gebhart/patrepeval huggingface dataset:
Automated docking of substrates to proteins by simulated annealing (1990)

The Metropolis technique of conformation searching is combined with rapid energy evaluation using molecular affinity potentials to give an efficient procedure for docking substrates to macromolecules of known structure. The procedure works well on a number of crystallographic test systems, functionally reproducing the observed binding modes of several substrates.
Signaling by IL‐12 and IL‐23 and the immunoregulatory roles of STAT4 (2004)

Produced in response to a variety of pathogenic organisms, interleukin (IL)-12 and IL-23 are key immunoregulatory cytokines that coordinate innate and adaptive immune responses. These dimeric cytokines share a subunit, designated p40, and bind to a common receptor chain, IL-12R beta 1. The receptor for IL-12 is composed of IL-12R beta 1 and IL-12R beta 2, whereas IL-23 binds to a receptor composed of IL-12R beta 1 and IL-23R. Both cytokines activate the Janus kinases Tyk2 and Jak2, the transcription factor signal transducer and activator of transcription 4 (STAT4), as well as other STATs. A major action of IL-12 is to promote the differentiation of naive CD4+ T cells into T-helper (Th) 1 cells, which produce interferon (IFN)-gamma, and deficiency of IL-12, IL-12R subunits or STAT4 is similar in many respects. In contrast, IL-23 promotes end-stage inflammation. Targeting IL-12, IL-23, and their downstream signaling elements would therefore be logical strategies for the treatment of immune-mediated diseases.
Histology and physiology of Fusarium head blight. (2003)

Trisomy 21 (Down syndrome) is the most common congenital anomaly, and it occurs in one out of 700-1000 births. Current techniques such as amniocentesis and chorionic villi sampling (CVS) require lengthy laboratory culture procedures and high costs. This study was undertaken to establish a rapid prenatal diagnosis of trisomy 21 using real-time quantitative polymerase chain reaction (PCR) of fetal DNA from amniotic fluid. Real-time quantitative PCR was performed with DNA templates obtained from 14 normal blood samples, 10 normal amniotic fluid samples, 14 Down syndrome blood samples, and 7 Down syndrome amniotic fluid samples. Primers for D21S167 and S100B of chromosome 21 were used. Primers that direct the amplification of the 165-bp fragment of the insulin-like growth factor (IGF)-1 gene on chromosome 12 using a PCR primer were included to generate an internal standard for quantitation. The relative levels of D21S167 and S100B were 2.6 and 2.4 times higher in the blood of Down syndrome patients than those in the control group. The differences between these two groups were statistically significant (p-values were 0.0012 and 0.0016, respectively). The relative levels of D21S167 and S100B were 2.1 and 2.7 times higher in the amniotic fluid of Down syndrome fetuses than those in the control group. The difference between these two groups was statistically significant (p-values were 0.0379 and 0.0379, respectively). Prenatal diagnosis of trisomy 21 by real-time quantitative PCR using STR (small tandem repeats) amplification of D21S167 and S100B is a useful, accurate and rapid diagnostic method. Furthermore, it may also be useful for prenatal diagnosis with fetal DNA from maternal blood, and for preimplantation genetic diagnosis and prenatal counseling.
Inflammation in Human Brain Injury: Intracerebral Concentrations of IL-1 α , IL-1 β , and Their Endogenous Inhibitor IL-1ra (2007)

