gebhart/patrepeval huggingface dataset:
Cultured human trophoblast cells reproduce the initial events of placental biology. (1993)

Term placenta trophoblast cultures can be viewed and used as a model system mimicking morphological and biochemical events of placenta biology and differentiation.
Genome-wide signals of positive selection in human evolution (2014)

The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci, and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1000 Genomes Project and detect signatures of positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to argue that the observed signatures require a high rate of strongly adaptive substitutions near amino acid changes. We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes.
Immune Checkpoint Blockade to Improve Tumor Infiltrating Lymphocytes for Adoptive Cell Therapy (2016)

Tumor-infiltrating lymphocytes (TIL) has been associated with improved survival in cancer patients. Within the tumor microenvironment, regulatory cells and expression of co-inhibitory immune checkpoint molecules can lead to the inactivation of TIL. Hence, there is a need to develop strategies that disrupt these negative regulators to achieve robust anti-tumor immune responses. We evaluated the blockade of immune checkpoints and their effect on T cell infiltration and function. We examined the ability of TIL to induce tumor-specific immune responses in vitro and in vivo. TIL isolated from tumor bearing mice were tumor-specific and expressed co-inhibitory immune checkpoint molecules. Administration of monoclonal antibodies against immune checkpoints led to a significant delay in tumor growth. However, anti-PD-L1 antibody treated mice had a significant increase in T cell infiltration and IFN-γ production compared to other groups. Adoptive transfer of in vitro expanded TIL from tumors of anti-PD-L1 antibody treated mice led to a significant delay in tumor growth. Blockade of co-inhibitory immune checkpoints could be an effective strategy to improve TIL infiltration and function.
Compressing Polygon Mesh Connectivity with Degree Duality Prediction (2002)

In this paper we present a coder for polygon mesh connectivity that delivers the best connectivity compression rates meshes reported so far. Our coder is an extension of the vertex-based coder for triangle mesh connectivity by Touma and Gotsman[GI98]. We code polygonal connectivity as a sequence of face and vertex degrees and exploit the correlation between them for mutual predictive compression. Because low-degree vertices are likely to be surrounded by high-degree faces and vice versa, we predict vertex degrees based on neighboring face degrees and face degrees based on neighboring vertex degrees.
A diffusible lymphokine produced by CD8+ T lymphocytes suppresses HIV replication. (1989)

Peripheral blood CD8+ T lymphocytes from human immunodeficiency virus (HIV)-infected individuals suppress replication of HIV in peripheral blood mononuclear cells (PBMC). This anti-viral activity appears to be mediated in part by a diffusible factor. Production of this lymphokine varies among infected individuals and may reflect the intrinsic ability of an individual's CD8+ cells to control HIV infection. In some cases in which factor activity is not apparent, contact of the CD8+ cells with infected CD4+ cells can produce for suppression of virus replication. These observations could lead to approaches for enhancing anti-viral responses in HIV-infected individuals.
Managing the Impact of Customer Support Disruptions on New Product Development Projects (2004)

Knowledge-worker development projects are often performed where multiple projects are always in progress, and where preemption often occurs for solving time-critical customer service projects. The following nonlinear model for learning-intense situations demonstrates that the choice of preemption policy significantly impacts project completion times. Within this model, the authors identify policies that reduce the detrimental effects of preemption. The best policy preempts the activity that has the most slack and has been in progress the shortest time, and restarts the activity quickly with qualified resources as soon as possible.
A statistical approach to 3d object detection applied to faces and cars (2000)

