gebhart/patrepeval huggingface dataset:
Marigold, Castor Bean, and Chrysanthemum as Controls of Meloidogyne incognita and Pratylenchus alleni. (1975)

Root and soil populations of Meloidogyne incognita were significantly fewer from marigold, castor bean, and chrysanthemum than from tomato roots and soil, but not from fallow soil. Root populations of Pratvlenchus alleni were significantly fewer from marigold, castor bean, and chrysanthemum than from tomato: marigold had the fewest. Root populations of M. incognita and P. alleni from tomato simultaneously cultivated with marigold, castor bean, and chrysanthemum were significantly fewer than from tomato cultivated alone. Aborted giant cells and dead M. incognita (larvae and females) were observed in roots of marigold and castor bean, but not in chrysanthemum or tomato. Significantly more males than females occurred in castor bean roots. lnfcction sites of P. alleni appeared normal in all hosts. Thin-layer and column chromatography of alcoholic extracts from castor bean revealed no nematicidal thiophenc derivatives.
Superoxide Dismutase in Plants (1994)

Abstract Superoxide dismutases (SODs) are metal-containing enzymes that catalyze the dismutation of superoxide radicals to oxygen and hydrogen peroxide. The enzyme has been found in all aerobic organisms examined where it plays a major role in the defense against toxic-reduced oxygen species, which are generated as byproducts of many biological oxidations. The generation of oxygen radicals can be further exacerbated during environmental adversity and consequently SOD has been proposed to be important for plant stress tolerance. In plants, three forms of the enzyme exist, as classified by their active site metal ion: copper/zinc, manganese, and iron forms. The distribution of these enzymes has been studied both at the subcellular level and at the phylogenic level. It is only in plants that all three different types of SOD coexist. Their occurrence in the different subcellular compartments of plant cells allows a study of their molecular evolution and the possibility of understanding why three functionally equivalent but structurally different types of SOD have been maintained. Several cDNA sequences that encode the different SODs have recently become available, and the use of molecular techniques have greatly increased our knowledge about this enzyme system and about oxidative stress in plants in general, such that now is an appropriate time to review our current knowledge.
Inducing a Lexicon of Abusive Words – a Feature-Based Approach (2018)

Michael Wiegand, Josef Ruppenhofer, Anna Schmidt, Clayton Greenberg. Proceedings of the 2018 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies, Volume 1 (Long Papers). 2018.
Structure in Protein Chemistry (2nd edition) (2007)

The second edition of Structure in Protein Chemistry showcases the latest developments and innovations in the field of protein structure analysis and prediction. The book begins by explaining how proteins are purified and describes methods for elucidating their sequences of amino acids and defining their posttranslational modifications. Comprehensive explanations of crystallography and of noncovalent forces-ionic interactions, hydrogen bonding, and the hydrophobic effect-act as a prelude to an exhaustive description of the atomic details of the structures of proteins. The resulting understanding of protein molecular structure forms the basis for discussions of the evolution of proteins, the symmetry of the oligomeric associations that produce them, and the chemical, mathematical, and physical basis of the techniques used to study their structures. The latter include image reconstruction, nuclear magnetic resonance spectroscopy, proton exchange, optical spectroscopy, electrophoresis, covalent cross-linking, chemical modification, immunochemistry, hydrodynamics, and the scattering of light, X-radiation, and neutrons. These procedures are applied to study the folding of polypeptides and the assembly of oligomers. Biological membranes and their proteins are also discussed.
Nivolumab for Metastatic Renal Cell Carcinoma: Results of a Randomized Phase II Trial (2014)

Nivolumab demonstrated antitumor activity with a manageable safety profile across the three doses studied in mRCC. No dose-response relationship was detected as measured by PFS. These efficacy and safety results in mRCC support study in the phase III setting.
Microdevice for continuous flow magnetic separation for bioengineering applications (2017)

A novel continuous flow microfluidic device, integrated with soft-magnetic wire (permalloy), is fabricated and tested for magnetophoresis based separation. The flow-invasive permalloy wire, magnetized using an external bias field, is positioned perpendicular to the external magnetic field and with its length traversing the introduced sample flow. The microfluidic device is realized in PDMS; the mold for PDMS microstructures is cut out of Plexiglas® sheets with controllable dimensions. Microfluidic devices with microchannel height ranging between 0.5 mm and 2 mm are fabricated. Experiments are carried out with and without sheath flow; with sheath flow the microparticles are focused at the center of the microchannel.
Direct and Indirect Modulation of the N-Methyl D-Aspartate Receptor: Potential for the Development of Novel Antipsychotic Therapies (2002)

