gebhart/patrepeval huggingface dataset:
FOXP3 mRNA profile prognostic of T cell mediated rejection and human kidney allograft survival (2020)

Abstract Background and objectives T cell mediated rejection (TCMR) is the most frequent type of acute rejection and is associated with kidney allograft failure. Almost 40% of TCMR episodes fail to respond to anti-rejection therapy. FOXP3 is a specification factor for regulatory T cells and our single center study of 83 kidney allograft recipients showed that urinary cell FOXP3 mRNA level is diagnostic of TCMR and predicts TCMR reversibility and allograft survival. The objective of the current study is to determine whether our original findings could be replicated in an independent cohort of 480 kidney allograft recipients enrolled in the multicenter Clinical Trials of Organ Transplantation (CTOT)-04. Design, setting, participants, and measurements We measured levels of FOXP3 mRNA and levels of mRNA for CD25, CD3E, and perforin, and 18S rRNA in 3559 urines from 480 kidney allograft recipients prospectively enrolled in CTOT-04. RNA was isolated from the urinary cells and preamplification-enhanced real-time quantitative PCR assays were used to measure mRNAs. Results 18S rRNA normalized levels of mRNA for FOXP3 ( P =0.01, Kruskal-Wallis test), CD25 ( P =0.01), CD3E ( P <0.0001), and perforin ( P <0.0001) distinguished patients with TCMR biopsies from those with No Rejection biopsies and those with stable graft function. FOXP3 mRNA level, but not the levels of mRNA for CD25, CD3E, or perforin, predicted TCMR reversal (AUC=0.764; 95% confidence interval, 0.611 to 0.917; P =0.008). Multivariable logistic regression analysis showed that FOXP3 mRNA level remains predictive after adjustment for potential cofounders. Kaplan-Meier survival curve analysis showed that FOXP3 mRNA level ( P =0.0306) but not the levels of mRNA for CD25, CD3E, or perforin, is associated with kidney allograft survival. Conclusion In the independent CTOT-04 cohort, we demonstrate that urinary cell level of FOXP3 mRNA is diagnostic of TCMR, predicts its reversibility, and is prognostic of kidney allograft survival following an episode of TCMR.
Production and Characterization of Anti-Cocaine Catalytic Antibodies (2004)

Cocaine abuse has become a major health problem in recent decades, and the problem has been greatly accentuated by the appearance of crack cocaine, the more potent free base of the natural alkaloid. Cocaine’s primary molecular target is the dopamine reuptake transporter at the nucleus accumbens. By blocking reuptake, cocaine enhances dopaminergic neurotransmission, which activates the reward pathway. The result is reinforcement of drug-taking behavior in species ranging from mouse to man, and in human subjects, the perception of euphoria. This peculiar mechanism of action has limited the therapeutic approaches to the treatment of cocaine abuse because of the inherent difficulty of “blocking a blocker.” One plausible alternative is the neutralization of the drug before it reaches its target in the brain, and antibodies, a class of natural binders, would appear to be well-suited for the task. Several active and passive cocaine vaccines have already been tested with a fair degree of success (,), but the elevated concentration of antibody required for binding and neutralizing cocaine blood levels is still a problem to be overcome. This hurdle is less difficult for a catalytic antibody, which not only binds, but also destroys what it binds to.
Improved quantum circuits for elliptic curve discrete logarithms (2020)

We present improved quantum circuits for elliptic curve scalar multiplication, the most costly component in Shor's algorithm to compute discrete logarithms in elliptic curve groups. We optimize low-level components such as reversible integer and modular arithmetic through windowing techniques and more adaptive placement of uncomputing steps, and improve over previous quantum circuits for modular inversion by reformulating the binary Euclidean algorithm. Overall, we obtain an affine Weierstrass point addition circuit that has lower depth and uses fewer $T$ gates than previous circuits. While previous work mostly focuses on minimizing the total number of qubits, we present various trade-offs between different cost metrics including the number of qubits, circuit depth and $T$-gate count. Finally, we provide a full implementation of point addition in the Q# quantum programming language that allows unit tests and automatic quantum resource estimation for all components.
Compressive Mining: Fast and Optimal Data Mining in the Compressed Domain (2014)