In this thesis, we describe a statistical method for 3D object detection. In this method, we decompose the 3D geometry of each object into a small number of viewpoints. For each view-point, we construct a decision rule that determines if the object is present at that specific orienta-tion. Each decision rule uses the statistics of both object appearance and “non-object ” visual appearance. We represent each set of statistics using a product of histograms. Each histogram represents the joint statistics of a subset of wavelet coefficients and their position on the object. Our approach is to use many such histograms representing a wide variety of visual attributes. Using this method, we have developed the first algorithm that can reliably detect faces that vary from frontal view to full profile view and the first algorithm that can reliably detect cars over a wide range of viewpoints. Acknowledgments I would like to thank my advisor, Takeo Kanade, for his guidance in this research. His ideas, insights, suggestions, questions, and enthusiasm were great help in stimulating my thought and in bringing this research forward. I would like to thank the other members of my dissertation com-
Palladium-catalyzed copper(i)-mediated cross-coupling of arylboronic acids and 2(1H)-pyrazinones facilitated by microwave irradiation with simultaneous cooling (2007)

The application of a palladium-catalyzed Cu(I)-mediated Liebeskind-Srogl protocol for the decoration of the 2(1H)-pyrazinone scaffold resulted in significantly improved yields and rates when performed under microwave irradiation with simultaneous cooling.
Rapid bioassay of pesticide residues in vegetable sample from Laguna, Philippines (1997)

A rapid bioassay technique for the detection of pesticide residues was used in screening organophosphates and carbamate insecticides in vegetable samples from Laguna, Philippines. The rapid bioassay is based on the inhibition of the enzyme acetylcholinesterase (AChE) by organophosphate or carbamate insecticides. This enzyme is responsible for hydrolyzing acetylcholine, a chemical transmitter of stimuli from one nerve cell to another. Generally slightly lower sensitivities were obtained for the crude AChE than the purified enzyme. The activity of the crude AChE compared well with the Taiwan Agricultural Research Institute (TARI) purified acetylcholinesterase with activity of 1.09 x 10 raised to the negative 2 power mol/min/ml and 1.02 x 10 raised to the negative 2 power mol/min/ml, respectively. These results indicate that freshly prepared crude AChE may be used in screening for pesticide contamination in vegetables using the rapid bioassay method. A total of 168 vegetable samples were assayed and 11.3 percent gave more than 20 percent inhibition of acetylcholinesterase, a clear indication of the presence of insecticide residues. The higher the degree of enzyme inhibition, the higher the residues of insecticides. Gas chromatographic analysis revealed that samples which exhibited an inhibition 43 percent exceeded the maximum residue limit (MRL) set by FAO/WHO for methomyl, triazophos and diazinon. Samples which exhibited 20-40 percent inhibition contained residues of methyl parathion, chlorpyrifos and malathion at levels within the MRL set by FAO/WHO
Direct activation of mTOR in B lymphocytes confers impairment in B‐cell maturation andloss of marginal zone B cells (2011)

Abstract The tuberous sclerosis complex (TSC), composed of TSC1/TSC2 heterodimers, is inhibitory to the mammalian target of rapamycin (mTOR). Deletion of either TSC1 or TSC2 renders mTOR constitutively active. To directly explore the impact of mTOR activation on B‐cell development, we conditionally deleted TSC1 in murine B cells. This led to impairment in B‐cell maturation. Unexpectedly, and in contrast to Akt activation, marginal zone (MZ) B cells were significantly reduced. Administration of rapamycin partially corrected the MZ defect, indicating a direct role for mTOR in controlling MZ development. When challenged with a T‐cell‐dependent antigen, TSC1 KO mice responded less efficiently. Consistent with the MZ defects, TSC1 KO mice did not respond at all to T‐independent antigens. Because activation of Akt upstream of TSC and mTOR yields the reverse phenotype with respect to MZ development, we conclude that, physiologically, Akt simultaneously emits two opposing signals that counterbalance each other in the control of B‐cell differentiation.
HLA-Haploidentical Bone Marrow Transplantation for Hematologic Malignancies Using Nonmyeloablative Conditioning and High-Dose, Posttransplantation Cyclophosphamide (2008)

