gebhart/patrepeval huggingface dataset:
Increased serum levels of tumor necrosis factor alpha precede major complications of bone marrow transplantation [see comments] (1990)

Acute graft-versus-host disease, interstitial pneumonitis, endothelial leakage syndrome, and veno-occlusive disease are major complications of bone marrow transplantation. Though several new regimens for prophylaxis and treatment of these syndromes have been introduced, the overall incidence has been only slightly reduced over the last few years. We retrospectively analyzed tumor necrosis factor alpha (TNF alpha) serum levels between day -8 and day 100 after bone marrow transplantation in 56 patients transplanted in our unit for a variety of hematological diseases. In 34 patients with uneventful courses, mean TNF alpha levels rose to a maximum of 76 +/- 29 pg/mL. In contrast, 22 patients with major transplant related complications showed mean increases of TNF alpha of 492 +/- 235 pg/mL (P less than .0001). Increases of TNF alpha occurred before interstitial pneumonitis and severe acute graft-versus-host disease with a latency of 25 to 54 days. Early complications such as endothelial leakage syndrome and veno-occlusive disease were closely associated with increases of TNF alpha serum levels. Our study suggests two pathways of TNF alpha release: activation of host macrophages and stimulation of donor cells in the course of acute graft-versus-host disease. Cytokine monitoring should be helpful for prediction and earlier treatment of major transplant related complications.
Influence of circulating insulin-like growth factor-I compared with that of intrarenal insulin-like growth factor-I on proximal nephron receptor density in rats (1992)

1. We examined the effects of dietary protein manipulations in partially nephrectomized (one and one-third nephrectomy) and normal rats to gain perspective on the relative importance of circulating versus intrarenal (collecting tubule) insulin-like growth factor-I in the control of proximal nephron receptor density. In addition, we studied the factors that influence liver insulin-like growth factor-I secretion in partially nephrectomized rats. 2. Dietary protein restriction (6% versus 40%) lowered circulating levels of insulin and insulin-like growth factor-I in both normal and partially nephrectomized rats up to 3 weeks after institution of the diets; however, growth hormone levels were little changed. Reduced renal mass stimulated intrarenal production of insulin-like growth factor-I regardless of the diet. 3. Scatchard analysis revealed that the density of insulin-like growth factor-I receptors on glomerular and proximal tubule basolateral membranes increased when circulating levels of insulin-like growth factor-I were diminished, despite raised levels of intrarenal insulin-like growth factor-I, in partially nephrectomized rats. 4. Circulating insulin-like growth factor-I, rather than the tissue level, plays the dominant role in the control of proximal nephron receptor density under physiological conditions. Insulin, but not growth hormone, may play a role in liver insulin-like growth factor-I secretion in partially nephrectomized rats during dietary manipulations.
T-cell–based Immunotherapy: Adoptive Cell Transfer and Checkpoint Inhibition (2015)

Tumor immunotherapy has had demonstrable efficacy in patients with cancer. The most promising results have been with T-cell-based therapies. These include adoptive cell transfer of tumor-infiltrating lymphocytes, genetically engineered T cells, and immune checkpoint inhibitor antibodies. In this review, we describe the different T-cell-based strategies currently in clinical trials and put their applications, present and future, into perspective.
Identification of N-(4-Piperidinyl)-4-(2,6-dichlorobenzoylamino)-1H-pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design (2008)

The application of fragment-based screening techniques to cyclin dependent kinase 2 (CDK2) identified multiple (>30) efficient, synthetically tractable small molecule hits for further optimization. Structure-based design approaches led to the identification of multiple lead series, which retained the key interactions of the initial binding fragments and additionally explored other areas of the ATP binding site. The majority of this paper details the structure-guided optimization of indazole (6) using information gained from multiple ligand-CDK2 cocrystal structures. Identification of key binding features for this class of compounds resulted in a series of molecules with low nM affinity for CDK2. Optimisation of cellular activity and characterization of pharmacokinetic properties led to the identification of 33 (AT7519), which is currently being evaluated in clinical trials for the treatment of human cancers.
Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution (2009)