Following traumatic brain injury (TBI), cascades of inflammatory processes occur. Laboratory studies implicate the cytokines interleukin-1alpha (IL-1alpha) and IL-1beta in the pathophysiology of TBI and cerebral ischemia, whilst exogenous and endogenous interleukin-1 receptor antagonist (IL-1ra) is neuroprotective. We analyzed IL-1alpha, IL-1beta, and IL-1ra in brain microdialysates (100-kDa membrane) in 15 TBI patients. We also analyzed energy-related molecules (glucose, lactate, pyruvate, glutamate, and the lactate/pyruvate ratio) in these brain microdialysates. Mean of mean (+/-SD) in vitro microdialysis percentage recoveries (extraction efficiencies) were IL-1alpha 19.7+/-7.6%, IL-1beta 23.9+/-10.5%, and IL-1ra 20.9+/-6.3%. In the patients' brain microdialysates, mean of mean cytokine concentrations (not corrected for percentage recovery) were IL-1alpha 5.6+/-14.8 pg/mL, IL-1beta 10.4+/-14.7 pg/mL, and IL-1ra 2796+/-2918 pg/mL. IL-1ra was consistently much higher than IL-1alpha and IL-1beta. There were no significant relationships between IL-1 family cytokines and energy-related molecules. There was a significant correlation between increasing IL-1beta and increasing IL-1ra (Spearman r=0.59, p=0.028). There was also a significant relationship between increasing IL-1ra and decreasing intracranial pressure (Spearman r=-0.57, p=0.041). High concentrations of IL-1ra, and also high IL-1ra/IL-1beta ratio, were associated with better outcome (Mann Whitney, p=0.018 and p=0.0201, respectively), within these 15 patients. It is unclear whether these IL-1ra concentrations are sufficient to antagonize the effects of IL-1beta in vivo. This study demonstrates feasibility of our microdialysis methodology in recovering IL-1 family cytokines for assessing their inter-relationships in the injured human brain, and suggests a neuroprotective role for IL-1ra. It remains to be seen whether exogenous IL-1ra or other agents can be used to manipulate cytokine levels in the brain, for potential therapeutic effect.
Synthesis, Characterization, and Applications of Magnetic Nanoparticles Featuring Polyzwitterionic Coatings (2018)

Throughout the last decades, magnetic nanoparticles (MNP) have gained tremendous interest in different fields of applications like biomedicine (e.g., magnetic resonance imaging (MRI), drug delivery, hyperthermia), but also more technical applications (e.g., catalysis, waste water treatment) have been pursued. Different surfactants and polymers are extensively used for surface coating of MNP to passivate the surface and avoid or decrease agglomeration, decrease or modulate biomolecule absorption, and in most cases increase dispersion stability. For this purpose, electrostatic or steric repulsion can be exploited and, in that regard, surface charge is the most important (hybrid) particle property. Therefore, polyelectrolytes are of great interest for nanoparticle coating, as they are able to stabilize the particles in dispersion by electrostatic repulsion due to their high charge densities. In this review article, we focus on polyzwitterions as a subclass of polyelectrolytes and their use as coating materials for MNP. In the context of biomedical applications, polyzwitterions are widely used as they exhibit antifouling properties and thus can lead to minimized protein adsorption and also long circulation times.
Effective multi-label active learning for text classification (2009)

Labeling text data is quite time-consuming but essential for automatic text classification. Especially, manually creating multiple labels for each document may become impractical when a very large amount of data is needed for training multi-label text classifiers. To minimize the human-labeling efforts, we propose a novel multi-label active learning approach which can reduce the required labeled data without sacrificing the classification accuracy. Traditional active learning algorithms can only handle single-label problems, that is, each data is restricted to have one label. Our approach takes into account the multi-label information, and select the unlabeled data which can lead to the largest reduction of the expected model loss. Specifically, the model loss is approximated by the size of version space, and the reduction rate of the size of version space is optimized with Support Vector Machines (SVM). An effective label prediction method is designed to predict possible labels for each unlabeled data point, and the expected loss for multi-label data is approximated by summing up losses on all labels according to the most confident result of label prediction. Experiments on several real-world data sets (all are publicly available) demonstrate that our approach can obtain promising classification result with much fewer labeled data than state-of-the-art methods.
Optimal Dynamic Prioritization of Scarce COVID-19 Vaccines (2020)

COVID-19 vaccines have been authorized in multiple countries and more are under rapid development. Careful design of a vaccine prioritization strategy across socio-demographic groups is a crucial public policy challenge given that (1) vaccine supply will be constrained for the first several months of the vaccination campaign, (2) there are stark differences in transmission and severity of impacts from SARS-CoV-2 across groups, and (3) SARS-CoV-2 differs markedly from previous pandemic viruses. We assess the optimal allocation of a limited vaccine supply in the U.S. across groups differentiated by age and also essential worker status, which constrains opportunities for social distancing. We model transmission dynamics using a compartmental model parameterized to capture current understanding of the epidemiological characteristics of COVID-19, including key sources of group heterogeneity (susceptibility, severity, and contact rates). We investigate three alternative policy objectives (minimizing infections, years of life lost, or deaths) and model a dynamic strategy that evolves with the population epidemiological status. We find that this temporal flexibility contributes substantially to public health goals. Older essential workers are typically targeted first. However, depending on the objective, younger essential workers are prioritized to control spread or seniors to directly control mortality. When the objective is minimizing deaths, relative to an untargeted approach, prioritization averts deaths on a range between 20,000 (when non-pharmaceutical interventions are strong) and 300,000 (when these interventions are weak). We illustrate how optimal prioritization is sensitive to several factors, most notably vaccine effectiveness and supply, rate of transmission, and the magnitude of initial infections.
Preferential interaction of α‐tocopherol with phosphatidylcholines in mixed aqueous dispersions of phosphatidylcholine and phosphatidylethanolamine (2000)