Real-world data typically contain repeated and periodic patterns. This suggests that they can be effectively represented and compressed using only a few coefficients of an appropriate basis (e.g., Fourier, Wavelets, etc.). However, distance estimation when the data are represented using different sets of coefficients is still a largely unexplored area. This work studies the optimization problems related to obtaining the \emph{tightest} lower/upper bound on Euclidean distances when each data object is potentially compressed using a different set of orthonormal coefficients. Our technique leads to tighter distance estimates, which translates into more accurate search, learning and mining operations \textit{directly} in the compressed domain. We formulate the problem of estimating lower/upper distance bounds as an optimization problem. We establish the properties of optimal solutions, and leverage the theoretical analysis to develop a fast algorithm to obtain an \emph{exact} solution to the problem. The suggested solution provides the tightest estimation of the $L_2$-norm or the correlation. We show that typical data-analysis operations, such as k-NN search or k-Means clustering, can operate more accurately using the proposed compression and distance reconstruction technique. We compare it with many other prevalent compression and reconstruction techniques, including random projections and PCA-based techniques. We highlight a surprising result, namely that when the data are highly sparse in some basis, our technique may even outperform PCA-based compression. The contributions of this work are generic as our methodology is applicable to any sequential or high-dimensional data as well as to any orthogonal data transformation used for the underlying data compression scheme.
164. Improvement of Gene Therapy for Wilson Disease (2016)

Wilson's disease (WD) is an autosomal recessively inherited copper storage disorder due to mutations in ATP7B gene that causes hepatic and neurologic symptoms. Current treatments are based on lifelong copper chelating drugs, which may cause side effects and do not restore normal copper metabolism. We have recently demonstrated that the administration of an AAV vector expressing ATP7B under the control of a liver specific promoter induces full restoration of copper homeostasis in a mouse model of Wilson's disease. However, the size of the vector genome surpasses the optimal size for AAV packaging, limiting the use of large promoters or additional regulatory sequences such as introns or bigger poly A sequences. In the present work we have designed two truncated versions of ATP7B protein (T1 and T2), and have analyzed their functionality and therapeutic efficacy. ATP7B contains 6 metal binding sites (MBS) in the N-terminal region. T1 presents a deletion of 1 MBS and a fragment of the adjacent one, whereas T2 lacks the first 4 MBS. Both proteins were active since they were able eliminate intracellular excess of copper in an in vitro system. The administration of recombinant AAV vectors carrying the truncated proteins under the control of a liver specific promoter was able to reduce liver damage and urinary copper excretion in the murine model, but T1 was less efficient than the WT ATP7B gene. In contrast, T2 showed full capacity to normalize these parameters. Furthermore, T2 was more efficient than WT in restoring ceruloplasmin oxidase activity in serum. In conclusion, we have identified a fully functional truncated version of ATP7B protein that will reduce the size of the therapeutic AAV vector genome and allow the introduction of additional regulatory elements.
Solvent-Free Synthesis of Zeolites from Anhydrous Starting Raw Solids (2015)

Development of sustainable routes for synthesis of zeolites is very important because of wide applications of zeolites at large scale in the fields of catalysis, adsorption, and separation. Here we report a novel and generalized route for synthesis of zeolites in the presence of NH4F from grinding the anhydrous starting solid materials and heating at 140-240 °C. Accordingly, zeolites of MFI, BEA*, EUO, and TON structures have been successfully synthesized. The presence of F(-) drives the crystallization of these zeolites from amorphous phase. Compared with conventional hydrothermal synthesis, the synthesis in this work not only simplifies the synthesis process but also significantly enhances the zeolite yields. These features should be potentially of great importance for industrial production of zeolites at large scale in the future.
Structure, self-assembly, and properties of a truncated reflectin variant (2020)