Verification of candidate biomarkers requires specific assays to selectively detect and quantify target proteins in accessible biofluids. The primary objective of verification is to screen potential biomarkers to ensure that only the highest quality candidates from the discovery phase are taken forward into preclinical validation. Because antibody reagents for a clinical grade immunoassay often exist for a small number of candidates, alternative methodologies are required to credential new and unproven candidates in a statistically viable number of serum or plasma samples. Using multiple reaction monitoring coupled with stable isotope dilution MS, we developed quantitative, multiplexed assays in plasma for six proteins of clinical relevance to cardiac injury. The process described does not require antibodies for immunoaffinity enrichment of either proteins or peptides. Limits of detection and quantitation for each signature peptide used as surrogates for the target proteins were determined by the method of standard addition using synthetic peptides and plasma from a healthy donor. Limits of quantitation ranged from 2 to 15 ng/ml for most of the target proteins. Quantitative measurements were obtained for one to two signature peptides derived from each target protein, including low abundance protein markers of cardiac injury in the nanogram/milliliter range such as the cardiac troponins. Intra- and interassay coefficients of variation were predominantly <10 and 25%, respectively. The configured multiplex assay was then used to measure levels of these proteins across three time points in six patients undergoing alcohol septal ablation for hypertrophic obstructive cardiomyopathy. These results are the first demonstration of a multiplexed, MS-based assay for detection and quantification of changes in concentration of proteins associated with cardiac injury in the low nanogram/milliliter range. Our results also demonstrate that these assays retain the necessary precision, reproducibility, and sensitivity to be applied to novel and uncharacterized candidate biomarkers for verification of proteins in blood.
Secretion imbalance between tumour necrosis factor and its inhibitor in inflammatory bowel disease (1998)

Results showed enhanced secretion of TNF-alpha but failure to release enhanced amounts of soluble TNF receptor in lamina propria mononuclear cells of patients with IBD. An imbalance in secretion between TNF and TNF inhibitor may be implicated in the pathogenesis of IBD.
Preparation and Properties of Biodiesel from Cynara cardunculus L. Oil (1999)

A study was made of the reaction of transesterification of Cynara cardunculus L. oil by means of methanol, using sodium hydroxide, potassium hydroxide, and sodium methoxide as catalysts. The objective of the work was to characterize the methyl esters for use as biodiesels in internal combustion motors. The operation variables used were methanol concentration (5−21 wt %), catalyst concentration (0.1−1 wt %), and temperature (25−60 °C). The evolution of the process was followed by gas chromatography, determining the concentration of the methyl esters at different reaction times. The biodiesel was characterized by determining its density, viscosity, high heating value, cetane index, cloud and pour points, Ramsbottom carbon residue, characteristics of distillation, and flash and combustion points according to ISO norms. The biodiesel with the best properties was obtained using 15% methanol, sodium methoxide as catalyst (1%), and 60 °C temperature. This biodiesel has very similar properties to those of diesel no. 2.
Synthesis and Antitumor Activities of Novel Benzoylphenylurea Derivatives. (1991)

Seventy novel benzoylphenylurea compounds were synthesized and their antitumor activities were examined in vivo against P388 leukemia. N-(2-Nitrobenzoyl)-N'-[4-(2-pyrimidinyloxy)phenyl]ureas showed the highest antitumor activities when dosed intraperitoneally or orally. Their structure-activity relationships were examined with particular focus on the position and the variety of substituent on each aryl ring.
Development, structure and senescence of colleters in Gardenia lucida Roxb. (Rubiaceae) (2014)

Colleters are found on the adaxial basal part of the stipule and calyx of &lt;em&gt;Gardenia lucida&lt;/em&gt;. They secrete a yellow transparent resinous substance commonly known as "Dikamali gum". They develop on both the stipule and calyx from a group of epidermal and hypodermal initials. A mature colleter consists of a central core of elongated parenchymatous cells surrounded by a palisade-like secretory epidermis. Druses type crystals of calcium oxalate are frequent in the colleters. At the time of senescence the central cells show lignification and the presence of tannin.
Length limited coding and optimal height-limited binary trees (1988)