The effect of alpha-tocopherol on the structure and phase behaviour of mixed aqueous dispersions of phosphatidylcholine and phosphatidylethanolamine has been examined by synchrotron X-ray diffraction and freeze-fracture electron microscopy. Equimolar mixtures of fully saturated derivatives of phospholipids that show gel phase immiscibility were examined including dimyristoylglycerophosphocholine/dipalmitoylglycerophosphoethanolamin e and distearoylglycerophosphocholine/dilauroylglycerophosphoethanolamine++ +. Analysis of the X-ray scattering intensities recorded at wide angles during heating scans of mixed aqueous dispersions containing 2.5 or 5 mol% alpha-tocopherol showed that alpha-tocopherol disordered the acyl chain packing of the phosphatidylcholine to a greater extent than the phosphatidylethanolamine component of the mixture. This suggested that alpha-tocopherol preferentially interacts with phosphatidylcholine rather than phosphatidylethanolamine, irrespective of whether this was the high or low melting point component of the mixture. The presence of 20 mol% alpha-tocopherol in either phospholipid mixture prevented gel phase separation during the prior cooling scan and no conclusions could be drawn as to the distribution of alpha-tocopherol in these mixtures.
Microfluidic-Based Multi-Organ Platforms for Drug Discovery (2016)

Development of predictive multi-organ models before implementing costly clinical trials is central for screening the toxicity, efficacy, and side effects of new therapeutic agents. Despite significant efforts that have been recently made to develop biomimetic in vitro tissue models, the clinical application of such platforms is still far from reality. Recent advances in physiologically-based pharmacokinetic and pharmacodynamic (PBPK-PD) modeling, micro- and nanotechnology, and in silico modeling have enabled single- and multi-organ platforms for investigation of new chemical agents and tissue-tissue interactions. This review provides an overview of the principles of designing microfluidic-based organ-on-chip models for drug testing and highlights current state-of-the-art in developing predictive multi-organ models for studying the cross-talk of interconnected organs. We further discuss the challenges associated with establishing a predictive body-on-chip (BOC) model such as the scaling, cell types, the common medium, and principles of the study design for characterizing the interaction of drugs with multiple targets.
Scalable fault tolerant image communication and storage grid (2003)

Increasing production and use of digital medical imagery are driving new approaches to information storage and management. Traditional, centralized approaches to image communication, storage and archiving are becoming increasingly expensive to scale and operate with high levels of reliability. Multi-site, geographically-distributed deployments connected by limited-bandwidth networks present further scalability, reliability, and availability challenges. A grid storage architecture built from a distributed network of low cost, off-the-shelf servers (nodes) provides scalable data and metadata storage, processing, and communication without single points of failure. Imaging studies are stored, replicated, cached, managed, and retrieved based on defined rules, and nodes within the grid can acquire studies and respond to queries. Grid nodes transparently load-balance queries, storage/retrieval requests, and replicate data for automated backup and disaster recovery. This approach reduces latency, increases availability, provides near-linear scalability and allows the creation of a geographically distributed medical imaging network infrastructure. This paper presents some key concepts in grid storage and discusses the results of a clinical deployment of a multi-site storage grid for cancer care in the province of British Columbia.
Autonomous Hyperspectral Target Detection with Quasi-Stationarity Violation at Background Boundaries (2006)

