gebhart/patrepeval huggingface dataset:
Quaternary pollen analysis: recent progress in palaeoecology and palaeoclimatology (2003)

During the last decade Quaternary pollen analysis has developed towards improved pollen-taxonomical precision, automated pollen identification and more rigorous definition of pollen assemblage zones. There have been significant efforts to model the spatial representation of pollen records in lake sediments which is important for more precise interpretation of the pollen records in terms of past vegetation patterns. We review the difficulties in matching modelled post-glacial plant migration patterns with pollen-based palaeorecords and discuss the potential of DNA analysis of pollen to investigate the ancestry and past migration pathways of the plants. In population ecology there has been an acceleration of the widely advocated conceptual advance of pollen-analytical research from vaguely defined ‘environmental reconstructions’ towards investigating more precisely defined ecological problems aligned with the current ecological theories. Examples of such research have included an increasing number of investigations about the ecological impacts of past disturbances, often integrating pollen records with other palaeoecological data. Such an approach has also been applied to incorporate a time perspective to the questions of ecosystem restoration, nature conservation and forest management. New lines of research are the use of pollen analysis to study long-term patterns of vegetation diversity, such as the role of glacial-age vegetation fragmentation as a cause of Amazonian rain forest diversity, and to investigate links between pollen richness and past plant diversity. Palaeoclimatological use of pollen records has become more quantitative and has included more precise and rigorous testing of pollen-climate calibration models with modern climate data. These tests show the approximate nature of the models and warn against a too straightforward climatic interpretation of the small-scale variation in reconstructions. Pollen-based climate reconstructions over the Late Glacial-early Holocene boundary have indicated that pollen-stratigraphical changes have been rapid with no evidence for response lags. This does not rule out the possibility of migrational disequilibrium, however, as the rapid changes may be mostly due to nonmigrational responses of existing vegetation. It is therefore difficult to assess whether the amplitude of reconstructed climate change reflects real climate change. Other outstanding problems remain the obscure relationship of pollen production and climate, the role of human impact and other nonclimatic factors, and nonanalogue situations.
Synthesis and Characterization of a Novel 6-Heteroaryl-3,6-dihydro-2H-pyran-2-acetic Acid (1987)

Cis and ~-6-~2-I3-(4-fluorophenyl)-l-(l-methylethyl-lH-idol-2-yllethenyll-3,4, --5,6-tetrahydro-4-hydroxy-2H-pyran-2dne (lb and La) rearrange under mildly acidic conditrons giving only ~-6-[3-(4-fluorophenyl)-l-(l-methylethyl)-1H-indol-2-yll-3,6dlhydro-2H-pyran-Zacetic acid (3).A mechanism is proposed for the acid catalyzed rearrangement.In the course of our nudies on the synthesis and evaluation of 7-(3,1-disubstitutedll,l'-biphenyl]-2-yl)-3,5-1 dihydroxyd-heptenoic acid lactones (e.g., Compound 2) as HMG-CoA reductase inhibitors, a patent describing indolyl lactone la as a potent HMG-CoA reductase inhibitor war irsued.'A sample of La was prepared in order to compare its chemical and biological properties with those of compound 2, one of our most potent biphenyl lactones.It readily became apparent that lactone la was unstable to mildly acidic conditions.Biphenyl lactone 2, as well as the other biphenyl lactoner prepared in our previous study, undergo a rapid
Site-Specific Fluorescent Labeling of DNA Using Staudinger Ligation (2003)

We report the site-specific fluorescent labeling of DNA using Staudinger ligation with high efficiency and high selectivity. An oligonucleotide modified at its 5' end by an azido group was selectively reacted with 5-[(N-(3'-diphenylphosphinyl-4'-methoxycarbonyl)phenylcarbonyl)aminoacetamido]fluorescein (Fam) under aqueous conditions to produce a Fam-labeled oligonucleotide with a high yield (approximately 90%). The fluorescent oligonucleotide was characterized by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Because of the relatively high yield of the Staudinger ligation, simple purification of the product by size-exclusion chromatography and desalting is sufficient for the resulting fluorescent oligonucleotide to be used as a primer in a Sanger dideoxy sequencing reaction to produce fluorescent DNA extension fragments, which are analyzed by a fluorescent electrophoresis DNA sequencer. The results indicate that the Staudinger ligation can be used successfully and site-specifically to prepare fluorescent oligonucleotides to produce DNA sequencing products, which are detected with single base resolution in a capillary electrophoresis DNA sequencer using laser-induced fluorescence detection.
Cold-Start Reinforcement Learning with Softmax Policy Gradient (2017)

