gebhart/patrepeval huggingface dataset:
Intramacrophage growth of Mycobacterium avium during infection of mice (1991)

Growth of the virulent Mycobacterium avium strain TMC 724 in host tissues during persistent infection of mice was studied. Following intravenous infection of C57BL/6 mice, the kinetics of bacterial growth was biphasic in the spleen and liver, with a significant reduction of the multiplication rate after day 21 to 28 of infection. An electron-microscopic study of the liver and spleen of infected mice showed that the bacteria were strictly intracellular. They were observed within inflammatory macrophages populating granulomas disseminated in host tissues. The bacteria were confined to the phagosome compartment, and they were encapsulated. Phagosome-lysosome fusions were encountered, but the bacteria showed no visible signs of degradation and continued to multiply. These results are the first in vivo evidence that virulent M. avium multiplies exclusively intracellularly and that encapsulated bacteria resist the microbicidal mechanisms of macrophages inside the phagosomal compartment.
Computerized Real-Time Analysis of Football Games (2005)

Computer systems support many coaching activities performed before and after competitions, such as strategy development and performance evaluation, but competent assistance during games is much more demanding. It requires real-time interpretation of sensor data, the recognition and classification of ball actions, and fast-action game analysis and assessment. Only recently has high-precision microwave technology enabled computer systems to simultaneously track the position of players and the ball. Consequently, real-time game analysis systems must be able to automatically recognize intentional activities in a multiagent system with continually acting agents. To meet these demands, we've developed the football interaction and process model and a software system that can acquire, interpret, and analyze this model. Our FIPM system can acquire models of player skills, infer action-selection criteria, and determine player and team strengths and weaknesses.
Cultural Materiality and Spiritual Alienation (2013)

This article takes its point of departure in Phillip Blond’s Christian criticism of secular materialisms and the failure of modern thought to appreciate the true materiality of creation. He challenges secular thought and returns to a combination of Greek and Christian Trinitarian thought, in order to reach for a new ground for political theology. Blond’s Christian ontological claims are contested, but an aspect of them is brought into the context of cultural creation and related to questions of the spiritual dimension of cultural arte-facts in a secular setting. Against the background of Friedrich Nietzsche’s struggle with the difficulty of singling out a pure secular culture from the old and (in his view) stifling religious heritage in society and culture, this article suggests that a radical notion of human intentional (but finite) creation, analogous to Blond’s idea of God’s infinite creative intention, may be helpful for a construction of a materialistic critical theory about contingent spiritual obstacles to political change.
BAFF and LPS cooperate to induce B cells to become susceptible to CD95/Fas‐mediated cell death (2007)

Microorganisms with pathogen-associated molecular patterns (PAMP) activate B cells directly by binding to TLR and also indirectly by inducing APC to release cytokines such as BAFF that promote B cell survival. We found that murine B cells activated concomitantly with LPS (TLR-4 ligand) and BAFF are protected from spontaneous apoptosis, but are more susceptible to Fas/CD95-mediated cell death. This increased susceptibility to Fas-induced apoptosis is associated with a dramatic coordinated up-regulation of Fas/CD95 and IRF-4 expression through a mechanism mediated, at least in part, by inhibition of the MEK/ERK pathway. Up-regulation of Fas/CD95 by BAFF is restricted to B cells activated through TLR-4, but not through TLR-9, BCR or CD40. TLR ligands differ in the BAFF family receptors (R) they induce on B cells: BAFF-R is increased by the TLR4 ligand, LPS, but not by the TLR9 ligand, CpG-containing oligodeoxynucleotides, which, in contrast, strongly up-regulates transmembrane activator and CAML interactor (TACI). This suggests the up-regulation of Fas by BAFF is mediated by BAFF-R and not by TACI. Consistently, APRIL, which binds to TACI and B cell maturation antigen but not BAFF-R, did not enhance Fas expression on LPS-activated B cells. Increased susceptibility to Fas-mediated killing of B cells activated with LPS and BAFF may be a fail-safe mechanism to avoid overexpansion of nonspecific or autoreactive B cells.
Autonomous satellite rendezvous and docking using lidar and model based vision (2005)