The dopamine hypothesis of schizophrenia has been a driving force in guiding both theories of pathophysiology of schizophrenia, and drug discovery efforts in this area. While this path has been fruitful in producing a deeper understanding of the disorder and a variety of antipsychotic drugs, it is generally recognized that targeting the D(2) dopamine receptor has multiple shortcomings. Recently, alterations in the glutamatergic system have been proposed to play a key role in the neurochemical disruptions underlying schizophrenia. In particular, the similarities between the symptoms of schizophrenia and the psychotomimetic effects of non-competitive N-methyl D-aspartate (NMDA) receptor antagonists such as phencyclidine have spurred interest in the possibility that an NMDA receptor hypofunctional state might underlie schizophrenia. In this review, we summarize the NMDA hypofunction hypothesis of schizophrenia, and focus on the NMDA receptor as a potential target for novel antipsychotic agents. Both modulatory sites on the NMDA receptor, as well as G-protein coupled receptors such as the muscarinic and metabotropic glutamate receptors that modulate the NMDA receptor, are potential targets for the development of novel compounds that could ameliorate the symptoms of schizophrenia.
Performance analysis of digital radio links with nonlinear transmit amplifier and data predistorter with memory (2003)

A method of introducing an adaptive digital predistortion circuit to compensate for the nonlinearity produced in digital radio systems by the high-power amplifier (HPA) is proposed. The method is attractive for its simplicity (two digital finite-impulse response (FIR) filters) and because of the inherent adaptability to any nonlinearity. The simplicity of the predistorter is worth noting; only two parameters ( alpha /sub 1/ and alpha /sub 3/) need to be estimated in place of tens of the third-order kernel coefficients, as proposed in previous schemes. The performance gain is about 3 dB for a 64 quadrature amplitude modulation (QAM) system without predistortion and 1 dB for a system with memoryless data predistortion. The corresponding values for the 256 QAM system are 4 dB and 1.5 dB, respectively.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Closed-Cycle Capillary Polymerase Chain Reaction Machine (2001)

A novel thermocycling machine based on a microcapillary equipped with bidirectional pressure-driven flow and in situ optical position sensors is described. A 1-microL droplet of reaction mixture moves between three heat zones in a 1-mm-i.d., oil-filled capillary using a multielement scattered light detector and active feedback. Dwell times and accelerations can be adjusted independently. As a demonstration of the device, 30 cycles of a 500-base pair product were performed in 23 min with 78% amplification efficiency. This result compares well with previous high-speed thermocyclers. Theoretically, the arrangement can approach a time of 2.5 min for 30 cycle amplifications of a 500-base pair product.
Fragmentation and Labeling of Probe DNA for Whole-Mount FISH in Drosophila (2011)

Good probes for whole-mount fluorescent in situ hybridization (FISH) must meet two criteria: The DNA fragments must be very small and they must be highly labeled. This article describes an effective labeling scheme that involves fragmenting the probe DNA and then adding a mixture of labeled and unlabeled nucleotides to the 3' ends using the enzyme terminal deoxynucleotidyl transferase (TdT). This method can be used to label a variety of DNA probes, regardless of their initial size (e.g., plasmid, cosmid, or P1 clones, polymerase chain reaction [PCR] products, or total genomic DNA). Short oligonucleotides may also be labeled in this way without digestion, because their small size allows them to diffuse through thick tissues. A potential advantage of end-labeling is that the modified nucleotides are not incorporated into the complementary probe sequence itself and may thus interfere less with hybridization. The free 3' tail may also make haptens more accessible to detection reagents.
Intention-based Segmentation: Human Reliability and Correlation with Linguistic Cues (1994)