Naturally occurring and recombinant protein-based materials are frequently employed for the study of fundamental biological processes and are often leveraged for applications in areas as diverse as electronics, optics, bioengineering, medicine, and even fashion. Within this context, unique structural proteins known as reflectins have recently attracted substantial attention due to their key roles in the fascinating color-changing capabilities of cephalopods and their technological potential as biophotonic and bioelectronic materials. However, progress toward understanding reflectins has been hindered by their atypical aromatic and charged residue-enriched sequences, extreme sensitivities to subtle changes in environmental conditions, and well-known propensities for aggregation. Herein, we elucidate the structure of a reflectin variant at the molecular level, demonstrate a straightforward mechanical agitation-based methodology for controlling this variant's hierarchical assembly, and establish a direct correlation between the protein's structural characteristics and intrinsic optical properties. Altogether, our findings address multiple challenges associated with the development of reflectins as materials, furnish molecular-level insight into the mechanistic underpinnings of cephalopod skin cells' color-changing functionalities, and may inform new research directions across biochemistry, cellular biology, bioengineering, and optics.
Effective Treatment of Mycobacterium avium subsp. hominissuis and Mycobacterium abscessus Species Infections in Macrophages, Biofilm, and Mice by Using Liposomal Ciprofloxacin (2018)

Nontuberculous mycobacteria (NTM) affect an increasing number of individuals worldwide. Infection with these organisms is more common in patients with chronic lung conditions, and treatment is challenging. Quinolones, such as ciprofloxacin, have been used to treat patients, but the results have not been encouraging. In this report, we evaluate novel formulations of liposome-encapsulated ciprofloxacin (liposomal ciprofloxacin) <i>in vitro</i> and <i>in vivo</i> Its efficacy against <i>Mycobacterium avium</i> and <i>Mycobacterium abscessus</i> was examined in macrophages, in biofilms, and <i>in vivo</i> using intranasal instillation mouse models. Liposomal ciprofloxacin was significantly more active than free ciprofloxacin against both pathogens in macrophages and biofilms. When evaluated <i>in vivo</i>, treatment with the liposomal ciprofloxacin formulations was associated with significant decreases in the bacterial loads in the lungs of animals infected with <i>M. avium</i> and <i>M. abscessus</i> In summary, topical delivery of liposomal ciprofloxacin in the lung at concentrations greater than those achieved in the serum can be effective in the treatment of NTM, and further evaluation is warranted.
Molecular Interactions between the TSH Receptor and a Thyroid-Stimulating Monoclonal Autoantibody (2007)

Mutation of both the TSHR and M22 Fab has allowed identification of some residues critical for the receptor-autoantibody interaction. This approach should lead to detailed mapping of the amino acids important for M22 biological activity.
Asymmetric half bridge soft-switching PFC converter with direct energy transfer (2003)

A single-stage power factor correction (PFC) AC/DC converter with a direct energy transfer feature is proposed in this paper. An asymmetric half-bridge topology is used as the DC-DC cell for its inherent ZVS capability, and a direct energy transfer PFC cell is introduced to improve the conversion efficiency. Its operational principles are discussed in detail, and simulation and experimental results are also presented to verify the functionality of this converter.
Design of embedded compute-intensive processing elements and their scheduling in a reconfigurable environment Conception d'éléments intégrés de traitement à calcul intensif et leur ordonnancement dans un environnement reconfigurable (2005)

This paper addresses the problem of solving computationally intensive algorithms such as multimedia and graphics applications. A novel methodology to design embedded compute-intensive processing elements (ECIPEs) is proposed. In order to identify common data flow patterns among core data flow graphs (DFGs), a low-complexity and parallelism-aware common subgraph extraction algorithm is proposed. In addition, a reconfiguration-aware static scheduling technique to manage task and resource dependencies is proposed. To validate the success of this approach, estimates of reconfiguration times obtained by performing several experiments (on an assorted set of algorithms taken from media standards such as MPEG-4 and frequently used graphics algorithms) are provided, and the potential for reduction in the number of reconfiguration cycles is shown.
Impact of High-Yield Pulp Substitution on the Brightness Stability of Uncoated Wood-Free Paper (2010)

