gebhart/patrepeval huggingface dataset:
EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization (2007)

In recent years, protein-ligand docking has become a powerful tool for drug development. Although several approaches suitable for high throughput screening are available, there is a need for methods able to identify binding modes with high accuracy. This accuracy is essential to reliably compute the binding free energy of the ligand. Such methods are needed when the binding mode of lead compounds is not determined experimentally but is needed for structure-based lead optimization. We present here a new docking software, called EADock, that aims at this goal. It uses an hybrid evolutionary algorithm with two fitness functions, in combination with a sophisticated management of the diversity. EADock is interfaced with the CHARMM package for energy calculations and coordinate handling. A validation was carried out on 37 crystallized protein-ligand complexes featuring 11 different proteins. The search space was defined as a sphere of 15 A around the center of mass of the ligand position in the crystal structure, and on the contrary to other benchmarks, our algorithm was fed with optimized ligand positions up to 10 A root mean square deviation (RMSD) from the crystal structure, excluding the latter. This validation illustrates the efficiency of our sampling strategy, as correct binding modes, defined by a RMSD to the crystal structure lower than 2 A, were identified and ranked first for 68% of the complexes. The success rate increases to 78% when considering the five best ranked clusters, and 92% when all clusters present in the last generation are taken into account. Most failures could be explained by the presence of crystal contacts in the experimental structure. Finally, the ability of EADock to accurately predict binding modes on a real application was illustrated by the successful docking of the RGD cyclic pentapeptide on the alphaVbeta3 integrin, starting far away from the binding pocket.
State Laws Criminalizing Female Circumcision: A Violation of the Equal Protection Clause of the Fourteenth Amendment, 32 J. Marshall L. Rev. 353 (1999) (1999)

circumcision has been the most frequently performed surgery in the United States").3. Fishbeck v. North Dakota, 115 F
Blepharospasm: a review of 264 patients. (1988)

The natural history and response to different treatments have been evaluated in 264 patients with blepharospasm. The mean age of onset was 55.8 years and there was a female preponderance of 1.8 to 1. Dystonia elsewhere was found in 78% of patients, usually in the cranial-cervical region, and appeared to follow a somatotopic progression. A family history of blepharospasm or dystonia elsewhere was found in 9.5% of cases, which suggests a genetic predisposition. Ocular lesions preceded the onset of blepharospasm in 12.1% of cases. The response to drugs was inconsistent, although initial improvement was experienced by one fifth of patients treated with anticholinergics. Twenty-nine bilateral facial nerve avulsion operations were performed with benefit in 27 cases; but recurrences appeared in 22, on average one year after surgery. Botulinum toxin injections were performed in 151 patients. Significant improvement was achieved in 118 cases. Mean duration of benefit was 9.2 weeks. Transient ptosis and diplopia were the commonest side effects.
A high throughput deblocking filter design supporting multiple video coding standards (2009)

This paper presents a high throughput, VLSI architecture for multi-standard in-loop deblocking filter (ILF) supporting H.264 BP/MP/HP, AVS, and VC-1 video decoding. It comprises 38.4 Kgates and 672 bytes of local memory using TSMC 0.13 mum CMOS technology when operating at 225 MHz which meets the real-time processing requirement for high-resolution video decoding. We develop a PDB scheme and an integrated 1-D filter to realize various coding tools of the deblocking filter supporting multiple video coding standards.
Nonlinear model predictive control methodology for efficiency and durability improvement in a fuel cell power system (2016)

Trabajo presentado al 21st World Hydrogen Energy Conference (WHEC), celebrado en Zaragoza (España) del 13 al 16 de junio de 2016.
Crosstalk reduction for VLSI (1997)