Policy-gradient approaches to reinforcement learning have two common and undesirable overhead procedures, namely warm-start training and sample variance reduction. In this paper, we describe a reinforcement learning method based on a softmax value function that requires neither of these procedures. Our method combines the advantages of policy-gradient methods with the efficiency and simplicity of maximum-likelihood approaches. We apply this new cold-start reinforcement learning method in training sequence generation models for structured output prediction problems. Empirical evidence validates this method on automatic summarization and image captioning tasks.
4H-SiC Epitaxial Layers Grown on On-Axis Si-Face Substrate (2007)

We report on the growth of 4H-SiC epitaxial layer on Si-face polished nominally on-axis 2” full wafer, using Hot-Wall CVD epitaxy. The polytype stability has been maintained over the larger part of the wafer, but 3C inclusions have not been possible to avoid. Special attention has given to the mechanism of generation and propagation of 3C polytype in 4H-SiC epilayer. Different optical and structural techniques were used to characterize the material and to understand the growth mechanisms. It was found that all 3C inclusions were generated at the interface between the substrate and the epitaxial layer, and no 3C inclusions were initiated at later stages of the growth.
Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties (2004)

Abstract Single-stranded DNA molecules with ligand-binding ability and catalytic function, referred to as DNA aptamers and DNA enzymes, respectively, are special DNA sequences isolated from random-sequence DNA libraries by “in vitro selection”. These two new classes of artificial DNA molecules have the potential of being used as molecular tools in a variety of innovative applications ranging from biosensing to gene regulation. Our laboratory is interested in engineering fluorescence-signaling DNA aptamers and DNA enzymes that can be widely exploited for detection-directed applications. In this article, we will first discuss our recent efforts on the rational design of a new class of signaling aptamers denoted “structure- switching signaling aptamers”, which report target binding by switching structures from DNA/DNA duplex to DNA/target complex. We will then describe the in vitro selection of fluorescence-signaling DNA enzymes that exhibit a synchronized catalysis-signaling capability by cleaving a chimeric RNA/DNA substrate at the lone RNA linkage surrounded by closely spaced fluorophore-quencher pair. Potential utilities of these signaling DNA molecules will also be discussed.
Eye center localization and detection using radial mapping (2016)

We propose a geometrical method, applied over eye-specific features, to improve the accuracy of the art of eye-center localization. Our solution is built upon: (a) checking radially constrained gradient vectors, (b) adding weightage to iris specific features and (c) considering bi-directional image gradients to eliminate errors due to reflection on pupil. Our system outperforms the state of the art methods, when compared collectively across multiple benchmark databases, such as BioID and FERET. Our process is lightweight, robust and significantly fast: achieving 50-60 fps for eye center localization, using a single threaded approach on a 2.4 GHz CPU with no GPU. This makes it practicable for real-life applications.
Enhancement of the activity of immunotoxins made with either ricin A chain or Pseudomonas exotoxin in human ovarian and epidermoid carcinoma cell lines. (1988)