We evaluated the safety and efficacy of high-dose, posttransplantation cyclophosphamide (Cy) to prevent graft rejection and graft-versus-host disease (GVHD) after outpatient nonmyeloablative conditioning and T cell-replete bone marrow transplantation from partially HLA-mismatched (haploidentical) related donors. Patients with advanced hematologic malignancies (n = 67) or paroxysmal nocturnal hemoglobinuria (n = 1) received Cy 50 mg/kg i.v. on day 3 (n = 28) or on days 3 and 4 (n = 40) after transplantation. The median times to neutrophil (>500/microL) and platelet recovery (>20,000/microL) were 15 and 24 days, respectively. Graft failure occurred in 9 of 66 (13%) evaluable patients, and was fatal in 1. The cumulative incidences of grades II-IV and grades III-IV acute (aGVHD) by day 200 were 34% and 6%, respectively. There was a trend toward a lower risk of extensive chronic GVHD (cGVHD) among recipients of 2 versus 1 dose of posttransplantation Cy (P = .05), the only difference between these groups. The cumulative incidences of nonrelapse mortality (NRM) and relapse at 1 year were 15% and 51%, respectively. Actuarial overall survival (OS) and event-free survival (EFS) at 2 years after transplantation were 36% and 26%, respectively. Patients with lymphoid malignancies had an improved EFS compared to those with myelogenous malignancies (P = .02). Nonmyeloablative HLA-haploidentical BMT with posttransplantation Cy is associated with acceptable rates of fatal graft failure and severe aGVHD or cGVHD.
Magnetic order of rare-earth tritelluride CeTe<sub>3</sub>at low temperature (2009)

Rare-earth tritelluride CeTe3, which belongs to the family of quasi-two dimensional compounds RTe3 (where R = Y, La-Sm, Gd-Tm), has highly two-dimensional crystal structure. Fermi surfaces consist of inner and outer square sheets, large regions of which are nested by a single incommensurate wave-vector. Because of the characteristic quasi-two-dimensional nature of square Fermi surfaces, the charge density wave of RTe3 is formed with an extremely large gap and extensively investigated. Despite the extensive studies on the charge density wave in recent years, remarkably little is known about magnetism and low-temperature properties of CeTe3. We have investigated the low-temperature magnetic-ordered-phases of the rare-earth tritelluride CeTe3 with single crystals. We measured specific heat, electrical resistivity and differential magnetic susceptibility using a 3He cryostat down to about 0.45 K and a 3He/4He dilution refrigerator down to 0.1 K. We have found that heavy quasi-particles form spin density wave at low temperatures, reflecting the square Fermi surfaces with the quasi-one-dimensional nature.
Efficient duty cycle mac protocols for dynamic traffic loads in wireless sensor networks (2009)

Idle listening is one of the most significant causes of energy consumption in wireless sensor networks (WSNs), and many protocols have been proposed based on duty cycling to reduce this cost. These protocols, either synchronous or asynchronous, are mainly optimized for light traffic loads. A WSN, however, could often experience bursty and high traffic loads, as may happen for example with broadcast or convergecast traffic. In this thesis, I design and evaluate a new synchronous protocol, DW-MAC (Demand Wakeup MAC), and a new asynchronous protocol, RI-MAC (Receiver Initiated MAC), that are both efficient under dynamic traffic loads, including light or heavy loads. I also design and evaluate ADB (Asynchronous Duty-cycle Broadcasting), a new protocol for efficient multihop broadcasting in WSNs using asynchronous duty cycling. 
DW-MAC introduces a new low-overhead scheduling algorithm that allows nodes to wake up on demand during the Sleep period of an operational cycle and ensures that data transmissions do not collide at their intended receivers; this demand wakeup adaptively increases effective channel capacity as traffic load increases. RI-MAC, instead, uses receiver-initiated transmissions, in which each transmitter passively waits until its intended receiver wakes up and transmits a beacon frame; this technique minimizes the time a sender and its intended receiver occupy the wireless medium to find a rendezvous time for exchanging data. ADB is integrated with RI-MAC to exploit information only available at this layer; rather than treating the data transmission from a node to all of its neighbors as the basic unit of progress for the multihop broadcast. ADB dynamically optimizes the broadcast at the level of transmission to each individual neighbor of a node as the neighbors asynchronously wakeup, avoiding redundant transmissions and transmissions over poor links, and allowing a transmitter to go to sleep as early as possible. In detailed simulation of all three protocols using ns-2, they each substantially outperform earlier competing protocols in terms of reduced energy and latency and increased packet delivery ratio. I also implemented RI-MAC and ADB in a testbed of MICAz motes using TinyOS and further demonstrate the significant performance improvements made over prior protocols.
Determination of Halogenated Pyrenes in Water by High Performance Liquid Chromatography. (1992)