Servicing satellites on-orbit requires ability to rendezvous and dock by an unmanned spacecraft with no or minimum human input. Novel imaging sensors and computer vision technologies are required to detect a target spacecraft at a distance of several kilometers and to guide the approaching spacecraft to contact. Current optical systems operate at much shorter distances, provide only bearing and range towards the target, or rely on visual targets. Emergence of novel LIDAR technologies and computer vision algorithms will lead to a new generation of rendezvous and docking systems in the near future. Such systems will be capable of autonomously detecting a target satellite at a distance of a few kilometers, estimating its bearing, range and relative orientation under virtually any illumination, and in any satellite pose. At MDA Space Missions we have developed a proof-of-concept vision system that uses a scanning LIDAR to estimate pose of a known satellite. First, the vision system detects a target satellite, and estimates its bearing and range. Next, the system estimates the full pose of the satellite using a 3D model. Finally, the system tracks satellite pose with high accuracy and update rate. Estimated pose provides information where the docking port is located even if the port is not visible and enables selecting more efficient flight trajectory. The proof-of-concept vision system has been integrated with a commercial time-of-flight LIDAR and tested using a moving scaled satellite replica in the MDA Vision Testbed.
Fine-grained network time synchronization using reference broadcasts (2002)

Recent advances in miniaturization and low-cost, low-power design have led to active research in large-scale networks of small, wireless, low-power sensors and actuators. Time synchronization is critical in sensor networks for diverse purposes including sensor data fusion, coordinated actuation, and power-efficient duty cycling. Though the clock accuracy and precision requirements are often stricter than in traditional distributed systems, strict energy constraints limit the resources available to meet these goals.We present Reference-Broadcast Synchronization , a scheme in which nodes send reference beacons to their neighbors using physical-layer broadcasts. A reference broadcast does not contain an explicit timestamp; instead, receivers use its arrival time as a point of reference for comparing their clocks. In this paper, we use measurements from two wireless implementations to show that removing the sender's nondeterminism from the critical path in this way produces high-precision clock agreement (1.85 ± 1.28μsec, using off-the-shelf 802.11 wireless Ethernet), while using minimal energy. We also describe a novel algorithm that uses this same broadcast property to federate clocks across broadcast domains with a slow decay in precision (3.68 ± 2.57μsec after 4 hops). RBS can be used without external references, forming a precise relative timescale, or can maintain microsecond-level synchronization to an external timescale such as UTC. We show a significant improvement over the Network Time Protocol (NTP) under similar conditions.
Discrete stochastic microfacet models (2014)

This paper investigates rendering glittery surfaces, ones which exhibit shifting random patterns of glints as the surface or viewer moves. It applies both to dramatically glittery surfaces that contain mirror-like flakes and also to rough surfaces that exhibit more subtle small scale glitter, without which most glossy surfaces appear too smooth in close-up. These phenomena can in principle be simulated by high-resolution normal maps, but maps with tiny features create severe aliasing problems under narrow-angle illumination. In this paper we present a stochastic model for the effects of random subpixel structures that generates glitter and spatial noise that behave correctly under different illumination conditions and viewing distances, while also being temporally coherent so that they look right in motion. The model is based on microfacet theory, but it replaces the usual continuous microfacet distribution with a discrete distribution of scattering particles on the surface. A novel stochastic hierarchy allows efficient evaluation in the presence of large numbers of random particles, without ever having to consider the particles individually. This leads to a multiscale procedural BRDF that is readily implemented in standard rendering systems, and which converges back to the smooth case in the limit.
Influence of Hydration and Electrolyte Supplementation on Incidence and Time to Onset of Exercise-Associated Muscle Cramps. (2005)

Context: Exercise-associated muscle cramps (EAMCs) are common among physically active individuals and are temporarily disabling; therefore, prevention is of great interest.Objective: To determine the role of hydration and electrolyte supplementation in the prevention of EAMCs.Design: Each subject completed 2 counterbalanced trials in a repeated-measures design.Setting: University of Alabama.Patients or Other Participants: College-aged men (n = 13) with a history of EAMCs.Intervention(s): In each trial, participants performed a calf-fatiguing protocol to induce EAMCs in the calf muscle group. Each trial was performed in a hot environment (dry bulb temperature of 37 degrees C, relative humidity of 60%). In the carbohydrate-electrolyte trial, subjects consumed, at a rate similar to sweat loss, a carbohydrate-electrolyte beverage with sodium chloride added. In the hypohydration trial, subjects were not allowed to consume any fluids.Main Outcome Measure(s): We measured the incidence and time to onset of EAMCs.Results: Nine participants experienced cramps in the carbohydrate-electrolyte trial, compared with 7 in the hypohydration trial. Of the 7 individuals who had EAMCs in both trials, exercise duration before onset was more than doubled in the carbohydrate-electrolyte trial (36.8 +/- 17.3 minutes) compared with the hypohydration trial (14.6 +/- 5.0 minutes, P < .01).Conclusions: Consumption of a carbohydrate-electrolyte beverage before and during exercise in a hot environment may delay the onset of EAMCs, thereby allowing participants to exercise longer. However, it appears that dehydration and electrolyte loss are not the sole causes of EAMCs, because 69% of the subjects experienced EAMCs when they were hydrated and supplemented with electrolytes.
Propionyl-CoA carboxylase from Streptomyces coelicolor A3(2) : cloning of the gene encoding the biotinlcontaining subunit (1996)