The present study evaluates whether the in vitro activity of immunotoxins can be enhanced by verapamil or by various antagonists of calmodulin (dansylcadaverine, trifluoperazine, chlorpromazine). The following immunotoxins made with either Pseudomonas exotoxin (PE), recombinant ricin A chain (rRTA), or ricin A chain (RTA) were used: HB21-PE and 454A12-rRTA that both recognize the human transferrin receptor; and 260F9-rRTA and 454C11-RTA that both react with human ovarian and breast cancer cells. The cytotoxicity of these immunotoxins was determined in human ovarian carcinoma cell lines and KB cells. Verapamil, that was demonstrated previously to enhance the cell-killing activity of PE immunotoxins, enhanced the activity of several ricin A chain immunotoxins, including 454A12-rRTA, 260F9-rRTA, and 454C11-RTA. Comparing 50% inhibitory dose values for inhibition of protein synthesis by 454A12-rRTA, enhancement ranged from 2- to greater than 25-fold, was dependent on the concentration of verapamil, and was greatest at short incubation times. In addition, the cytotoxicity of HB21-PE and of selected RTA immunotoxins was increased up to 30-fold by the addition of various calmodulin antagonists. The enhancing drugs did not decrease the specificity of the immunotoxins.
Screening Derivatized Peptide Libraries for Tight Binding Inhibitors to Carbonic Anhydrase II by Electrospray Ionization-Mass Spectrometry (1996)

This paper describes the use of electrospray ionization-mass spectrometry (ESI-MS) to screen two libraries of soluble compounds to search for tight binding inhibitors for carbonic anhydrase II (EC 4.2.1.1). The two libraries, H2NO2SC6H4C(O)NH-AA1-AA2-C(O)NHCH2CH2CO2H where AA1 and AA2 are L-amino acids (library size: 289 compounds) or D-amino acids (256 compounds), were constructed by attaching tripeptides to the carboxyl group of 4-carboxybenzenesulfonamide. Screening of both libraries yielded, as the tightest binding inhibitor, compound 1 (AA1 = AA2 = L-Leu; binding constant Kb = 1.4 x 10(8) M-1). The ability of ESI-MS to estimate simultaneously the relative binding affinities of a protein to soluble ligands in a library, if general, should be useful in drug development.
The effect of the E2 prostaglandin enprostil, and the somatostatin analogue sms 201 995, on the growth of a human gastric cell line, MKN45G (1990)

The effect of enprostil and the somatostatin analogue SMS 201 995 on the growth of a clonal variant of the human gastric adenocarcinoma cell line, MKN45, was studied. The derived cell line grew twice as fast as MKN45 when grown as a xenograft line in nude mice. However, it did not respond trophically to gastrin either in vitro or in vivo (unlike MKN45) although it possessed the same number of gastrin receptors as the parental line. Gastrin production by the cell line during in vitro culture was twice that of MKN45; thus, the cell line was denoted MKN45G. When MKN45G was grown as xenografts in nude mice (n = 10/group), enprostil (20 micrograms/kg/day) significantly inhibited tumour growth when administered continuously by an osmotic mini-pump from day 1 to day 7 of a 20-day experiment, and induced tumour regression when administered from day 7 to day 14. Enprostil reduced postprandial serum gastrin levels when administered from day 7 to day 14 and prevented gastrin release by MKN45 in vitro. SMS 201 995 at doses of 25 and 240 micrograms/kg/day induced tumour regression when administered from day 1 to day 7 and the former dose reduced post-prandial serum gastrin levels at day 5. Gastrin release by MKN45G was not affected by SMS 201 995 in vitro, thus its effect may not be mediated directly via gastrin, requiring interaction between other hormones or growth factors in the in vivo situation.
Data Mining Session-Based Patient Reported Outcomes (PROs) in a Mental Health Setting: Toward Data-Driven Clinical Decision Support and Personalized Treatment (2011)

The CDOI outcome measure -- a patient-reported outcome (PRO) instrument utilizing direct client feedback -- was implemented in a large, real-world behavioral healthcare setting in order to evaluate previous findings from smaller controlled studies. PROs provide an alternative window into treatment effectiveness based on client perception and facilitate detection of problems/symptoms for which there is no discernible measure (e.g. pain). The principal focus of the study was to evaluate the utility of the CDOI for predictive modeling of outcomes in a live clinical setting. Implementation factors were also addressed within the framework of the Theory of Planned Behavior by linking adoption rates to implementation practices and clinician perceptions. The results showed that the CDOI does contain significant capacity to predict outcome delta over time based on baseline and early change scores in a large, real-world clinical setting, as suggested in previous research. The implementation analysis revealed a number of critical factors affecting successful implementation and adoption of the CDOI outcome measure, though there was a notable disconnect between clinician intentions and actual behavior. Most importantly, the predictive capacity of the CDOI underscores the utility of direct client feedback measures such as PROs and their potential use as the basis for next generation clinical decision support tools and personalized treatment approaches.
Cutting Edge: Persistence of Transferred Lymphocyte Clonotypes Correlates with Cancer Regression in Patients Receiving Cell Transfer Therapy (2004)

