gebhart/patrepeval huggingface dataset:
Ectopic expression of ABI3 gene enhances freezing tolerance in response to abscisic acid and low temperature in Arabidopsis thaliana (2001)

The plant hormone abscisic acid (ABA) regulates several physiological and developmental processes in plants, including stress adaptation and seed maturation. ABA-mediated processes appear to be central in plant cold acclimation and expression of cold acclimation-related genes. Ectopic expression of ABI3 encoding a seed-specific transcriptional activator confers on Arabidopsis vegetative tissues the ability to accumulate seed-specific transcripts in response to ABA, and also influences some ABA-mediated vegetative responses. In the present study we characterized the effect of ectopic expression of ABI3 on cold acclimation and development of freezing tolerance in Arabidopsis. We first determined the effect of ABI3 on ABA-induced expression of cold acclimation-related genes. Expression of ABI3 increased the ABA-induced accumulation of transcripts for several ABA/cold/drought-responsive genes such as RAB18 and LTI78. Enhanced expression of these genes was evident even after transient application of ABA, and the enhanced expression was correlated with increased freezing tolerance in ABI3 transgenic plants. Ectopic expression of ABI3 also appeared to modulate low temperature-induced freezing tolerance. The ABI3 transgenic plants acclimated faster than the wild-type plants, and the maximum tolerance obtained was significantly higher. These data showed that lower levels of ABA were needed to trigger the expression of the genes and to maintain the freezing-tolerant state in the ABI3 transgenic plants, and indicate that ectopic expression of ABI3 leads to enhanced responsiveness to ABA. The ectopic expression of ABI3 could provide a new strategy for engineering plant stress tolerance.
Cooperative diversity in wireless networks: algorithms and architectures (2002)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.
A Convenient One-Pot Preparative Method for 4,5-Diarylisoxazoles Involving Amine Exchange Reactions (1996)

4,5-Diarylisoxazoles 1 are efficiently prepared by submitting enaminones 2, readily obtained from deoxybenzoins 3, to oximation conditions. This conversion implies an uncommon amine group exchange reaction. Preparation of 4-isoxazolines 5 and ring-opening transformations to β-keto nitriles 4 and 1,3-amino alcohol derivatives 7 are also described.
Antigenic variation of gonococcal pilin expression in vivo: analysis of the strain FA1090 pilin repertoire and identification of the pilS gene copies recombining with pilE during experimental human infection The GenBank accession numbers for the sequences reported in this paper are U58840–U58851, U61269, L28978, L28980, L28987 and L28990–L28992. (2001)

Antigenic variation of gonococcal pilin involves a family of variable genes that undergo homologous recombination, resulting in transfer of variant sequences from the pilS silent gene copies into the complete pilE expression locus. Little is known about the specific recombination events that are involved in assembling new variant pilin genes in vivo. One approach to understanding pilin variation in vivo is to carry out experimental human infections with a gonococcal strain having a fully characterized repertoire of pilin genes, so that the specific recombination events occurring in vivo can be determined. To this end, the authors cloned, sequenced and mapped the pilin genes of strain FA1090 of Neisseria gonorrhoeae. This strain contains one pilE locus and 19 silent gene copies that are arranged in five pilS loci; the pilE locus and four of the pilS loci are clustered in a 35 kb region of the chromosome. The general features of the pilin loci in FA1090 are similar to those in strain MS11, in which the mechanism of pilin variation has been extensively studied. However, none of the silent copy sequences are identical in the two strains, which emphasizes the extreme variability in this gene family among gonococci. Three male volunteers were inoculated with the same variant of strain FA1090 and developed urethritis within 2–4 d. The pilE gene sequences from a total of 23 colonies cultured from the subjects were analysed, determining which pilS silent copy donated each portion of the expressed pilE genes. There were 12 different pilin variants, one of which was the original inoculum variant, among the in vivo-expressed pilE gene sequences. The pilE of the inoculum variant was derived entirely from a single silent copy (pilS6c1). However, the pilE genes in the majority of the colonies cultured from the infected subjects were chimeras of sequence derived from two or three silent copies. Recombination to generate new pilE sequences involved exchange of single variable minicassettes, multiple minicassettes, entire silent gene copies, or (rarely) recombination within a minicassette.
Efficient and robust automated machine learning (2015)

