gebhart/patrepeval huggingface dataset:
A VLSI algorithm for direct and reverse conversion from weighted binary number system to residue number system (1984)

Residue Number Systems (RNS) are proved to be useful in many applications, as for example in signal processing. In this paper, a VLSI computing architecture is proposed for converting an integer number N from the weighted binary representation into and out a residue code based on s moduli. For this architecture a possible layout is given and its complexity is evaluated in terms of area and time. Under several hypotheses on RNS parameters, constructive upper bounds ranging from <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0(n^{2} \log n)</tex> to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0(n^{2}</tex> <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\log \log n)</tex> and from <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0(\log^{2} n)</tex> to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0(\log n)</tex> for area and time, respectively, have been obtained for the direct conversion. On the contrary, constructive upper bounds <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">A = 0(n^{2} \log n)</tex> and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T = 0(\log^{2} n)</tex> have been found independent of the formed hypotheses, for the reverse conversion.
Coronary CT Angiography–derived Fractional Flow Reserve: Machine Learning Algorithm versus Computational Fluid Dynamics Modeling (2018)

Purpose To compare two technical approaches for determination of coronary computed tomography (CT) angiography-derived fractional flow reserve (FFR)-FFR derived from coronary CT angiography based on computational fluid dynamics (hereafter, FFR<sub>CFD</sub>) and FFR derived from coronary CT angiography based on machine learning algorithm (hereafter, FFR<sub>ML</sub>)-against coronary CT angiography and quantitative coronary angiography (QCA). Materials and Methods A total of 85 patients (mean age, 62 years ± 11 [standard deviation]; 62% men) who had undergone coronary CT angiography followed by invasive FFR were included in this single-center retrospective study. FFR values were derived on-site from coronary CT angiography data sets by using both FFR<sub>CFD</sub> and FFR<sub>ML</sub>. The performance of both techniques for detecting lesion-specific ischemia was compared against visual stenosis grading at coronary CT angiography, QCA, and invasive FFR as the reference standard. Results On a per-lesion and per-patient level, FFR<sub>ML</sub> showed a sensitivity of 79% and 90% and a specificity of 94% and 95%, respectively, for detecting lesion-specific ischemia. Meanwhile, FFR<sub>CFD</sub> resulted in a sensitivity of 79% and 89% and a specificity of 93% and 93%, respectively, on a per-lesion and per-patient basis (P = .86 and P = .92). On a per-lesion level, the area under the receiver operating characteristics curve (AUC) of 0.89 for FFR<sub>ML</sub> and 0.89 for FFR<sub>CFD</sub> showed significantly higher discriminatory power for detecting lesion-specific ischemia compared with that of coronary CT angiography (AUC, 0.61) and QCA (AUC, 0.69) (all P < .0001). Also, on a per-patient level, FFR<sub>ML</sub> (AUC, 0.91) and FFR<sub>CFD</sub> (AUC, 0.91) performed significantly better than did coronary CT angiography (AUC, 0.65) and QCA (AUC, 0.68) (all P < .0001). Processing time for FFR<sub>ML</sub> was significantly shorter compared with that of FFR<sub>CFD</sub> (40.5 minutes ± 6.3 vs 43.4 minutes ± 7.1; P = .042). Conclusion The FFR<sub>ML</sub> algorithm performs equally in detecting lesion-specific ischemia when compared with the FFR<sub>CFD</sub> approach. Both methods outperform accuracy of coronary CT angiography and QCA in the detection of flow-limiting stenosis.
Rescue of Monocrotaline-Induced Pulmonary Arterial Hypertension Using Bone Marrow–Derived Endothelial-Like Progenitor Cells (2005)