The performance of high-speed electronic systems is limited by interconnect-related failure modes such as coupled noise. We propose new techniques for alleviating the problems caused by coupling between signal lines on integrated circuits. We show that models used by previous work on coupled noise-constrained layout synthesis do not allow the use of several important degrees of freedom. These degrees of freedom include the ability to utilize dynamic noise margins rather than static noise margins, the dependence of coupled noise on drive strength, and the possibility of using overlaps to reduce susceptibility to noise. We derive an expression for the coupled noise integral and a bound for the peak coupled noise voltage which shows order of magnitude improvements in both accuracy and fidelity compared to the charge sharing model used in previous work. We use the new bounds to guide a greedy channel router, which manipulates exact adjacency information at every stage, allowing it to introduce jogs or doglegs when necessary for coupled noise reduction. Experimental results indicate that our algorithm compares favorably to previous work. The coupled noise is significantly reduced on benchmark instances.
Efficient priming of protein antigen–specific human CD4+ T cells by monocyte-derived dendritic cells (2000)

Dendritic cells (DCs) have the unique ability to initiate an immune response in vivo by capturing antigens (Ags) in peripheral tissues and migrating to secondary lymphoid organs, where they sensitize naive CD4(+) T cells. To mimic this process in vitro, previous studies have shown that DCs directly isolated from peripheral blood can be used to elicit primary responses to neoantigens (neoAgs). In other studies, when monocyte-derived DCs have been utilized to sensitize total CD4(+) T cells in vitro, only secondary proliferation to neoAgs could be elicited. In the present study, the relative abilities of CD40 ligation, protein kinase C activation, and culture in tumor necrosis factor alpha (TNF-alpha) to induce functional and phenotypic maturation of human DCs from monocyte precursors were compared. Optimal TNF-alpha-induced maturation of DCs required a prolonged 4-day culture. It was then found that loading immature DCs with the neoAgs keyhole limpet hemocyanin or human immunodeficiency virus-1 p24 gag prior to TNF-alpha-induced maturation, rather than after maturation, was crucial to sensitize CD4(+) T cells to new Ags. This primary proliferation to neoAgs was initiated from the CD4(+) CD45RA(+) naive T-cell population. Finally, it was found that monocyte-derived DCs acquired the ability to secrete interleukin-12 p70, after contact with Ag-specific T cells. The ability to prime and expand Ag-specific CD4(+) T cells ex vivo to neoAgs in serum-free conditions has potential application for cellular vaccination and adoptive immunotherapy.
Ferroelectric Polymer Nanocomposites for Room‐Temperature Electrocaloric Refrigeration (2015)

Solution-processable ferroelectric polymer nanocomposites are developed as a new form of electrocaloric materials that can be effectively operated under both modest and high electric fields at ambient temperature. By integrating the complementary properties of the constituents, the nanocomposites exhibit state-of-the-art cooling energy densities. Greatly improved thermal conductivity also yields superior cooling power densities validated by finite volume simulations.
Effects of sensor orientation on AC electromagnetic tracking system accuracy in a CT scanner environment (2008)

The purpose of this study was to examine the effects of different sensor orientation on the positional accuracy of an AC electromagnetic tracking system, the second generation NDI Aurora, within a CT scanner environment. A three-axis positioning robot was used to move three electromagnetically tracked needles above the CT table throughout a 30cm by 30cm by 30cm volume sampled in 2.5cm steps. All three needle tips were held within 2mm of each other, with the needle axes orthogonally located in the +x, +y, and +z directions of the Aurora coordinate system. The corresponding position data was captured from the Aurora for each needle and was registered to the positioning system data using a rigid body transformation minimizing the least squares L2-norm. For all three needle orientations the largest errors were observed farthest from the field generator and closest to the CT table. However, the 3D distortion error patterns were different for each needle, demonstrating that the sensor orientation has an effect on the positional measurement of the sensor. This suggests that the effectiveness of using arrays of reference sensors to model and correct for metal distortions may depend strongly on the orientation of the reference sensors in relation to the orientation of the tracked device. In an ideal situation, the reference sensors should be oriented in the same direction as the tracked needle.
Satellite radar interferometry: Two‐dimensional phase unwrapping (1988)