The success of machine learning in a broad range of applications has led to an ever-growing demand for machine learning systems that can be used off the shelf by non-experts. To be effective in practice, such systems need to automatically choose a good algorithm and feature preprocessing steps for a new dataset at hand, and also set their respective hyperparameters. Recent work has started to tackle this automated machine learning (AutoML) problem with the help of efficient Bayesian optimization methods. Building on this, we introduce a robust new AutoML system based on scikit-learn (using 15 classifiers, 14 feature preprocessing methods, and 4 data preprocessing methods, giving rise to a structured hypothesis space with 110 hyperparameters). This system, which we dub AUTO-SKLEARN, improves on existing AutoML methods by automatically taking into account past performance on similar datasets, and by constructing ensembles from the models evaluated during the optimization. Our system won the first phase of the ongoing ChaLearn AutoML challenge, and our comprehensive analysis on over 100 diverse datasets shows that it substantially outperforms the previous state of the art in AutoML. We also demonstrate the performance gains due to each of our contributions and derive insights into the effectiveness of the individual components of AUTO-SKLEARN.
Effect of neoadjuvant chemotherapy on CXCR4 expression in human breast cancer (2007)

3487 Introduction: The overexpression of chemokine receptor CXCR4 has been shown to play a pivotal role in breast cancer metastasis. In vitro and animal studies have demonstrated decreased cell migration and abrogation of metastatic disease when agents that specifically block CXCR4 are given. Its clinical significance, however, is still being elucidated. Studies have shown CXCR4 to be overexpressed in human breast cancer tissue versus benign breast tissue. In recent literature, CXCR4 overexpression has also been associated with lymph node metastasis. In this study, we examined the effect of neoadjuvant chemotherapy on CXCR4 overexpression in breast cancer patients. Methods: A prospective database of 1202 breast cancer patients was culled for this study. Eleven patients were identified with both pre- and post-neoadjuvant chemotherapy tissue specimens in our tissue bank. The patients were all diagnosed with locally advanced breast cancer (Stage IIB - III), and were found to have no evidence of systemic metastasis on subsequent staging work-up. The standard neoadjuvant chemotherapy regimen was four cycles of adriamycin and cyclophosphamide. Ten patients underwent post-neoadjuvant modified radical mastectomy, and one underwent breast conservation therapy. All eleven patients had either complete or partial response to chemotherapy. CXCR4 overexpression was quantified by western blot analysis and reported as x-fold elevated compared to Hela cells. Statistical analysis included Wilcoxon Rank Sum, Chi Square, Kaplan-Meier survival analysis and log-rank test. Results: The mean CXCR4 level was 8.8 ± 5 fold (mean ± standard deviation over benign controls). Neoadjuvant chemotherapy reduced the mean CXCR4 level to 3.2 ± 2.7 fold, resulting in a mean difference of 5.6 ± 4.0 (62% reduction) and a statistically significant reduction in CXCR4 levels (p=0.002 Wilcoxon Rank Sum Test). Both pre-neoadjuvant and post-neoadjuvant CXCR4 levels were found to have no statistically significant correlation to tumor size, nodal, HER2, ER, PR status, or pathological stage (Chi Square Analysis). A persistently elevated post-neoadjuvant chemotherapy CXCR4 level above the mean (3.2) was associated with an increased risk of cancer recurrence (p=0.041 Log-rank test). Conclusions: Neoadjuvant chemotherapy significantly reduces levels of CXCR4 overexpression in breast cancer. Elevated post-neoadjuvant chemotherapy CXCR4 expression appears to predict cancer recurrence in breast cancer patients, but a larger patient sample is necessary for proper evaluation.
Studies on the amide and C-terminal residues in proteins. 3. The esterification of proteins (1958)