Certain spans of utterances in a discourse, referred to here as segments, are widely assumed to form coherent units. Further, the segmental structure of discourse has been claimed to constrain and be constrained by many phenomena. However, there is weak consensus on the nature of segments and the criteria for recognizing or generating them. We present quantitative results of a two part study using a corpus of spontaneous, narrative monologues. The first part evaluates the statistical reliability of human segmentation of our corpus, where speaker intention is the segmentation criterion. We then use the subjects' segmentations to evaluate the correlation of discourse segmentation with three linguistic cues (referential noun phrases, cue words, and pauses), using information retrieval metrics.
Kekerasan Dalam Rumah Tangga (KDRT) Dalam Perspektif Fiqh (2017)

Keadilan sangat sulit diperoleh bagi perempuan, terbukti dengan maraknya korban Kekerasan Dalam Rumah Tangga (KDRT). Keadilan disimbolkan dengan Dewi Themis, yang notabene adalah perempuan. Dewi Themis digambarkan mengenakan tutup mata, memegang timbangan, dan membawa pedang bermata dua untuk menjamin kekuatan pertimbangan dan keadilan. Tutup mata yang dikenakan Dewi Themis manandakan agar keadilan dapat diberikan secara objektif tanpa pandang bulu. Namun sepertinya tutup mata ini menjadi hambatan bagi Sang Dewi Themis akhirnya tidak dapat melihat bahwa timbangan yang di bawahnya tidak seimbang. Tutup mata itu membuat Dewi Themis tidak mampu melihat bahwa pedang bermata dua yang dibawanya malah membuat korban kembali, menjadi korban karena tertusuk oleh sisi mata pedang yang terarah kepadanya. Akhirnya dengan tutup mata itu, Dewi Themis tidak mampu lagi melihat kebenaran untuk dapat memberikan keadilan pada pihak yang berhak menerimanya. Apakah fiqh termasuk seperti Dewi Themis tersebut yang sudah tertutup matanya sehingga sudah tidak bisa lagi melihat realitas kebenaran dan keadilan di depannya, sehingga dengan dawuhnya mensubordinatkan nilai keadilan bagi perempuan. Padahal pencarian keadilan merupakan salah satu fitrah kemanusiaan, yang harus tetap ditegakkan sebagaimana firman Allah Q.S. al-Maidah (5) : 8 “I’dilu, huwa aqrabu littaqwâ” yang artinya “berbuat adillah, hal itu lebih mendekatkan ke takwa”, begitupun menurut ahli filsafat zaman Romawi kuno, M.Tullius Cicero (106-43 SM) yang terkenal “Fiat Justitia Fereat Mundus” yang artinya “laksanakan keadilan walaupun langit akan runtuh”
IL-2-inducible T-cell kinase deficiency: clinical presentation and therapeutic approach (2010)

Mutations in the IL-2-inducible T-cell kinase gene have recently been shown to cause an autosomal recessive fatal Epstein Barr virus (EBV) associated lymphoproliferation. We report 3 cases from a single family who presented with EBV-positive B-cell proliferation diagnosed as Hodgkin's lymphoma. Single nucleotide polymorphism array-based genome-wide linkage analysis revealed IL-2-inducible T-cell kinase as a candidate gene for this disorder. All 3 patients harbored the same novel homozygous nonsense mutation C1764G which causes a premature stop-codon in the kinase domain. All cases were initially treated with chemotherapy. One patient remains in durable remission, the second patient subsequently developed severe hemophagocytic lymphohistiocytosis with multi-organ failure and died, and the third patient underwent a successful allogeneic bone marrow transplantation. IL-2-inducible T-cell kinase deficiency underlies a new primary immune deficiency which may account for part of the spectrum of Epstein Barr virus related lymphoproliferative disorders which can be successfully corrected by bone marrow transplantation.
Iron Chelators in Cancer Chemotherapy (2004)