Interferometric synthetic aperture radar observations provide a means for obtaining high‐resolution digital topographic maps from measurements of amplitude and phase of two complex radar images. The phase of the radar echoes may only be measured modulo 2π; however, the whole phase at each point in the image is needed to obtain elevations. We present here our approach to “unwrapping” the 2π ambiguities in the two‐dimensional data set. We find that noise and geometrical radar layover corrupt our measurements locally, and these local errors can propagate to form global phase errors that affect the entire image. We show that the local errors, or residues, can be readily identified and avoided in the global phase estimation. We present a rectified digital topographic map derived from our unwrapped phase values.
Integration challenges for multi-gate devices (2005)

The FinFET transistor is the most widely studied and known multi-gate architecture that has the potential to be scaled to beyond the 45 nm technology node. In this paper a number of integration issues have been addressed. In first section the patterning challenges have been discussed. Due to the particular layout of the FinFET devices a variation in fin width is seen due to the rounding of the fin opening. This problem can be addressed by looking at alternative litho settings and OPC. Next to that topography plays an important in patterning the gate. It is seen that the optimization of the different OE times is key in achieving a controlled gate profile without poly residues. Techniques like poly etch-back can be used to alleviate the topography issues as much as possible. Threshold voltage tuning with implantation is extremely difficult for narrow fin devices. Workfunction tuning by either deposited metal gate or full silicidation is seen as a more viable solution. The extensions and deep source/drain areas need to be as conformal as possible in order to avoid the dominance of the top channel over the sidewalls. However, conventional implantation techniques are unsuitable and alternative implantation techniques need to be investigated. Next to that, when high density is needed, the fin spacing will limit the allowed tilt angle due to implant shadowing. The sidewall crystal orientation is different from that of the top channel and this will impact the mobility of holes and electrons in a different way. Rotation of the fins over 45 degrees, the use of strained layers and strained SiGe source/drain have been briefly discussed as possible solutions to tackle this problem. Finally, the impact of the fin width on R/sub SD/ has been shown. Elevated source/drain has been brought forward as a solution to this problem.
Infrared absorption in low-loss KCl single crystals near 10.6 μm (1974)

The infrared absorption in KCl single crystals near 10.6 μm has been studied using calorimetric techniques with fixed-frequency and tunable CO2 laser sources. By use of crystals grown in a reactive CCl4 atmosphere, with surfaces carefully prepared by chemical polishing, it is possible to obtain absorption coefficients of 0.0002 cm−1 or less in samples several centimeters thick. This residual absorption is composed of a surface and a bulk part. It is possible to show that the bulk absorption approaches the estimated intrinsic limit of 0.00008 cm−1. An absorption band near 9.8 μm is present in all samples examined and appears to be largely associated with the surface.
Remote Optical Cardiopulmonary Signal Extraction With Noise Artifact Removal, Multiple Subject Detection &amp; Long-Distance (2018)

Most existing imaging technologies are prone to noise artifact resulting from movement of subjects, movement of the camera, facial expressions, talking, skin tone, and lighting variations. In addition, these technologies have been limited to detecting physiological signs from a single subject at a time. Still, another challenge facing these technologies is that they have only been demonstrated over a limited range to a subject. This paper proposes an efficient remote imaging system with a new, low-complexity method for noise artifact removal to extract the cardiopulmonary signal from a number of subjects (up to six people) and at long-distances (up to 60 m). The experimental results of the proposed system showed a strong agreement, high correlation, and low noise level with the reference measurements and outperformed the conventional measurement methods such as independent component analysis and principle component analysis in both the stationary and non-stationary scenarios.
High mobility group box 1 protein interacts with multiple Toll-like receptors (2005)

High mobility group box 1 (HMGB1), originally described as a DNA-binding protein, can also be released extracellularly and functions as a late mediator of inflammatory responses. Although recent reports have indicated that the receptor for advanced glycation end products (RAGE) as well as Toll-like receptor (TLR)2 and TLR4 are involved in cellular activation by HMGB1, there has been little evidence of direct association between HMGB1 and these receptors. To examine this issue, we used fluorescence resonance energy transfer (FRET) and immunoprecipitation to directly investigate cell surface interactions of HMGB1 with TLR2, TLR4, and RAGE. FRET images in RAW264.7 macrophages demonstrated association of HMGB1 with TLR2 and TLR4 but not RAGE. Transient transfections into human embryonic kidney-293 cells showed that HMGB1 induced cellular activation and NF-kappaB-dependent transcription through TLR2 or TLR4 but not RAGE. Coimmunoprecipitation also found interaction between HMGB1 and TLR2 as well as TLR4, but not with RAGE. These studies provide the first direct evidence that HMGB1 can interact with both TLR2 and TLR4 and also supply an explanation for the ability of HMGB1 to induce cellular activation and generate inflammatory responses that are similar to those initiated by LPS.
Serum free light-chain measurements for identifying and monitoring patients with nonsecretory multiple myeloma (2001)