The lack of persistence of transferred autologous mature lymphocytes in humans has been a major limitation to the application of effective cell transfer therapies. The results of a pilot clinical trial in 13 patients with metastatic melanoma suggested that conditioning with nonmyeloablative chemotherapy before adoptive transfer of activated tumor-reactive T cells enhances tumor regression and increases the overall rates of objective clinical responses. The present report examines the relationship between T cell persistence and tumor regression through analysis of the TCR beta-chain V region gene products expressed in samples obtained from 25 patients treated with this protocol. Sequence analysis demonstrated that there was a significant correlation between tumor regression and the degree of persistence in peripheral blood of adoptively transferred T cell clones, suggesting that inadequate T cell persistence may represent a major factor limiting responses to adoptive immunotherapy.
New therapeutic approaches in atopic dermatitis. (1993)

Novel approaches to the therapy for atopic dermatitis (AD) can now be considered because of recent advances in the pathogenesis of the disease. Several of these concepts are being tested in clinical trials. The effectiveness of cyclosporin A, plus reports of adoptive transfer of AD, or its clearing, following bone marrow transplantation, verify the criticalness of immune cells in AD pathogenesis. Thus, there is renewed interest in immunosuppressives, such as azathioprine and methotrexate, as well as new adhesion molecule and T-cell activation inhibitors. Therapy with the T-cell lymphokine, interferon-gamma, or the thymic hormone, thymopentin, is designed to inhibit the IL-4-dominated response of AD T-cells. This approach, rather than directly suppressing all immune responsiveness, represents a more specific targeting to improve the balance of a chronically disordered immune response. Recent findings of a therapeutic advantage of longer-wavelength phototherapy over UVB therapy may relate to specific immunologic events following UVB vs UVA photoinjury that are critical to the exacerbation of AD. Complex herbal mixtures used in traditional Chinese medicine are currently being evaluated, but toxicity and palatability may be limiting. Other dietary approaches, such as modifying the lipid balance, have generally not had much benefit. Because the safety and efficacy of the above treatments need further exploration, the physician must continue to utilize fundamental methods, such as mitigating trigger factors (i.e., microbes and stress, and certain foods in persons with documented sensitivity), on improving the abnormal epidermal lipid barrier to irritation, and on reducing cutaneous inflammation with mild topical steroids.
Phagocytosis: A Fundamental Process in Immunity (2017)

One hundred years have passed since the death of Élie Metchnikoff (1845-1916). He was the first to observe the uptake of particles by cells and realized the importance of this process for the host response to injury and infection. He also was a strong advocate of the role of phagocytosis in cellular immunity, and with this he gave us the basis for our modern understanding of inflammation and the innate and acquired immune responses. Phagocytosis is an elegant but complex process for the ingestion and elimination of pathogens, but it is also important for the elimination of apoptotic cells and hence fundamental for tissue homeostasis. Phagocytosis can be divided into four main steps: (i) recognition of the target particle, (ii) signaling to activate the internalization machinery, (iii) phagosome formation, and (iv) phagolysosome maturation. In recent years, the use of new tools of molecular biology and microscopy has provided new insights into the cellular mechanisms of phagocytosis. In this review, we present a general view of our current knowledge on phagocytosis. We emphasize novel molecular findings, particularly on phagosome formation and maturation, and discuss aspects that remain incompletely understood.
Detection of non‐covalent interaction of single and double stranded DNA with peptides by MALDI‐TOF (1998)