Iron chelators may be of value as therapeutic agents in the treatment of cancer. They may act by depleting iron, a necessary nutrient, and limiting tumor growth. Alternatively or additionally, they may form redox-active metal complexes that cause oxidative stress via production of reactive oxygen species, damaging critical intracellular targets and thereby eliciting a cytotoxic response. Studies in vitro have evaluated the structure-activity relationships and mechanism of action of many classes of iron chelators, including desferrioxamine (DFO), pyridoxal isonicotinoyl hydrazone (PIH) analogs, desferrithiocin (DFT) analogs, tachpyridine, the heterocyclic carboxaldehyde thiosemicarbazones, and O-Trensox. Animal studies have confirmed the antitumor activity of several chelators. Dexrazoxane has been approved for use in combination with doxorubicin, and its effectiveness in allowing higher doses of doxorubicin to be administered is, in part, based on the interactions of both drugs with iron. Clinical trials of the antitumor activity of chelators have been largely limited to DFO, which has been extensively studied as a consequence of its approved use for treatment of secondary iron overload. While the modest antitumor effects of DFO are encouraging, it is likely that more effective iron chelators may be identified.
Use of Lambda Phage DNA as a Hybrid Internal Control in a PCR-Enzyme Immunoassay To Detect Chlamydia pneumoniae (1998)

An inherent problem in the diagnostic PCR assay is the presence of ill-defined inhibitors of amplification which may cause false-negative results. Addition of an amplifiable fragment of foreign DNA in the PCR to serve as a hybrid internal control (HIC) would allow for a simple way to identify specimens containing inhibitors. Two oligonucleotide hybrid primers were synthesized to contain nucleic acid sequences of the Chlamydia pneumoniae 16S rRNA primers in a position flanking two primers that target the sequences of a 650-bp lambda phage DNA segment. By using the hybrid primers, hybrid DNA comprising a large sequence of lambda phage DNA flanked by short pieces of chlamydia DNA was subsequently generated by PCR, cloned into a plasmid vector, and purified. Plasmids containing the hybrid DNA were diluted and used as a HIC by adding them to each C. pneumoniae PCR test. Consequently, C. pneumoniae primers were able to amplify both chlamydia DNA and the HIC DNA. The production of a 689-bp HIC DNA band on an acrylamide gel indicated that the specimen contained no inhibitors and that internal conditions were compatible with PCR. Subsequently, a biotinylated RNA probe for the HIC was transcribed from a nested sequence of the HIC and was used for its hybridization. Detection of the HIC DNA-RNA hybrid was achieved by enzyme immunoassay (EIA). This PCR-EIA system with a HIC was initially tested with 12 previously PCR-positive and 14 previously PCR-negative specimens. Of the 12 PCR-positive specimens, 11 were reconfirmed as positive; 1 had a negative HIC value, indicating inhibition. Of the 14 previously PCR-negative specimens, 13 were confirmed as true negative; 1 had a negative HIC value, indicating inhibition. The assay was then used with 237 nasopharyngeal specimens from patients with pneumonia. Twenty-one of 237 (8.9%) were positive for C. pneumoniae, and 42 (17.7%) were found to inhibit the PCR. Specimens showing inhibitory activity were diluted 1:10 and were retested. Ten specimens were still inhibitory to the PCR and required further DNA purification. No additional positive samples were detected and 3 nasopharyngeal specimens remained inhibitory to PCR. Coamplification of a HIC DNA can help confirm true-negative PCR results by ruling out the presence of inhibitors of DNA amplification.
Fused‐silica capillaries with surface‐bound dextran layer crosslinked with diepoxypolyethylene glycol for capillary electrophoresis of biological substances at reduced electroosmotic flow (1995)

This report is concerned with the introduction of novel surface modification involving the covalent attachment of branched, high molecular weight dextrans and subsequent crosslinking with polyether chains on the inner surface of fused silica capillaries with the aim of producing hydrophilic capillaries with reduced electroosmotic flow (EOF). Three different molecular mass dextrans, namely 45, 71 or 150 kDa were covalently attached to the capillary surface, and subsequently crosslinked with diepoxypolyethylene glycol (PEG). This chemistry produced stable coating over a wide range of conditions including high and low pH aqueous solutions. Moreover, the various dextran-PEG-coated capillaries exhibited reduced electroosmotic flow. These features of the dextran-PEG coatings were useful for the separations of basic and acidic proteins, and provided high resolution separation for closely related acidic monosaccharides and sialooligosaccharides.
Mast cell and macrophage chemokines CXCL1/CXCL2 control the early stage of neutrophil recruitment during tissue inflammation (2013)