Using sensitive, automated immunoassays, increased concentrations of either kappa or lambda free light chains (and abnormal kappa/lambda ratios) were detected in the sera of 19 of 28 patients with nonsecretory multiple myeloma. Four other patients had suppression of one or both light chains, and the remaining 5 sera had normal or raised free light-chain concentrations with substantially normal kappa/lambda ratios. Six of the patients with an elevated single free light chain, who were studied during follow-up, had changes in disease activity that were reflected by the changes in free light-chain concentrations. It is concluded that quantification of free light chains in serum should prove useful for the diagnosis and monitoring of many patients with nonsecretory myeloma.
Mobilization of tumor cells and hematopoietic progenitor cells into peripheral blood of patients with solid tumors [see comments] (1994)

Peripheral blood progenitor cells (PBPCs) are increasingly used for autografting after high-dose chemotherapy. One advantage of PBPCs over the use of autologous bone marrow would be a reduced risk of tumor-cell contamination. However, the actual level of tumor cells contaminating PBPC harvests is poorly investigated. It is currently not known whether mobilization of PBPCs might also result in mobilization of tumor cells. We evaluated 358 peripheral blood samples from 46 patients with stage IV or high-risk stage II/III breast cancer, small cell (SCLC) or non-small cell (NSCLC) lung cancer, as well as other advanced malignancies for the detection of epithelial tumor cells. Monoclonal antibodies against acidic and basic cytokeratin components and epithelial antigens (HEA) were used in an alkaline phosphatase-anti-alkaline phosphatase assay with a sensitivity of 1 tumor cell within 4 x 10(5) total cells. Before initiation of PBPC mobilization, circulating tumor cells were detected in 2/7 (29%) patients with stage IV breast cancer and in 2/10 (20%) patients with extensive-disease SCLC, respectively. In these patients, an even higher number of circulating tumor cells was detected after chemotherapy with VP16, ifosfamide, and cisplatin (VIP) followed by granulocyte colony-stimulating factor (G-CSF). This approach has previously been shown to be highly effective in mobilizing PBPCs. In the 42 patients without circulating tumor cells during steady state, tumor cells were mobilized in 9/42 (21%) patients after VIP+G-CSF induced recruitment of PBPCs. The overall incidence of tumor cells varied between 4 and 5,600 per 1.6 x 10(6) mononuclear cells analyzed. All stage IV breast cancer patients and 50% of SCLC patients were found to concomitantly mobilize tumor cells and PBPCs. Kinetic analyses showed two patterns of tumor cell recruitment depending on the presence or absence of bone marrow disease: (1) early after chemotherapy (between days 1 and 7) in patients without marrow infiltration, and (2) between days 9 and 16 in patients with marrow infiltration, ie, within the optimal time period for the collection of PBPCs. We show that there is a high proportion of patients with circulating tumor cells under steady-state conditions, and in addition a substantial risk of concomitant tumor cell recruitment upon mobilization of PBPCs, particularly in stage IV breast cancer patients with bone marrow infiltration. The biologic and clinical significance of this finding is unknown at present.
Asymmetric Synthesis of β-Amino Acids via the Michael Addition of Chiral Metal Amides (1997)