This paper describes high performance liquid chromatographic (HPLC) determinations of halogenated pyrenes in water by use of LiChrosorb RP-18 column as a stationary phase and acetonitrile/water as a mobile phase. The method consists of the following 3 procedures : extraction of halogenated pyrenes from water samples with benzene, cleaning up by one dimensional dual-band thin layer chromatography, identification and determination of halogenated pyrenes by HPLC. The calibration curves of pyrene (Py), 1-chloropyrene (PyCl), 1-bromopyrene (PyBr), 1, 8-, 1, 6-, 1, 3-dichloropyrene (PyCl2) and 1, 8-dibromopyrene (PyBr2) were linear over the range of 0-2 ng for Py and PyCl, 0-4 ng for each PyCl2, and 0-20 ng for PyBr and 1, 8-PyBr2. The minimum detectable amounts of Py and each halogenated pyrenes (s/n=4) were 0.1 ng for Py, 0.05 ng for PyCl, 0.2 ng for 1, 8-PyCl2, 0.25 ng for 1, 6-PyCl2, 0.7 ng for 1, 3-PyCl2 and 1.0 ng for PyBr and PyBr2. The proposed method has been applied to determine the halogenated compounds in chlorinated-river water spiked with 100 μg/l pyrene. The concentrations of halogenated compounds were 0.67 μg/l for PyCl, 17.1 μg/l for PyBr, 3.87 μg/l for PyCl2 and 14.0 μg/l for PyBr2.
Localization and Control of Magnetic Suture Needles in Cluttered Surgical Site with Blood and Tissue (2021)

Real-time visual localization of needles is necessary for various surgical applications, including surgical automation and visual feedback. In this study we investigate localization and autonomous robotic control of needles in the context of our magneto-suturing system. Our system holds the potential for surgical manipulation with the benefit of minimal invasiveness and reduced patient side effects. However, the nonlinear magnetic fields produce unintuitive forces and demand delicate position-based control that exceeds the capabilities of direct human manipulation. This makes automatic needle localization a necessity. Our localization method combines neural network-based segmentation and classical techniques, and we are able to consistently locate our needle with 0.73 mm RMS error in clean environments and 2.72 mm RMS error in challenging environments with blood and occlusion. The average localization RMS error is 2.16 mm for all environments we used in the experiments. We combine this localization method with our closed-loop feedback control system to demonstrate the further applicability of localization to autonomous control. Our needle is able to follow a running suture path in (1) no blood, no tissue; (2) heavy blood, no tissue; (3) no blood, with tissue; and (4) heavy blood, with tissue environments. The tip position tracking error ranges from 2.6 mm to 3.7 mm RMS, opening the door towards autonomous suturing tasks.
Limits on quality factors of localized defect modes in photonic crystals due to dielectric loss (1998)

The spectral widths of defect modes localized at line defects formed in a two-dimensional photonic crystal composed of a square lattice of dielectric cylinders were analyzed theoretically. The transmission spectra calculated by the layer-doubling method based on the vector–cylindrical–wave expansion of the internal field showed a rapid decrease of the spectral width with increasing number of the lattice layers when the dielectric loss is absent. Quality factors larger than 107 were predicted for the total lattice layers of 18. However, the numerical evaluation of the decay constant of the defect modes due to the imaginary part of the dielectric constant showed that the actual quality factor is limited by the dielectric loss. The calculated widths agreed qualitatively with the experimental observations by Lin et al. [Appl. Phys. Lett. 68, 3233 (1996)].
Towards an authorization mechanism for user-role based security in an object-oriented design model (2002)