Pulmonary arterial hypertension (PAH) is characterized by a progressive increase in pulmonary vascular resistance caused by narrowing and loss of pulmonary microvasculature, which in its late stages becomes refractory to traditional therapies. We hypothesized that bone marrow-derived endothelial progenitor cells (EPCs), which normally function to repair and regenerate blood vessels, would restore pulmonary hemodynamics and increase microvascular perfusion in the rat monocrotaline (MCT) model of PAH. Mononuclear cells were isolated from the bone marrow of syngeneic Fisher-344 rats by Ficoll gradient centrifugation and cultured for 7 to 10 days in endothelial growth medium. Fluorescently labeled endothelial-like progenitor cells (ELPCs) engrafted at the level of the distal pulmonary arterioles and incorporated into the endothelial lining in the MCT-injured lung. The administration of ELPCs 3 days after MCT nearly completely prevented the increase in right ventricular systolic pressure seen at 3 weeks with MCT alone (31.5+/-0.95 versus 48+/-3 mm Hg, respectively; P<0.001), whereas injection of skin fibroblasts had no protective effect (50.9+/-5.4 mm Hg). Delayed administration of progenitor cells 3 weeks after MCT prevented the further progression of PAH 2 weeks later (ie, 5 weeks after MCT), whereas only animals receiving ELPCs transduced with human endothelial NO-synthase (eNOS) exhibited significant reversal of established disease at day 35 (31+/-2 mm Hg, P<0.005) compared with day 21 (50+/-3 mm Hg). Fluorescent microangiography revealed widespread occlusion of pulmonary precapillary arterioles 3 weeks after MCT, whereas arteriolar-capillary continuity and microvascular architecture was preserved with the administration of syngeneic ELPCs. Moreover, the delivery of ELPCs to rats with established PAH resulted in marked improvement in survival, which was greatest in the group receiving eNOS-transduced cells. We conclude that bone marrow-derived ELPCs can engraft and repair the MCT-damaged lung, restoring microvasculature structure and function. Therefore, the regeneration of lung vascular endothelium by injection of progenitor cells may represent a novel treatment paradigm for patients with PAH.
Cathepsin L and Arg/Lys aminopeptidase: a distinct prohormone processing pathway for the biosynthesis of peptide neurotransmitters and hormones (2004)

Peptide neurotransmitters and hormones are synthesized as protein precursors that require proteolytic processing to generate smaller, biologically active peptides that are secreted to mediate neurotransmission and hormone actions. Neuropeptides within their precursors are typically flanked by pairs of basic residues, as well as by monobasic residues. In this review, evidence for secretory vesicle cathepsin L and Arg/Lys aminopeptidase as a distinct proteolytic pathway for processing the prohormone proenkephalin is presented. Cleavage of prohormone processing sites by secretory vesicle cathepsin L occurs at the NH2-terminal side of dibasic residues, as well as between the dibasic residues, resulting in peptide intermediates with Arg or Lys extensions at their NH2-termini. A subsequent Arg/Lys aminopeptidase step is then required to remove NH2-terminal basic residues to generate the final enkephalin neuropeptide. The cathepsin L and Arg/Lys aminopeptidase prohormone processing pathway is distinct from the proteolytic pathway mediated by the subtilisin-like prohormone convertases 1/3 and 2 (PC1/3 and PC2) with carboxypeptidase E/H. Differences in specific cleavage sites at paired basic residue sites distinguish these two pathways. These two proteolytic pathways demonstrate the increasing complexity of regulatory mechanisms for the production of peptide neurotransmitters and hormones.
PRO_LIGAND: An Approach to de Novo Molecular Design. 2. Design of Novel Molecules from Molecular Field Analysis (MFA) Models and Pharmacophores (1994)

A computational approach for molecular design, PRO_LIGAND, has been developed within the PROMETHEUS molecular design and simulation system in order to provide a unified framework for the de novo generation of diverse molecules which are either similar or complementary to a specified target. In this instance, the target is a pharmacophore derived from a series of active structures either by a novel interpretation of molecular field analysis data or by a pharmacophore-mapping procedure based on clique detection. After a brief introduction to PRO_LIGAND, a detailed description is given of the two pharmacophore generation procedures and their abilities are demonstrated by the elucidation of pharmacophores for steroid binding and ACE inhibition, respectively. As a further indication of its efficacy in aiding the rational drug design process, PRO_LIGAND is then employed to build novel organic molecules to satisfy the physicochemical constraints implied by the pharmacophores.
Empirical comparison of fast clustering algorithms for large data sets (2005)