Neutrophil recruitment is an important early step in controlling tissue infections or injury. Here, we report that this influx depends on both tissue-resident mast cells and macrophages. Mice with mast cell deficiency recruit reduced numbers of neutrophils in the first few hours of intraperitoneal lipopolysaccharide (LPS) stimulation. Conversely, in mice with clodronate-ablated macrophages, neutrophils extravasate, but have limited ability to reach the peritoneal fluid. Tissue macrophages synthesize neutrophil chemoattractants CXCL1/CXCL2 (CXC chemokine ligands 1/2) in response to LPS. Mast cells also produce these chemokines of which a proportion are preformed in granules. Release of the granules and new CXCL1/CXCL2 synthesis is Toll-like receptor 4-dependent. Both in vivo studies with blocking monoclonal antibodies and in vitro chemotaxis experiments show the neutrophil response to mast cells and macrophages to be CXCL1/CXCL2-dependent. The data are in keeping with the model that mast cells, optimally positioned in close proximity to the vasculature, initiate an early phase of neutrophil recruitment by releasing the chemoattractants CXCL1/CXCL2. Having arrived within the stimulated tissue, neutrophils penetrate further in a macrophage-dependent manner. Therefore, we demonstrate a positive role for mast cells in tissue inflammation and define how this comes about with contribution from a second tissue cell, the macrophage.
Phase-locked spin torque oscillators: Impact of device variability and time delay (2007)

We have carried out detailed Landau–Lifshitz-Gilbert simulations of pairs of serially connected spin torque oscillators (STOs) in parallel with a resistive load. To study the impact of realistic process variations on STO synchronization we let the two STOs have different in-plane anisotropy fields (Hk). The simulation also provides for a time delay (τ). We construct a phase diagram of the STO synchronization as a function of Hk and direct current (Idc) at different τ. The phase diagram turns out to be quite rich with different types of synchronized precession modes. While the synchronized state is originally very sensitive to STO process variations and can only sustain up to 4% Hk variation, the addition of a small time delay dramatically improves its robustness and allows as much as 145% Hk variation in the entire out-of-plane precession regime.
Tumour necrosis factor‐induced gene expression in human marrow stroma: clues to the pathophysiology of MDS? (2007)

Aberrant regulation of the tumour necrosis factor alpha gene (TNF) and stroma-derived signals are involved in the pathophysiology of myelodysplasia. Therefore, KG1a, a myeloid leukaemia cell line, was exposed to Tnf in the absence or presence of either HS-5 or HS-27a cells, two human stroma cell lines. While KG1a cells were resistant to Tnf-induced apoptosis in the absence of stroma cells, Tnf-promoted apoptosis of KG1a cells in co-culture experiments with stroma cells. To investigate the Tnf-induced signals from the stroma cells, we examined expression changes in HS-5 and HS-27a cells after Tnf exposure. DNA microarray studies found both discordant and concordant Tnf-induced expression responses in the two stroma cell lines. Tnf promoted an increased mRNA expression of pro-inflammatory cytokines [e.g. interleukin (IL)6, IL8 and IL32]. At the same time, Tnf decreased the mRNA expression of anti-apoptotic genes (e.g. BCL2L1) and increased the mRNA expression of pro-apoptotic genes (e.g. BID). Overall, the results suggested that Tnf induced a complex set of pro-inflammatory and pro-apoptotic signals in stroma cells that promote apoptosis in malignant myeloid clones. Additional studies will be required to determine which of these signals are critical for the induction of apoptosis in the malignant clones. Those insights, in turn, may point the way to novel therapeutic approaches.
Experience With a Pill-Swallowing Enhancement Aid (2010)

Barriers to swallowing tablets and capsules can impact adherence to medication regimens. Few tools are currently available to assist adolescent children who have difficulty swallowing tablets and capsules. A convenience sample of adolescent children, identified through selfreport as having difficulty in swallowing tablets or capsules in the past, were provided Pill Glide, a flavored spray promoted to aid swallowing. To emulate medication administration, a tic tac (candy) was placed in the middle of the tongue, and with a drink of water, the participant was instructed to swallow the tic tac. Success or failure to swallow the tic tac was recorded. A total of 11 adolescent children ranging in age from 9 to 17 years reported past difficulty with swallowing medication. Seven of the 11 participants were successful in swallowing the tic-tac with the use of Pill Glide. This initial assessment of Pill Glide spray demonstrates positive findings for improving the ease of swallowing tablets and capsules for adolescents.