the inability of some individuals to drive independently. In addition, the development of new interface technologies will necessitate the development of alternative training methods. This study compares a conventional position sensing joystick to a novel isometric joystick during a driving task in a virtual environment and a real environment. The results revealed that there were few differences in task completion time and root-mean-square error (RMSE) between the two types of joysticks. There were significant correlations between the RMSE in the virtual environment and the real environment for both types of joysticks. The data indicate that performance in the virtual environment was representative of driving ability in the real environment, and the isometric joystick performed comparably to the position sensing joystick.
Breathhold multiecho fast spin‐echo pulse sequence for accurate <i>R</i><sub>2</sub> measurement in the heart and liver (2009)

Measurement of proton transverse relaxation rates (R(2)) is a generally useful means for quantitative characterization of pathological changes in tissue with a variety of clinical applications. The most widely used R(2) measurement method is the Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence but its relatively long scan time requires respiratory gating for chest or body MRI, rendering this approach impractical for comprehensive assessment within a clinically-acceptable examination time. The purpose of our study was to develop a breathhold multiecho fast spin-echo (FSE) sequence for accurate measurement of R(2) in the liver and heart. Phantom experiments and studies of subjects in vivo were performed to compare the FSE data with the corresponding even-echo CPMG data. For pooled data, the R(2) measurements were strongly correlated (Pearson correlation coefficient = 0.99) and in excellent agreement (mean difference [CPMG - FSE] = 0.10 s(-1); 95% limits of agreement were 1.98 and -1.78 s(-1)) between the two pulse sequences.
KMED: a two step process to remove color from pulp mill wastewater (1998)

A reaction between caustic bleach water and potassium permanganate was examined for its ability to remove colloidal color. The effectiveness of this reaction was found to depend on concentration and was not affected by pH. Under certain conditions, a large floc formed that was easily removed. The supernatant of the reaction, after being mixed with both acid wastewater and process wastewater, was treated with ozone to further reduce the residual color. The product of the two step process yielded an overall color reduction of more than 97%.
Metal Coordination-Assisted Near-Infrared Photochromic Behavior:  A Large Perturbation on Absorption Wavelength Properties of N,N-Donor Ligands Containing Diarylethene Derivatives by Coordination to the Rhenium(I) Metal Center (2007)

A new series of diarylethene-containing 1-aryl-substituted 2-(2-pyridyl)imidazole (L) ligands have been prepared and characterized. Subsequent reactions of the 2-(2-pyridyl)imidazole ligands with Re(CO)5Cl under reflux conditions afforded [Re(CO)3(L)Cl]; one of the complexes has also been structurally determined. The open forms of the ligands showed an intense absorption band at ca. 320 nm corresponding to π → π* and n → π* transitions of the 1-aryl-2-(2-pyridyl)imidazole moiety, with mixing of π → π* and n → π* transitions of the thiophene moieties. The corresponding rhenium(I) complexes showed IL absorption bands at ca. 352 nm, with additional MLCT [dπ(Re) → π*(L)] transitions at ca. 425 nm. Upon photocyclization of the diarylethene moieties by UV irradiation, two new absorption bands emerged at ca. 410−425 and 576−586 nm for the ligands, while the rhenium(I) complexes showed three new absorption bands at ca. 288−290, 475−480, and 712−713 nm upon excitation into either the IL or MLCT bands. Such a large shift of the absorption bands of the closed forms of the rhenium(I) complexes to the NIR region could be attributed to the planarization of the four heterocyclic rings relative to the open forms. On the contrary, the organic ligand systems alone did not display such a shift of the absorption maxima to the NIR region upon photocyclization.
AFS: Accurate, Fast, and Scalable Error-Decoding for Fault-Tolerant Quantum Computers (2022)

Quantum computers promise computational advantages for many important problems across various application domains. Unfortunately, physical quantum devices are highly susceptible to errors that limit us from running most of these quantum applications. Quantum Error Correction (QEC) codes are required to implement Fault-Tolerant Quantum Computers (FTQC) on which computations can be performed without encountering errors. Error decoding is a critical component of quantum error correction and is responsible for transforming a set of qubit measurements generated by the QEC code, called the syndrome, into error locations and error types. For the feasibility of implementation, error decoders must not only identify errors with high accuracy, but also be fast and scalable to a large number of qubits. Unfortunately, most of the prior works on error decoding have focused primarily only on the accuracy and have relied on software implementations that are too slow to be of practical use. Furthermore, these studies only look at designing a single decoder and do not analyze the challenges involved in scaling the storage and bandwidth requirements when performing error correction in large systems with thousands of qubits.In this paper, we present AFS, an accurate, fast, and scalable decoder architecture that is designed to operate in the context of systems with hundreds of logical qubits. We present the hardware implementation of AFS, which is based on the Union Find decoding algorithm and employs a three-stage pipelined design. AFS provides orders of magnitude higher accuracy compared to recent SFQ-based hardware decoders (logical error rate of 6×10<sup>−10</sup> for physical error rate of 10<sup>−3</sup>) and low decoding latency (42ns on average), while being robust to measurement errors introduced while extracting syndromes during the QEC cycles. We also reduce the amount of decoding hardware required to perform QEC simultaneously on all the logical qubits by co-designing the micro-architecture across multiple decoding units. Our proposed Conjoined-Decoder Architecture (CDA) reduces the storage overhead by 70% (10MB to 2.8MB). Finally, we reduce the bandwidth overheads required to transmit syndromes from the qubits to the decoders by exploiting the sparsity in the syndromes and compressing the data. Our proposed Syndrome Compression reduces the bandwidth requirement by 30x, on an average.
Molecular Testing for miRNA, mRNA, and DNA on Fine-Needle Aspiration Improves the Preoperative Diagnosis of Thyroid Nodules With Indeterminate Cytology (2015)

Multiplatform testing for DNA, mRNA, and miRNA can accurately classify benign and malignant thyroid nodules, increase the diagnostic yield of molecular cytology, and further improve the preoperative risk-based management of benign nodules with AUS/FLUS or FN/SFN cytology.
Untranslated Element in Neurofilament mRNA Has Neuropathic Effect on Motor Neurons of Transgenic Mice (2002)

Studies of experimental motor neuron degeneration attributable to expression of neurofilament light chain (NF-L) transgenes have raised the possibility that the neuropathic effects result from overexpression of NF-L mRNA, independent of NF-L protein effects (Cañete-Soler et al., 1999). The present study was undertaken to test for an RNA-mediated pathogenesis. Transgenic mice were derived using either an enhanced green fluorescent protein reporter construct or modified chimeric constructs that differ only in their 3' untranslated regions (UTRs). Motor function and spinal cord histology were normal in mice expressing the unmodified reporter transgene. In mice expressing a chimeric transgene in which sequence of NF-L 3' UTR was inserted into the 3' UTR of the reporter transgene, we observed growth retardation and reduced kinetic activity during postnatal development. Older mice developed impairment of motor function and atrophy of nerve fibers in the ventral roots. A similar but more severe phenotype was observed when the chimeric transgene contained a 36 bp c-myc insert in an mRNA destabilizing element of the NF-L sequence. Our results suggest that neuropathic effects of overexpressing NF-L can occur at the level of transgene RNA and are mediated by sequences in the NF-L 3' UTR.