A lithium amide conjugate addition approach to the synthesis of β-amino acid derivatives is described. Lithium amides derived from α-methylbenzylamine, such as lithium (α-methylbenzyl) benzylamide undergo highly diastereoselective 1, 4-conjugate addition to a variety of α, β-unsaturated carbonyl compounds. The benzyl substituents on the amino group can be readily removed by hydrogenolysis to afford a wide range of β-amino acid derivatives. The enolate intermediate can be trapped by electrophiles such as alkylhalides and (camphorsulphonyl) oxaziridine to give α-alkyl and α-hydroxy-β-amino acids in a highly stereocontroled fashion. The synthetic utility of the methodology is demonstrated by the syntheses of numbers of natural products and other important synthetic intermediates such as taxol C-13 side chain, cispentacin, and (+) -negamycin. The origin of the stereoselectivity is briefly discussed.
Selective immunosuppression by administration of major histocompatibility complex class II-binding peptides. II. Preventive inhibition of primary and secondary in vivo antibody responses. (1993)

The self-mouse lysozyme peptide corresponding to residues 46-62 (ML46-62) binds to the major histocompatibility complex (MHC) class II molecules I-A(k) and it selectively inhibits, when coinjected with antigen, priming of I-A(k)-restricted, antigen-specific T cells. We demonstrate that administration of ML46-62 also inhibits in vivo antibody responses induced by I-A(k)-restricted T helper cells. ML46-62 is able to prevent the primary anti-hen egg white lysozyme (HEL) antibody response induced by the entire HEL molecule in B10.A(4R) mice, expressing only I-A(k) molecules, but not in mice of H-2d haplotype. ML46-62 also strongly decreases, in B10.A(4R) mice, the antibody response to ribonuclease A, a protein antigen unrelated to the MHC blocker, indicating that MHC blockade is the mechanism leading to inhibition of antibody response. This is further supported by the concomitant decrease, in vivo, of complex formation between immunodominant HEL peptides and I-A(k) molecules, preventing I-A(k)-restricted T cell induction. Administration of ML46-62 after antigen priming does not affect ongoing antibody responses, as expected from MHC blockade. A single injection of ML46-62 at the time of protein antigen priming precludes not only the primary, but also the secondary antibody response to a subsequent challenge with soluble protein, even when the challenge is performed several months after priming. Coinjection of antigen and MHC antagonist inhibits production of all antibody isotypes equally well, suggesting that MHC class II blockade affects both Th1- and Th2-type T helper cells. Therefore, these results indicate that administration of MHC class II-binding peptides can efficiently and selectively prevent the induction of T cell-dependent primary and secondary in vivo antibody responses by blocking antigen presentation to class II-restricted T helper cells.
Cyclosporin A reverses vincristine and daunorubicin resistance in acute lymphatic leukemia in vitro. (1986)

The development of drug resistance by tumor cells is a major obstacle to the cure of human malignancy. Cyclosporin A (CsA) completely reverses primary resistance to vincristine and cross resistance to daunorubicin in a pleiotropic drug-resistant subline of human T cell acute lymphatic leukemia. This subline is over 50-fold resistant to vincristine and fivefold resistant to daunorubicin. CsA has little effect on vincristine or daunorubicin activity in drug-sensitive parental leukemia and corrects daunorubicin resistance without altering cellular daunorubicin accumulation.
III-V-on-Silicon Photonic Devices for Optical Communication and Sensing (2015)

In the paper, we review our work on heterogeneous III-V-on-silicon photonic components and circuits for applications in optical communication and sensing. We elaborate on the integration strategy and describe a broad range of devices realized on this platform covering a wavelength range from 850 nm to 3.85 μm.
Combined Bisulfite Restriction Analysis (COBRA) (2003)

Most molecular biological techniques used to analyze specific loci in complex genomic DNA involve some form of sequence-specific amplification, whether it is biological amplification by cloning in Escherichia coli, direct amplification by polymerase chain reaction (PCR), or signal amplification by hybridization with a probe that can be visualized. Since DNA methylation is added postreplicatively by a dedicated maintenance DNA methyltransferase that is not present in either E. coli or in the PCR reaction, the methylation information is lost during molecular cloning or PCR amplification. Molecular hybridization does not discriminate between methylated and unmethylated DNA, since the methyl group on the cytosine does not participate in base pairing. The lack of a facile way to amplify the methylation information in complex genomic DNA has been a significant impediment to DNA methylation research.