In Streptomyces coelicolor A3(2), polyketides are made from malonyl-CoA, which is presumed to be derived from acetyl-CoA by the action of acetyl-CoA carboxylase (ACC). No ACC activity was found in cell-free extracts of S. coelicolor. However, propionyl-CoA carboxylase (PCC) activity was detected at substantial levels. Fixation of CO2 by ACC and PCC occurs by covalent bonding of CO2 to a biotin-containing protein. Most bacteria have a single small biotinylated protein of approximately 22 kDa, but S. coelicolor contains three larger biotin-containing proteins (approximately 145, 88 and 70 kDa). To determine which biotinylated protein was associated with PCC activity, the enzyme was purified and shown to comprise an alpha subunit (biotin-containing) of 88 kDa and a beta subunit of 66 kDa. The N-terminal sequences of these proteins were determined and, using an oligonucleotide probe, the gene for the alpha subunit (pccA) was cloned.
Chapter 12: Human Microbiome Analysis (2012)

Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.
Morphological Forms of Tobermorite in Hydrothermally Treated Calcium Silicate Hydrate Gels (1996)

The morphology of the calcium silicate hydrate phase, tobermorite, generally thought to be the bonding phase in ordinary portland cement, was studied. Tobermorite was hydrothermally synthesized at pH 12.6 at 150°C. The powder was characterized by XRD and SEM analysis. Modeling of the morphology was performed using the SHAPE and ATOMS programs. Two morphologies were produced: fibers and platelets. Computer calculations of equilibrium particle shape suggest that growth occurs on the (110)‐type planes for both morphologies.
A Region ofBacillus subtilisCodY Protein Required for Interaction with DNA (2005)

Bacillus subtilis CodY protein is the best-studied member of a novel family of global transcriptional regulators found ubiquitously in low-G+C gram-positive bacteria. As for many DNA-binding proteins, CodY appears to have a helix-turn-helix (HTH) motif thought to be critical for interaction with DNA. This putative HTH motif was found to be highly conserved in the CodY homologs. Site-directed mutagenesis was used to identify amino acids within this motif that are important for DNA recognition and binding. The effects of each mutation on DNA binding in vitro and on the regulation of transcription in vivo from two target promoters were tested. Each of the mutations had similar effects on binding to the two promoters in vitro, but some mutations had differential effects in vivo.
Recursive Prediction of Traffic Conditions with Neural Network Models (2000)

This paper presents a recursive traffic flow prediction algorithm using artificial neural networks. The system prediction model is specified based on the understanding of how disturbances in traffic flow are propagated, and the order of the model is determined by correlation analysis. The parameters of the model, on the other hand, can be obtained through nonlinear optimization. Preliminary studies show that this approach can yield reasonably accurate results.
Predominant selection of T cells specific for the glycosylated collagen type II epitope (263–270) in humanized transgenic mice and in rheumatoid arthritis (2002)

Rheumatoid arthritis (RA) is associated with certain MHC class II alleles and is characterized by a chronic autoimmune response in the joints. Using transgenic mice expressing human DR4 (DRB1*0401) and human CD4, but lacking endogenous MHC class II, we show that posttranslational glycosylation of type II collagen (CII) influences the level of T cell tolerance to this candidate cartilage-specific autoantigen. In such mice, the expression of human CII resulted in a tolerized murine T cell response to human CII. However, tolerance induction remained incomplete, preferentially deleting responses to the nonmodified CII 263-270 epitope, whereas T cell recognition of a glycosylated variant of this epitope was affected to a lesser degree. A similar dominance of T cell responses to CII-glycopeptides was recorded in a cohort of severely affected RA-patients (n = 14). Thus, RA T cells predominantly recognize the immunodominant CII peptide in its glycosylated form and may explain why previously it has been difficult to detect T cell responses to CII in RA patients.
Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes (2015)

Whole-genome sequencing has become an indispensible tool of modern biology. However, the cost of sample preparation relative to the cost of sequencing remains high, especially for small genomes where the former is dominant. Here we present a protocol for rapid and inexpensive preparation of hundreds of multiplexed genomic libraries for Illumina sequencing. By carrying out the Nextera tagmentation reaction in small volumes, replacing costly reagents with cheaper equivalents, and omitting unnecessary steps, we achieve a cost of library preparation of $8 per sample, approximately 6 times cheaper than the standard Nextera XT protocol. Furthermore, our procedure takes less than 5 hours for 96 samples. Several hundred samples can then be pooled on the same HiSeq lane via custom barcodes. Our method will be useful for re-sequencing of microbial or viral genomes, including those from evolution experiments, genetic screens, and environmental samples, as well as for other sequencing applications including large amplicon, open chromosome, artificial chromosomes, and RNA sequencing.
Human T cells express specific binding sites for C1q. Role in T cell activation and proliferation. (1994)