Several fast algorithms for clustering very large data sets have been proposed in the literature. CLARA is a combination of a sampling procedure and the classical PAM algorithm, while CLARANS adopts a serial randomized search strategy to find the optimal set of medoids. GAC-R/sup 3/ and GAC-RAR/sub w/ exploit genetic search heuristics for solving clustering problems. In this research, we conducted an empirical comparison of these four clustering algorithms over a wide range of data characteristics. According to the experimental results, CLARANS outperforms its counterparts both in clustering quality and execution time when the number of clusters increases, clusters are more closely related, more asymmetric clusters are present, or more random objects exist in the data set. With a specific number of clusters, CLARA can efficiently achieve satisfactory clustering quality when the data size is larger, whereas GAC-R/sup 3/ and GAC-RAR/sub w/ can achieve satisfactory clustering quality and efficiency when the data size is small, the number of clusters is small, and clusters are more distinct or symmetric.
Autonomous UAV System Development for Payload Dropping Mission (2015)

— In this paper, power and autonomous system in UAV (Unmanned Aerial Vehicle) for payload dropping mission will be presented. The UAV consists of two main parts, airframe and the avionics system. There are two important subsystems of avionics system which will be discussed, power system and autonomous system. There are three Li-Poly batteries applied in this system to power the autonomous system. The autonomous system consists of an Ardupilot Mega v2.4.2 board (autonomous board), a GPS (Global Positioning System) sensor, attitude sensors, ESC (Electronic Speed Controller), servos, a brushless motor, a camera, a data transmitter, an Audio/Video transmitter, and also a Radio RC receiver. This UAV was designed to participate Kontes Robot Terbang Indonesia 2013 (Indonesia Aerial Robot Contest 2013), payload dropping category, at Institut Teknologi Bandung, Indonesia. In this competition, provided a mission which the UAV has to drop payloads in some target points which is only known when UAV in the flight time. The UAV has to fly autonomously point-to-point while it also search the true point to drop the payloads by camera capturing. By integrating UAV’s system with GCS (Ground Control System), the true point will be known by the operators in the ground control station and the mission can be accomplished. Keywords —airframe, power system, autonomous system, Kontes Robot Terbang Indonesia 2013 , dropping payloads.
Ultra-high quality factor planar Si_3N_4 ring resonators on Si substrates (2011)

We demonstrate planar Si3N4 ring resonators with ultra-high quality factors (Q) of 19 million, 28 million, and 7 million at 1060 nm, 1310 nm, and 1550 nm, respectively. By integrating the ultra-low-loss Si3N4 ring resonators with laterally offset planar waveguide directional couplers, optical add-drop and notch filters are demonstrated to have ultra-narrow bandwidths of 16 MHz, 38 MHz, and 300 MHz at 1060 nm, 1310 nm, and 1550 nm, respectively. These are the highest Qs reported for ring resonators with planar directional couplers, and ultra-narrowband microwave photonic filters can be realized based on these high-Q ring resonators.
Enhanced tumor outgrowth after peptide vaccination. Functional deletion of tumor-specific CTL induced by peptide vaccination can lead to the inability to reject tumors (1996)

CTL can play an important role in the defense against tumors. Protective CTL-mediated immunity can be established in animal tumor models after vaccination with synthetic peptides representing CTL epitopes. We now report that immunization with synthetic peptides can also lead to CTL tolerance associated with the inability to reject tumors. B6 tumor cells transformed by the human adenovirus early region 1 (Ad5E1) present an Ad5E1A- and an Ad5E1B-encoded CTL epitope to the immune system. CTL clones directed against either of these epitopes are able to eradicate established Ad5E1-induced tumors, showing that these CTL epitopes are targets of CTL that can mediate tumor regression. Here, we show that protective immunity against Ad5E1-expressing tumor cells can be established by immunization with Ad5E1-transformed cells and with an adenovirus vector containing the Ad5E1 region. Protective immunity, in either case, is associated with specific CTL memory. To test whether vaccination with synthetic peptides leads to protection against Ad5E1-expressing tumor cells, we vaccinated mice s.c. with a low dose of the Ad5E1B peptide. This peptide was chosen because the CTL response against the Ad5E1B-encoded CTL epitope contributes most to the antitumor response in B6 mice after vaccination with Ad5E1-transformed cells. Ad5E1B peptide-vaccinated mice were not protected against the outgrowth of Ad5E1-expressing tumor cells, but instead were no longer able to reject a tumor inoculum that was rejected by nonvaccinated mice. Moreover, the protection induced by tumor cell vaccination against Ad5E1B-expressing tumors was gone when the Ad5E1B-encoded CTL epitope was injected a few days before tumor challenge. This is associated with peptide-induced tolerance of Ad5E1B-specific CTL activity. These findings are relevant for the design of therapeutic approaches against both malignancies and T cell-mediated autoimmune diseases.
TAB2 Is Essential for Prevention of Apoptosis in Fetal Liver but Not for Interleukin-1 Signaling (2003)