Without any fillers and optical brightening agents (OBAOBAOBAs), 15%–20% substitution of high-yield pulps (HYPs) for the hardwood bleached kraft pulp (BKP) in a paper furnish can decrease the brightness stability significantly because HYP contains a large amount of lignin. However, using mineral fillers such as precipitated calcium carbonate (PCC) and OBAOBAOBA in a HYP-containing paper can essentially eliminate the negative effect of HYP substitution on the brightness stability of uncoated wood-free paper. During the commercial production of traditional wood-free paper products, which usually use both PCC and OBAOBAOBA, 15%–20% HYP substitution for the hardwood BKP will not have practical impact on the paper brightness stability. Results from commercial printing and writing paper production support the same conclusion.
Synthesis of very small diameter silica nanofibers using sound waves (2014)

Silica nanofibers of an average diameter ≈30 nm and length ≈100 μm have been synthesized using an unprecedented strategy: sound waves. A new phenomenon, spinning off the nanofibers at silica rod tips, is also observed.
Absorption of low molecular weight compounds in aqueous dispersions of polymer‐oligomer particles, 2. A two step swelling process of polymer particles giving an enormous increase in absorption capacity (1979)

Abstract A novel method for preparation of stable emulsions of slightly water soluble compounds is described. The method implies that the slightly water soluble compound diffuses through water and becomes absorbed into polymer particles which in a previous step have been brought to absorb a water insoluble, relatively low molecular weight compound. By this two step swelling process the polymer particles can be brought to absorb more than 100 times their own volume of the low molecular weight compounds to form stable o/w emulsions of the latter, with high oil content, and with a droplet size and size distribution which is completely determined by the size of the polymer particles in the latex applied initially. Monodisperse emulsions with large droplet size could easily be prepared. When the slightly water soluble compound added in the second step is a vinyl monomer which may subsequently be polymerized, the method represents a seed technique which is especially favourable for preparation of latexes with large particles size, including monodisperse latexes, with high solid content.
3D Cross-Point Spin Transfer Torque Magnetic Random Access Memory (2017)

We explore a 3D cross-point spin transfer torque magnetic random access memory (STT-MRAM) array based on the integration of a perpendicular magnetic tunneling junction (pMTJ) with a matching two-terminal selector. The integrated two-terminal device provides a unique opportunity for a high density, low cost stackable storage class memory that can achieve a fast operation speed, long data retention, low bit error rate (BER) and high endurance. 55[Formula: see text]nm size pillar shaped pMTJ and selector devices have been fabricated and characterized. The selector is compatible with pMTJ whether it is in the high or low resistance state. The pMTJ can be RESET and SET after the selector turns on. We model the dynamic switching of the coupled pMTJ and selector devices. Our model shows the importance of the optimal matching of pMTJ magnetic properties with selector resistive properties to achieve high performance.
Ruthenium‐Catalyzed Asymmetric Epoxidation of Olefins Using H<sub>2</sub>O<sub>2</sub>, Part II: Catalytic Activities and Mechanism (2006)

Asymmetric epoxidation of olefins with 30 % H2O2 in the presence of [Ru(pybox)(pydic)] 1 and [Ru(pyboxazine)(pydic)] 2 has been studied in detail (pybox = pyridine-2,6-bisoxazoline, pyboxazine = pyridine-2,6-bisoxazine, pydic = 2,6-pyridinedicarboxylate). 35 Ruthenium complexes with sterically and electronically different substituents have been tested in environmentally benign epoxidation reactions. Mono-, 1,1-di-, cis- and trans-1,2-di-, tri-, and tetra-substituted aromatic olefins with versatile functional groups can be epoxidized with this type of catalyst in good to excellent yields (up to 100 %) with moderate to good enantioselectivies (up to 84 % ee). Additive and solvent effects as well as the relative rate of reaction with different catalysts have been established. It is shown that the presence of weak organic acids or an electron-withdrawing group on the catalyst increases the reactivity. New insights on the reaction intermediates and reaction pathway of the ruthenium-catalyzed epoxidation are proposed on the basis of density functional theory calculation and experiments.
Performance Evaluation of EEG Based Mental Stress Assessment Approaches for Wearable Devices (2022)