A new O(nL)-time algorithm is given for finding an optimal prefix-free binary code for a weighted alphabet of size n, with the restriction that no code string be longer than L. An O(nL logn)-time algorithm is given for the corresponding alphabetic problem problem, which is equivalent to optimizing a dictionary of n words, implemented as a binary tree of height h
Gating-Dependent Mechanisms for Flecainide Action inSCN5A-Linked Arrhythmia Syndromes (2001)

We have linked 2 inactivation gating defects ("closed-state" fast inactivation and intermediate inactivation) to flecainide sensitivity in patients carrying LQT3 and Brugada syndrome mutations. These results provide a mechanistic rationale for predicting proarrhythmic sensitivity to flecainide based on the identification of specific SCN5A inactivation gating defects.
Overcoming Chronic Rejection—Can it B? (2009)

Despite the success of immunosuppressive drug therapy to reduce the incidence of acute rejection in organ transplantation, chronic rejection is still an impediment to long-term graft survival and tolerance. There is a growing body of evidence that B-cell production of alloantibody is an important element in the genesis of chronic rejection. Effector function of B cells in transplantation is not specifically targeted by current T-cell-directed therapeutic approaches. We briefly discuss the origin, animal models, diagnostic methods, and currently available B cell reagents that might be used in combination with existing immunosuppressive regimens to address B-cell-mediated allograft injury.
Intralesional Cytokine Therapy in Cancer (1998)

Systemic cytokine therapy in cancer has major side effects, and we reasoned that the local infusion of cytokines into tumors could induce local immunologic responses with minimal toxicity and potentially strong systemic anticancer effects. This study investigated the toxicity and effectiveness of intralesional granulocyte/macrophage-colony-stimulating factor (GM-CSF) infusion in solid-tumor masses. We studied 14 patients (12 men, two women) with malignant mesothelioma (MM), aged 60 years (range, 46–70 years), with stage 2 disease, in whom the tumor was of sufficient size and accessibility for an intralesional catheter to be inserted. Re-combinant human GM-CSF (Molgramostim; Schering Plough) was infused intralesionally for 8 weeks, by using a portable pump, at a dose of 2.5–10 μg/kg/day. One patient using GM-CSF developed histologically confirmed necrosis of tumor surrounding the distal catheter, one developed a marked lymphocytic infiltrate in the tumor and had a partial response measured by chest computed tomography (CT) scan, 10 progressed, and three had no response. Neutrophilia with morphologic evidence of neutrophil activation and clinical features suggestive of neutrophil plugging of blood vessels occurred at doses >5 μg/kg/day. In vitro, GM-CSF doubled human neutrophil/CD11b/CD18 expression, suggesting that neutrophil clumping as seen in vivo might be due to integrin upregulation. Intralesional infusion of cytokines is feasible but can be associated with systemic toxicity and has considerable technical problems. It produces a localized immune reaction with tumor regression in a minority of patients.
IL-4-Induced Arginase 1 Suppresses Alloreactive T Cells in Tumor-Bearing Mice (2003)

We previously demonstrated that a specialized subset of immature myeloid cells migrate to lymphoid organs as a result of tumor growth or immune stress, where they suppress B and T cell responses to Ags. Although NO was required for suppression of mitogen activation of T cells by myeloid suppressor cells (MSC), it was not required for suppression of allogenic responses. In this study, we describe a novel mechanism used by MSC to block T cell proliferation and CTL generation in response to alloantigen, which is mediated by the enzyme arginase 1 (Arg1). We show that Arg1 increases superoxide production in myeloid cells through a pathway that likely utilizes the reductase domain of inducible NO synthase (iNOS), and that superoxide is required for Arg1-dependent suppression of T cell function. Arg1 is induced by IL-4 in freshly isolated MSC or cloned MSC lines, and is therefore up-regulated by activated Th2, but not Th1, cells. In contrast, iNOS is induced by IFN-gamma and Th1 cells. Because Arg1 and iNOS share L-arginine as a common substrate, our results indicate that L-arginine metabolism in myeloid cells is a potential target for selective intervention in reversing myeloid-induced dysfunction in tumor-bearing hosts.
CLONING OF THE 1.4-kb mRNA SPECIES OF HUMAN COMPLEMENT FACTOR H REVEALS A NOVEL MEMBER OF THE SHORT CONSENSUS REPEAT FAMILY RELATED TO THE CARBOXY TERMINAL OF THE CLASSICAL 150-kDa MOLECULE (1991)