User-role based security (URBS) is a technique for characterizing database security that takes the responsibilities of individuals into consideration when determining the security requirements of an application. In previous work, the authors developed a set of techniques for defining and analyzing URBS for an application. They extend this work by considering an actual individual's authorized access rights in an application, and by focusing on specifying, analyzing, and validating these rights. Inconsistencies and conflicts not identified when the roles were defined and analyzed, might become apparent when different roles are combined to represent the privileges for an individual. This study serves as a fundamental step toward supporting an authorization mechanism for URBS, thereby achieving management and control over all authorized accesses to an object-oriented database.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Lead‐time reduction: the search for competitive advantage (1995)

Generic product offerings in a boundaryless competitive environment do not support economic viability. Time‐based dimensions of a product are becoming an increasingly important component in assessing strategic advantage. A generalized framework is provided for analyzing product environments based on production/consumption gaps that can lead to an augmented product. Traditional long lead times and high inventory levels are less appropriate and more costly endeavours that may not even achieve product parity.
Target Velocity Estimation and Antenna Placement for MIMO Radar With Widely Separated Antennas (2010)

This paper studies the velocity estimation performance for multiple-input multiple-output (MIMO) radar with widely spaced antennas. We derive the Cramer-Rao bound (CRB) for velocity estimation and study the optimized system/configuration design based on CRB. General results are presented for an extended target with reflectivity varying with look angle. Then detailed analysis is provided for a simplified case, assuming an isotropic scatterer. For given transmitted signals, optimal antenna placement is analyzed in the sense of minimizing the CRB of the velocity estimation error. We show that when all antennas are located at approximately the same distance from the target, symmetrical placement is optimal and the relative position of transmitters and receivers can be arbitrary under the orthogonal received signal assumption. In this case, it is also shown that for MIMO radar with optimal placement, velocity estimation accuracy can be improved by increasing either the signal time duration or the product of the number of transmit and receive antennas.
Choline Deprivation Induces Hyperhomocysteinemia in Rats Fed Low Methionine Diets (2008)

To clarify the relationship between dietary choline level and plasma homocysteine concentration, the effects of choline deprivation on plasma homocysteine concentration and related variables were investigated in rats fed a standard (25%) casein (25C) diet or standard soybean protein (25S) diet. Using the 25S diet, the time-dependent effect of choline deprivation and the comparative effects of three kinds of lipotropes were also investigated. Feeding rats with the choline-deprived 25S diet for 10 d significantly increased plasma total homocysteine concentration to a level 2.68-times higher than that of the control group, whereas choline deprivation had no effect in rats fed the 25C diet. Increases in hepatic S-adenosylhomocysteine and homocysteine concentrations, decreases in hepatic betaine concentration and the activity of cystathionine beta-synthase, but not betaine-homocysteine S-methyltransferase, and fatty liver also occurred in rats fed the choline-deprived 25S diet. Plasma homocysteine concentration increased when rats were fed the choline-deprived 25S diet for only 3 d, and the increase persisted up to 20 d. The hyperhomocysteinemia induced by choline deprivation was effectively suppressed by betaine or methionine supplementation. Choline deprivation caused hyperhomocysteinemia also in rats fed a choline-deprived low (10%) casein diet. The results indicate that choline deprivation can easily induce prominent hyperhomocysteinemia when rats are fed relatively low methionine diets such as a standard soybean protein diet and low casein diet, possibly through the suppression of homocysteine removal by both remethylation and cystathionine formation. This hyperhomocysteinemia might be a useful model for investigating the role of betaine in the regulation of plasma homocysteine concentration.