Mental stress has been identified as the root cause of various physical and psychological disorders. Therefore, it is crucial to conduct timely diagnosis and assessment considering the severe effects of mental stress. In contrast to other health-related wearable devices, wearable or portable devices for stress assessment have not been developed yet. A major requirement for the development of such a device is a time-efficient algorithm. This study investigates the performance of computer-aided approaches for mental stress assessment. Machine learning (ML) approaches are compared in terms of the time required for feature extraction and classification. After conducting tests on data for real-time experiments, it was observed that conventional ML approaches are time-consuming due to the computations required for feature extraction, whereas a deep learning (DL) approach results in a time-efficient classification due to automated unsupervised feature extraction. This study emphasizes that DL approaches can be used in wearable devices for real-time mental stress assessment.
Single-Crystalline CeB<sub>6</sub> Nanowires (2005)

Considered to be one of the best electron emission materials, CeB6 nanowires are of great scientific and industrial interest. CeB6 nanowires of square cross section with about 50 nm in lateral dimension and more than several micrometers in length have been successfully produced using a chemical vapor deposition method. The nanowires are grown in the 100 lattice direction, and both the tip top and the side surfaces are terminated with the {100} lattice planes.
<title>Three-dimensional ultrasound-guided breast biopsy system</title> (2001)

We introduce a mechanically constrained, 3D ultrasound- guided core-needle breast biopsy device. With modest breast compression, 3D ultrasound scans localize suspicious masses. A biopsy needle is mechanically guided into position for firing into the sampling region. Th needle is parallel to the transducer, allowing real-time guidance during needle insertion. Lesion sampling is verified by another ultrasound image after firing. Two procedures quantified targeting accuracy of this apparatus. First, we biopsied eleven breast phantoms containing 123 embedded, cylindrical lesions constructed from PVA-C (poly(vinyl alcohol) cryogel) with diameters ranging from 1.6 to 15.9mm. Identification of the colored lesion in the biopsy sample and analysis of the post-biopsy US images provided a model for the success rates. Using this, we predict that our apparatus will require six passes to biopsy a 3.0 mm lesion with 99% confidence. For the second experiment, agar phantoms were embedded with four rows of 0.8mm stainless steel beads. A 14-gauge needle was inserted to each bead position seen in a 3D ultrasound scan and the tip position was compared to the pre-insertion bead position. The inter-observer standard errors of measurement were less than 0.15 and 0.28mm for the bead and needle tip positions, respectively. The off-axis 3D 95% confidence intervals were determined to have widths between 0.43 and 1.71mm, depending on direction and bead position.
Why the Magnetic Loss Tangent Is Not a Relevant Constraint for Permeable Conformal Antennas (2016)

Recent experiments on high-efficiency permeable conformal antennas have drawn attention to a long-standing misconception on the theory of the ferrite rod antenna family. Deriving in closed form the radiation efficiency of these antennas and using full-wave simulations, we show that their radiation efficiency is not necessarily reduced by the loss tangent of the permeable material. It is shown that the key material parameter controlling the radiation efficiency of these antennas is not the loss tangent but the maximum of the Heaviside magnetic conductivity, a quantity proportional to Snoek's product. This yields the clear design rules for obtaining permeable antennas with maximized efficiency-bandwidth product (EBWP). Because the radiating currents of these antennas are the magnetic polarization currents in the material, they can be placed close to a metal ground plane or inside a low impedance medium without performance degradation while having an EBWP much higher than the metal-and-dielectric antennas having the same conformal volume, in spite of the presence of the magnetic loss. As an example, an antenna operating from HF to VHF can attain an EBWP 10 dB higher than the corresponding metal antenna. Similarly, using the Best-Yaghjian formalism, it is shown that these antennas are easier to match and can attain wider bandwidths than the equivalent conformal metal antennas.
Equitable quality video streaming for IP networks (2009)

We describe an equitable quality video streaming system where the video server dynamically selects between multiple versions of video content coded at different fixed quality levels, and dynamically selects transmission rates for each video session so that the network bandwidth is divided between concurrent users such that they receive equal video quality at each moment in time. By sharing the bandwidth in this way and allowing delivery to get arbitrarily ahead of decoding, equitable quality video streaming can significantly outperform constant bit rate coding and delivery, allowing 100% more video sessions to be delivered at the same overall perceptual quality.