Three factor H mRNA species of 4.3 kb, 1.8 kb, and 1.4 kb are constitutively expressed in human liver. Having previously characterized full-length cDNA clones derived from the 4.3-kb and 1.8-kb factor mRNA, we report here the isolation and eucaryotic expression of full-length cDNA clones coding for the 1.4-kb mRNA species. The 1266-bp cDNA codes for a polypeptide of 330 amino acids and contains two polyadenylation signals and a short poly(A)+tail. The protein is composed of a leader peptide followed by five short consensus repeat domains. It shows a hybrid structure with the last three domains being almost identical to the carboxy-terminal of the classical 150-kDa factor H molecule and the two first domains representing unique short consensus repeat structures. Eucaryotic expression in COS7 cells revealed two polypeptides derived from one cDNA clone that are also found in human serum. Differences between the cDNA clones within the last three domains indicate two distinct, possibly allelic sequences that, in addition, differ from the authentic 150-kDa factor H sequence. Southern blot results support the notion that the 4.3-kb factor H and the 1.4-kb factor H-related mRNA are transcribed from two separate but highly homologous genes.
Object Detection with Deep Learning: A Review (2018)

Due to object detection's close relationship with video analysis and image understanding, it has attracted much research attention in recent years. Traditional object detection methods are built on handcrafted features and shallow trainable architectures. Their performance easily stagnates by constructing complex ensembles which combine multiple low-level image features with high-level context from object detectors and scene classifiers. With the rapid development in deep learning, more powerful tools, which are able to learn semantic, high-level, deeper features, are introduced to address the problems existing in traditional architectures. These models behave differently in network architecture, training strategy and optimization function, etc. In this paper, we provide a review on deep learning based object detection frameworks. Our review begins with a brief introduction on the history of deep learning and its representative tool, namely Convolutional Neural Network (CNN). Then we focus on typical generic object detection architectures along with some modifications and useful tricks to improve detection performance further. As distinct specific detection tasks exhibit different characteristics, we also briefly survey several specific tasks, including salient object detection, face detection and pedestrian detection. Experimental analyses are also provided to compare various methods and draw some meaningful conclusions. Finally, several promising directions and tasks are provided to serve as guidelines for future work in both object detection and relevant neural network based learning systems.
Dissolution of Single-Walled Carbon Nanotubes (1999)

The solubility properties of single-walled carbon nanotubes (SWNTs) and the factors that control the dissolution of these materials have been investigated in detail. The authors report a number of strategies that lead to soluble SWNTs, in particular the covalent attachment of long alkyl chains to the carboxylic acid–terminated SWNTs shown in the Figure (produced by the purification process) via formation of amides and by formation of zwitterions by an acid–base reaction.
Discerning and Addressing Environmental Failures in Policy Scenarios Using Planning Support System (PSS) Technologies (2016)

The environmental consequences of planning decisions are often undervalued. This can result from a number of potential causes: (a) there might be a lack of adequate information to correctly assess environmental consequences; (b) stakeholders might discount the spatial and temporal impacts; (c) a failure to understand the dynamic interactions between socio-ecological systems including secondary and tertiary response mechanisms; or (d) the gravity of the status quo, i.e., blindly following a traditional discourse. In this paper, we argue that a Planning Support System (PSS) that enhances an assessment of environmental impacts and is integral to a community or regional planning process can help reveal the true environmental implications of scenario planning decisions, and thus improve communal planning and decision-making. We demonstrate our ideas through our experiences developing and deploying one such PSS—the Land-use Evolution and impact Assessment Model (LEAM) Planning Support System. University of Illinois researchers have worked directly with government planning officials and community stakeholders to analyze alternate future development scenarios and improve the planning process through a participatory, iterative process of visioning, model tuning, simulation, and discussion. The resulting information enables an evaluation of alternative policy or investment choices and their potential environmental implications that can change the way communities both generate and use plans.
Identification of Epitopes of Monoclonal Antibodies to Porcine Zona Pellucida 3β Glycoprotein, a Homologue of the Mouse/Human Sperm Receptor (1997)