The proinflammatory cytokine interleukin-1 (IL-1) transmits a signal via several critical cytoplasmic proteins such as MyD88, IRAKs and TRAF6. Recently, serine/threonine kinase TAK1 and TAK1 binding protein 1 and 2 (TAB1/2) have been identified as molecules involved in IL-1-induced TRAF6-mediated activation of AP-1 and NF-kappa B via mitogen-activated protein (MAP) kinases and I kappa B kinases, respectively. However, their physiological functions remain to be clarified. To elucidate their roles in vivo, we generated TAB2-deficient mice. The TAB2 deficiency was embryonic lethal due to liver degeneration and apoptosis. This phenotype was similar to that of NF-kappa B p65-, IKK beta-, and NEMO/IKK gamma-deficient mice. However, the IL-1-induced activation of NF-kappa B and MAP kinases was not impaired in TAB2-deficient embryonic fibroblasts. These findings demonstrate that TAB2 is essential for embryonic development through prevention of liver apoptosis but not for the IL-1 receptor-mediated signaling pathway.
Using computer vision to generate customized spatial audio (2003)

Creating high quality virtual spatial audio over headphones requires real-time head tracking, personalized head-related transfer functions (HRTFs) and customized room response models. While there are expensive solutions to address these issues based on costly head trackers, measured personalized HRTFs and room responses, these are not suitable for widespread or easy deployment and use. We report on the development of a system that uses computer vision to produce customizable models for both the HRTF and the room response, and to achieve head-tracking. The system uses relatively inexpensive cameras and widely available personal computers. Computer-vision based anthropometric measurements of the head, torso, and the external ears are used for HRTF customization. For low-frequency HRTF customization we employ a simple head-and-torso model developed recently [V. R. Algazi et al., 2002]. For high frequency customization we employ measured pinna characteristics as an index into a database of HRTFs [D. N. Zotkin et al., 2002]. For head tracking we employ an online implementation of the POSIT algorithm [D. DeMenthon and L. Davis, 1995] along with active markers to compute head pose in real-time. The system provides an enhanced virtual listening experience at low cost.
Postexposure antibody prophylaxis protects nonhuman primates from filovirus disease (2012)

Antibody therapies to prevent or limit filovirus infections have received modest interest in recent years, in part because of early negative experimental evidence. We have overcome the limitations of this approach, leveraging the use of antibody from nonhuman primates (NHPs) that survived challenge to filoviruses under controlled conditions. By using concentrated, polyclonal IgG antibody from these survivors, we treated filovirus-infected NHPs with multiple doses administered over the clinical phase of disease. In the first study, Marburg virus (MARV)-infected NHPs were treated 15 to 30 min postexposure with virus-specific IgG, with additional treatments on days 4 and 8 postexposure. The postexposure IgG treatment was completely protective, with no signs of disease or detectable viremia. MARV-specific IgM antibody responses were generated, and all macaques survived rechallenge with MARV, suggesting that they generated an immune response to virus replication. In the next set of studies, NHPs were infected with MARV or Ebola virus (EBOV), and treatments were delayed 48 h, with additional treatments on days 4 and 8 postexposure. The delayed treatments protected both MARV- and EBOV-challenged NHPs. In both studies, two of the three IgG-treated NHPs had no clinical signs of illness, with the third NHP developing mild and delayed signs of disease followed by full recovery. These studies clearly demonstrate that postexposure antibody treatments can protect NHPs and open avenues for filovirus therapies for human use using established Food and Drug Administration-approved polyclonal or monoclonal antibody technologies.
Single-step Protein A and Protein G avidity purification methods to support bispecific antibody discovery and development (2019)