DNA-histone interaction facilitates packaging of huge amounts of DNA in the confined space of the nucleus. The importance of this interaction underscores the need for new analytical techniques to acquire a better understanding of nuclear dynamics. Electrospray-ionization mass spectrometry made it possible to investigate non-covalently-bound biopolymers. We are enlarging the scope of available analytical tools by studying non-covalent interaction between single and double stranded DNA and peptides with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The interaction is an ionic one, between the negatively charged sugar-phosphate backbone of single stranded DNA and positively charged side chains of Arg- and Lys-rich peptides as demonstrated by Vertes' group1 with the dipeptides Arg-Lys and His-His. We replicated Lecchi and Pannell's work,2 which showed that double stranded DNA could be seen by MALDI using 6-aza-2-thiothymine (ATT) as matrix. We tried various peptides and found that as was demonstrated in DNA-histone interaction, a certain ratio and arrangement of basic residues was needed in order to generate ionic binding between DNA and peptide. We tested various single and double stranded DNA with the peptide of choice, and found that other variables such as pH value of solution, ionic strength, and matrix system did play a role. Proteins Suppl. 2:12–21, 1998. © 1998 Wiley-Liss, Inc.
High-Level Expression and Efficient Recovery of Ubiquitin Fusion Proteins from Escherichia coli (1996)

The transition in growth and induction of bacterial cultures expressing recombinant proteins from the laboratory bench to the pilot scale for production has been performed successfully for several ubiquitin fusion-expressing clones. Increased protein turnover and decreased metabolic efficiency of Escherichia coli at high cell densities are often responsible for failures in fermenter cultures. Current data indicate that (1) yields in shaker flask cultures are directly scalable to a 10 L fermenter, (2) higher cell densities actually augment the specific yield of ubiquitin fusion proteins, (3) an in vivo heat shock during fermentation increases the ubiquitin fusion yield, which provides an initial separation step in the fermenter, and (4) the ubiquitin fusion expression clone makes at least 3-fold more total protein, including host proteins, than the parent strain of E. coli. A series of three fermentations was performed, using the model strain, with varied temperature shift protocols. These fermentations showed that a maximal heat shock of 12 degrees C (from 30 to 42 degrees C), initiated simultaneously with induction, gave a maximal specific yield (over 90% of the total soluble protein by densitometry, 709 mg/L by protein assay), in which the recoverable ubiquitin fusion product comprised 16% of the wet weight of the cell paste. These results illustrate the enormous potential of ubiquitin fusion technology for the economical production of peptides, even in a 10 L fermenter.
The Effect of Pioglitazone on Peroxisome Proliferator-Activated Receptor-γ Target Genes Related to Lipid Storage In Vivo (2004)

Treatment with pioglitazone increased body weight, and this is associated with upregulation of some, but not all, genes previously demonstrated as "TZD responsive" in subcutaneous fat. The results suggest that TZDs might increase body weight through the upregulation of genes facilitating adipocyte lipid storage in vivo.
An audio-visual corpus for speech perception and automatic speech recognition (2006)

An audio-visual corpus has been collected to support the use of common material in speech perception and automatic speech recognition studies. The corpus consists of high-quality audio and video recordings of 1000 sentences spoken by each of 34 talkers. Sentences are simple, syntactically identical phrases such as "place green at B 4 now". Intelligibility tests using the audio signals suggest that the material is easily identifiable in quiet and low levels of stationary noise. The annotated corpus is available on the web for research use.
Is inducible nitric oxide synthase a target for chemoprevention? (2003)

The molecular messenger nitric oxide (NO) is synthesized endogenously from L-arginine by three isoforms of the enzyme NO synthase. The isoform most consistently associated with neoplasia is the inducible form, inducible nitric oxide synthase (iNOS). However, the role played by the NO/iNOS system in tumor development is complex, and both promoting and inhibitory effects on neoplasia have been reported. This review attempts to clarify the role of iNOS in carcinogenesis, with particular emphasis on the early stages of tumor development, offers possible explanations for the confused picture presented in the literature regarding the association of the NO/iNOS pathway with neoplasia, and identifies selective iNOS inhibitors that may have chemopreventive potential.