Collectively, these results describe peptide epitopes that will help in the design of an immunocontraceptive vaccine based on synthetic peptides corresponding to pZP3 beta or its homologues in other species.
Acid Mine Drainage Control and Treatment (2000)

Acid mine drainage (AMD) forms when sulfide minerals are exposed to oxidizing conditions in coal and metal mining, highway construction, and other large-scale excavations. The Surface Mining Control and Reclamation Act requires coal operators and regulators to predict whether AMD may occur on a potential mine site before disturbance. Accurate prediction of AMD before surface mining requires a complete understanding of many components at a mine site. Three of the most important factors are: overburden geochemistry, method and precision of overburden handling and placement in the backfill during reclamation, and the postmining hydrology of the site. AMD control technologies are measures that can be undertaken where AMD formation has either already taken place or is anticipated to be a problem in the future. Nearly all alkaline amendment schemes rely on ABA to identify the required alkalinity for neutralization of pyritic materials.
An Accurate and Rapid PCR-Based Zygosity Testing Method for Genetically Modified Maize (2010)

Using genetically modified NK603 maize as an example, an accurate and cost-effective PCR-based procedure was described for genetically modified maize zygosity testing. The method involved a simple PCR reaction with four primers. The primers were designed from the inserted transgene at 5' and 3' ends (5'TP and 3'TP), the 5' flanking genomic DNA (5'GP), and the 3' flanking genomic DNA (3'GP), respectively. If the plant was a null (wild type), genomic DNA between 5'GP and 3'GP were amplified and a single PCR product was produced; If the plant was a homozygote, DNA between 5'GP and 5'TP, 3'TP and 3'GP were amplified and two PCR products were produced; If the plant was a hemizygote, DNA between 5'GP and 5'TP, 3'TP and 3'GP, 5GP and 3'GP were all amplified, producing three PCR products. PCR products with different sizes were separated on an agarose gel, and one, two and three bands were easily scored, which represents null, homozygote and hemizygote, respectively. Compared to expensive quantitative PCR and time-consuming bioassay, this method coupled with high throughput genomic DNA extraction is of great assistance to corn breeders for zygosity selection. Hundreds of leaf discs from individual plants can be punched with eppendorf tubes in field and plant zygosity result is readily available. Similar strategy can be applied to develop event-specific zygosity testings for other maize genetically modified events such as Bt11, Event176, GA21, MON810, MON863 and TC1507 provided that their sequences at both insertion junctions are available.
MK-1775, a Novel Wee1 Kinase Inhibitor, Radiosensitizes p53-Defective Human Tumor Cells (2011)

These results indicate that p53-defective human tumor cells are significantly radiosensitized by the potent and selective wee1 kinase inhibitor, MK-1775, in both the in vitro and in vivo settings. Taken together, our findings strongly support the clinical evaluation of MK-1775 in combination with radiation.
Exchange magnetic field torques in YIG/Pt bilayers observed by the spin-Hall magnetoresistance (2013)

The effective field torque of an yttrium-iron-garnet (YIG) film on the spin accumulation in an attached platinum (Pt) film is measured by the spin-Hall magnetoresistance (SMR). As a result, the magnetization direction of a ferromagnetic insulating layer can be measured electrically. Experimental transverse and longitudinal resistances are well described by the theoretical model of SMR in terms of the direct and inverse spin-Hall effect, for different Pt thicknesses [3, 4, 8, and 35 nm]. Adopting a spin-Hall angle of Pt θSH=0.08, we obtain the spin diffusion length of Pt (λ=1.1±0.3 nm) as well as the real (Gr=(7±3)×1014 Ω−1m−2) and imaginary part (Gi=(5±3)×1013 Ω−1m−2) of the spin-mixing conductance and their ratio (Gr/Gi=16±4).