Heavy chain (Hc) heterodimers represent a majority of bispecific antibodies (bsAbs) under clinical development. Although recent technologies achieve high levels of Hc heterodimerization (HD), traces of homodimer contaminants are often present, and as a consequence robust purification techniques for generating highly pure heterodimers in a single step are needed. Here, we describe two different purification methods that exploit differences in Protein A (PA) or Protein G (PG) avidity between homo- and heterodimers. Differential elution between species was enabled by removing PA or PG binding in one of the Hcs of the bsAb. The PA method allowed the avidity purification of heterodimers based on the VH3 subclass, which naturally binds PA and interferes with separation, by using a combination of IgG3 Fc and a single amino acid change in VH3, N82aS. The PG method relied on a combination of three mutations that completely disrupts PG binding, M428G/N434A in IgG1 Fc and K213V in IgG1 CH1. Both methods achieved a high level of heterodimer purity as single-step techniques without Hc HD (93-98%). Since PA and PG have overlapping binding sites with the neonatal Fc receptor (FcRn), we investigated the effects of our engineering both <i>in vitro</i> and <i>in vivo</i>. Mild to moderate differences in FcRn binding and Fc thermal stability were observed, but these did not significantly change the serum half-lives of engineered control antibodies and heterodimers. The methods are conceptually compatible with various Hc HD platforms such as BEAT® (Bispecific Engagement by Antibodies based on the T cell receptor), in which the PA method has already been successfully implemented.
A B cell growth factor-like activity is secreted by cloned, neoplastic B cells. (1984)

Supernatants from synchronized clones of neoplastic B cells (BCL1) were found to contain a B cell growth factor (BCGFI)-like activity. The BCGF activity in the BCL1 supernatants (SN) could synergize with EL-4 SN in the late phases of an IL 1-dependent BCGF I assay (days 5 through 8). These SN did not contain any detectable BCGF II, IL, 1, or IL 2 activity. In contrast to EL-4-derived BCGF I, which has a m.w. of approximately 18,000, the BCL1-BCGF activity has a m.w. of approximately 4500. Because the BCGF activity in BCL1 SN fluctuates with cell cycle in synchronized cultures, this BCL1-BCGF may play an auto-stimulatory role in B cell proliferation.
Dynamic adaptation of access control policies (2004)

An architecture and algorithms for deriving an access control policy by composing access control requirements specified at multiple levels in a command hierarchy is described. Our method can detect conflicts in requirements, and find a policy that maximally satisfies the requirements, by satisfying higher priority requirements at the expense of lower priority ones. It also allows for easy verification of the final policy by an administrator. The architecture allows quick adaptation of policies to changing situations, by providing for delegation of authority while ensuring that high priority requirements will always be satisfied.
An Attenuated aroA Salmonella typhimurium Vaccine Elicits Humoral and Cellular Immunity to Cloned -Galactosidase in Mice (1987)

beta-Galactosidase (GZ) is an intracellular protein that is frequently used to express cloned antigens as fusion proteins in Escherichia coli. Salmonella typhimurium strain SL3261, an attenuated aroA vaccine strain, was used as a carrier for the plasmid pXY411, which directs the expression of GZ in salmonellae (which do not normally produce this protein). The resulting strain--SL3261(pXY411)--expressed GZ as an intracellular antigen. The plasmid was stable in vitro and in vivo and did not significantly alter the behavior of strain SL3261 in mice. Animals intravenously vaccinated with this construct developed circulating antibodies to GZ, as measured by ELISA, and delayed hypersensitivity to the antigen injected in the footpad. These results indicate that attenuated salmonellae may be expected to elicit both humoral and cellular responses to intracellular cloned antigens.