Operational real time hyperspectral reconnaissance systems adaptively estimate multivariate background statistics. Parameter values derived from these estimates feed autonomous onboard detection systems. However, inadequate adaptation occurs whenever an airborne sensor encounters a physical boundary between spectrally distinct regions. The transition area generates excessive false alarms, because standard detection algorithms rely on quasi- stationary models of background statistics. Here we describe a two-mode stochastic mixture model aimed at solving the boundary problem. It exploits deployed signal processing modules to solve a generalized eigenvalue problem, making a threshold test for targets computationally feasible.
Construction of broad-host-range cosmid cloning vectors: identification of genes necessary for growth of Methylobacterium organophilum on methanol (1985)

Four new cloning vectors have been constructed from the broad-host-range cloning vector pRK290. These vectors, pLA2901, pLA2905, pLA2910, and pLA2917, confer resistance to kanamycin and tetracycline. The latter two are cosmid derivatives of pLA2901. The new vectors can be mobilized into, and are stably maintained in, a variety of gram-negative bacteria. A Sau3A genomic bank of Methylobacterium organophilum strain xx DNA has been constructed in pLA2917, and complementation analysis, with a variety of mutants unable to grow on methanol, revealed at least five separate regions necessary for growth on methanol. Complementation analysis and Tn5 mutagenesis data suggest that at least three genes are responsible for expression of active methanol dehydrogenase.
mRNA sequence and deduced amino acid sequence of the mumps virus small hydrophobic protein gene (1989)

The mRNA of a putative small hydrophobic protein (SH) of mumps virus was identified in mumps virus-infected Vero cells, and its complete nucleotide sequence was determined by sequencing the genomic RNA and cDNA clones and partial sequencing of mRNA. The SH mRNA is 310 nucleotides long excluding the poly(A) and contains a single open reading frame encoding a protein of 57 amino acids with a calculated molecular weight of 6,719. The predicted protein is highly hydrophobic and contains a stretch of 25 hydrophobic amino acids near the amino terminus which could act as a membrane anchor region. There is no homology between the putative SH protein of mumps virus and the SH protein of simian virus 5, even though the SH genes are located in the same locus in the corresponding genome. One interesting observation is that the hydrophobic domain of simian virus 5 SH protein is at the carboxyl terminus, whereas that of mumps virus putative SH protein is near the amino terminus.
CD4+CD25+FOXP3+ Regulatory T Cells Suppress Anti-Tumor Immune Responses in Patients with Colorectal Cancer (2006)

Collectively, these data demonstrate that Treg capable of inhibiting tumor associated antigen-specific immune responses are enriched in patients with CRC. These results support a rationale for manipulating Treg to enhance cancer immunotherapy.
A macrophage receptor for apolipoprotein B48: Cloning, expression, and atherosclerosis (2000)

We have cloned a human macrophage receptor that binds to apolipoprotein (apo)B48 of dietary triglyceride (TG)-rich lipoproteins. TG-rich lipoprotein uptake by the apoB48R rapidly converts macrophages and apoB48R-transfected Chinese hamster ovary cells in vitro into lipid-filled foam cells, as seen in atherosclerotic lesions. The apoB48R cDNA (3,744 bp) encodes a protein with no known homologs. Its approximately 3.8-kb mRNA is expressed primarily by reticuloendothelial cells: monocytes, macrophages, and endothelial cells. Immunohistochemistry shows the apoB48R is in human atherosclerotic lesion foam cells. Normally, the apoB48R may provide essential lipids to reticuloendothelial cells. If overwhelmed, foam cell formation, endothelial dysfunction, and atherothrombogenesis may ensue, a mechanism for cardiovascular disease risk of elevated TG.
Self-Aligned Plasmonic Nanopores by Optically Controlled Dielectric Breakdown (2015)

We present a novel cost-efficient method for the fabrication of high-quality self-aligned plasmonic nanopores by means of an optically controlled dielectric breakdown. Excitation of a plasmonic bowtie nanoantenna on a dielectric membrane localizes the high-voltage-driven breakdown of the membrane to the hotspot of the enhanced optical field, creating a nanopore that is automatically self-aligned to the plasmonic hotspot of the bowtie. We show that the approach provides precise control over the nanopore size and that these plasmonic nanopores can be used as single molecule DNA sensors with a performance matching that of TEM-drilled nanopores. The principle of optically controlled breakdown can also be used to fabricate nonplasmonic nanopores at a controlled position. Our novel fabrication process guarantees alignment of the nanopore with the optical hotspot of the nanoantenna, thus ensuring that pore-translocating biomolecules interact with the concentrated optical field that can be used for detection and manipulation of analytes.
A Model of 3D Propagation in Discrete Cardiac Tissue. (2006)