Although the receptor that binds to the collagen-like domain of human C1q (C1qR) is expressed on a wide variety of cell types, the presence or absence of this receptor on human T lymphocytes has been debatable. The current studies were undertaken to re-examine whether human T cells possess specific binding sites for C1q by using a combination of techniques, including radioligand binding studies, flow cytometric analysis, and epifluorescence imaging techniques. Radioligand binding studies indicate that both peripheral T cells and the cultured T cell line, MOLT4, bind 125I-labeled C1q in a specific and apparently saturable manner, reaching equilibrium within 30 min at 37 degrees C under conditions of subphysiologic (90 mM NaCl) ionic strength. Western blot analysis with anti-C1qR of membrane proteins derived from Raji and MOLT4 cells showed an apparent single band of approximately 60 kDa under nonreducing conditions. Furthermore, when peripheral blood T cells were stimulated with 12,-o-tetradecanoyl phorbol-13-ester acetate for 5 days at 37 degrees C and assessed by FACS for their ability to bind anti-C1qR, the mitogen-induced cells were found to bind 40 to 50% more than their unstimulated counterparts. In addition, both CD4+ and CD8+ T cells were found to bind anti-C1qR. When the cells were mitogen induced with either 12,-o-tetradecanoyl phorbol-13-ester acetate, Con A, or PWM for 48 h in the presence or absence of 50 micrograms/ml C1q then pulsed with 1 microCi [3H]thymidine for 16 h at 37 degrees C, proliferation was significantly inhibited (40 to 80%, n = 7) as assessed by reduced [3H]thymidine incorporation. Taken together, the data suggest that: 1) Human T cells express C1qR in which immunoblots reveal a 60-kDa single chain protein. 2) C1qR expression is up-regulated by mitogens that induce T cell proliferation. 3) The primary ligand, C1q, induces an antiproliferative signal, which suggests that the C1qR plays a role in T cell activation and proliferation. In addition, the data contribute to the characterization of C1qRs on cells in peripheral blood and indicate that all cells, with the exception of erythrocytes, bear functional C1q receptors.
Considerations for the Clinical Application of Chimeric Antigen Receptor T Cells: Observations from a Recombinant DNA Advisory Committee Symposium Held June 15, 2010 (2011)

T cells that are genetically modified to express single-chain chimeric antigen receptors (CAR) have shown promise in early cancer immunotherapy clinical trials. Unfortunately, 2 recent deaths in cancer patients treated with CAR T cells have created some uncertainty on how to best mitigate patient risk, while continuing to advance this very promising therapeutic avenue. In order to address these concerns, the Recombinant DNA Advisory Committee (RAC) held a symposium, the objectives of which were to first review the reported treatment-associated toxicities and, second, to discuss methods for improving safety and efficacy. This report highlights the issues raised as part of this discussion, with a specific focus on protocols infusing CAR T cells. Because this was not a consensus conference, the opinions described should not be construed to represent those of any individual RAC member, the RAC as a body, conference participants, the National Institutes of Health, or the U.S. Food and Drug Administration.
Alz 50, a monoclonal antibody to Alzheimer's disease antigen, cross-reacts with tau proteins from bovine and normal human brain. (1988)

Microtubule-associated protein tau from bovine brain reacted on immunoblots and on enzyme-linked immunosorbent assay with a monoclonal antibody, Alz 50, which has previously been found to bind to an Alzheimer disease-specific antigen. The apparent affinity of binding of Alz 50 to tau was 2.1 X 10(-9) M on competitive enzyme-linked immunosorbent assay, and it was in the same range as for Tau-1 (0.5 X 10(-9) M), an antibody raised against purified bovine tau proteins. Immunoblotting of trypsin-digested tau revealed differences between Alz 50 and Tau-1 binding sites. The binding of both antibodies to tau was not affected by prior treatment with phosphatase, indicating that the cross-reactivity of Alz 50 with tau is due to the presence of phosphate-independent epitope. This epitope then differs from phosphate-dependent tau epitopes often shared with other cytoskeletal proteins. Alz 50 and Tau-1 binding sites were present in all isoelectric (pI 6-8) and molecular weight variants of tau. In contrast, phosphate-dependent epitopes recognized by another tau-reactive antibody (NP14) were found mostly in acidic tau variants. Similarly to tau proteins from bovine brain, tau-enriched preparations from normal human brain contained Alz 50 and Tau-1 reactive sites in all isoelectric (pI 6.5-8.5) and molecular weight variants. Our observation of Alz 50 cross-reactivity with tau suggests a relationship between tau and the novel protein identified recently in Alzheimer brains.