A model was developed of a bundle of cardiac fibers embedded in an extracellular space. In contrast to the classical bidomain approach, the model is constructed such that the intracellular and extracellular spaces are spatially distinct. The model was used to test the hypothesis that the distribution of the extracellular fluid in the tissue can affect the conduction velocity. The preliminary results suggest that under nominally normal conditions, the propagation speed depends on the fraction of extracellular space and less on the actual distribution of extracellular space within the bundle.
Identification and validation of P311 as a glioblastoma invasion gene using laser capture microdissection. (2001)

The mRNA expression profiles from glioblastoma cells residing at the tumor core and invasive rim of a human tumor resection were compared. From a single tumor specimen, 20,000 single cells from each region were collected by laser capture microdissection. Differential expression of 50-60 cDNA bands was detected. One of the sequences overexpressed by the invasive cells showed 99% homology to the P311 gene, the protein product of which is reported to localize at focal adhesions. Relative overexpression of P311 by invading glioblastoma cells compared with tumor core was confirmed by quantitative reverse transcription-PCR of six glioblastoma specimens after laser capture microdissection collection of rim and core cells. In vitro studies using antisense oligodeoxynucleotides and integrin activation confirmed the role of P311 in supporting migration of malignant glioma cells. Immunochemistry studies confirmed the presence of the P311 protein in tumor cells, particularly at the invasive edge of human glioblastoma specimens.
Does route of administration affect the outcome of TNF antagonist therapy? (2004)

The tumor necrosis factor (TNF) antagonists are parenterally administered biologic response modifiers indicated for the management of rheumatoid arthritis. Although infliximab, etanercept, and adalimumab are all members of this class, they differ in route of administration and dosing regimen. In the USA and in Europe, infliximab, in combination with oral methotrexate, is administered intravenously, initially at a dose of 3 mg/kg at weeks 0, 2, and 6, then every 8 weeks thereafter. The US Food and Drug Administration (FDA) has further approved that the dosage can be increased to 10 mg/kg and the doses can be given as often as every 4 weeks to optimize patient outcome (information based on the US package insert dated June 2002). Etanercept and adalimumab are given subcutaneously and can be self-injected. The FDA-approved dose of etanercept is 25 mg twice weekly, and of adalimumab is 40 mg every 2 weeks with methotrexate, or 40 mg alone. Medication adherence, possibly the most important factor in maintaining the benefits of anti-TNF therapy, is influenced by the interaction between the patient and his or her healthcare team, the patient's attitude toward the disease and medication regimen, and the choice of therapy.
Identifying alemtuzumab as an anti-myeloid cell antiangiogenic therapy for the treatment of ovarian cancer (2009)

These studies confirm VLC/myeloid cells as therapeutic targets in ovarian cancer. Our data provide critical pre-clinical evidence supporting the use of Alemtuzumab in clinical trials to test its efficacy as an anti-myeloid cell antiangiogenic therapeutic in ovarian cancer. The identification of an FDA approved anti-VLC agent with a history of clinical use will allow immediate proof-of-principle clinical trials in patients with ovarian cancer.
Tolerance to and Dependence on Alprazolam are Due to Changes in GABAa Receptor Function and Are Independent of Exposure to Experimental Set-up (1998)

The development of tolerance to and dependence on BDZs was investigated by monitoring locomotor activity in mice. Alprazolam (6 mg/kg twice daily s.c.) or solvent were administered over 12 days. The treatment schedule at least 50% BDZ receptor occupancy throughout treatment. Receptor occupancy half-lives were determined to be 2.6 hrs and 4.8 hrs. after cessation of 4 and 12 days of alprazolam administration, respectively. To assess if the tolerance to and dependence on alprazolam were due to repeated exposure of mice to the experimental set-up, some groups of mice were tested repeatedly, while other groups were subjected only to a single exposure. The observed locomotor activity, measured as horizontal activity and total distance travelled, indicated that the development of tolerance and of withdrawal symptoms to alprazolam is not related to repeated exposure of the mice to the experimental set-up, but is due to changes in function of the GABAa receptor.