The carboxyl groups of a protein can be esterified with diazomethane, but more conveniently with methanolic hydrochloric acid. In the present research, however, neither reagent has proved to be entirely satisfactory, for in our hands the first has not given full esterification and the second would do this only at the expense of the amide N, which we were particularly anxious to keep intact. They
Electrolyte homeostasis in urothelial neoplasia: the effects of amiloride (1995)

These results were consistent with the concept that activation of the amiloride-sensitive Na+/H+ membrane exchanger is a primary event in neoplasia.
Tietz Textbook of Clinical Chemistry (1999)

Part I: Laboratory Principles. General Laboratory Techniques and Procedures. Specimen Collection and Processing, Sources of Biological Variation. Part II: Analytical Techniques and Instrumentation. Spectrophotometric Techniques. Fluorometry, Nephelometry, And Turbidimetry. Basic Principles of Radioactivity and Its Measurement. Electrochemistry. Electrophoresis. Chromatography/Mass Spectrometry. Principlesof Immunochemical Techniques. Automation in the Clinical Laboratory. Part III: Chemometrics. Statistical Procedures. Selection and Interpretation of Laboratory Procedures. Selection and Evaluation of Methods. Establishment and Use of Reference Values. Part IV: Laboratory Management. Clinical Laboratory Informatics. Laboratory Management. Quality Management. Part V: Analytes. Nucleic Acid Biochemistry and Diagnostic Applications. Amino Acids. Proteins. Cytokines. Clinical Enzymology. Tumour Markers. Carbohydrates. Lipids, Lipoproteins, And Apolipoproteins. Therapeutic Drug Monitoring. Clinical Toxicology. Toxic Metals. Vitamins. Trace Elements. Electrolytes and Blood Gases. Part VI: Pathophysiology. Physiology and Disorders of Wates, Electrolyte, And Acid-Base Metabolism. Liver Function. Cardiac Function. Renal Function and Nitrogen Metabolics. Gastric, Pancreatic, And Intestinal Function. Organ Transplantation. Nutritional Assessment, Therapy, And Monitoring. Mineral and Bone Metabolism. General Endocrine Function. Pituitary Function. Thyroid Function. Function of the Adrenal Cortex. Cathecol Amines and Serotonin. Reproductive Endocrine Function. Biochemical Aspects of Hematology. Porphyrins and Disorders of Porphyrin Metabolism. Clinical Chemistry of Pregnancy. Lysosomal Storage Disease. Appendix.
Shining New Light on an Old Problem: Retooling MALDI Mass Spectrometry for Organotransition‐Metal Catalysis (2007)

Getting the air out: A bottleneck in transition-metal chemistry is the laborious process of identifying organometallic molecules. Anaerobic, charge-transfer MALDI-MS is a powerful new tool for observation of these reactive, often fragile species. Examples are drawn from catalysts relevant to olefin metathesis, hydrogenation, polymerization, and cyclopropanation. IMes=N,N′-bis(mesityl)imidazol-2-ylidene. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2008/z704489_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Recent advances in mid- and near-infrared spectroscopy with applications for research and teaching, focusing on petrochemistry and biotechnology relevant products (2013)

Mid- and near-infrared spectroscopy is introduced as a versatile analytical method for characterizing liquid and solid chemicals as obtained from petrochemistry and biotechnology processes. Besides normal transmission measurements, special equipment with silver halide fiber-optic probes allowing efficient analysis based on mid-infrared attenuated total reflection, and an accessory for near-infrared diffuse reflection measurements, are presented. The latter technique can be used advantageously for powdered samples such as microalgae biomass and polysaccharides, as well as for different tissues such as meat samples. The advantages and disadvantages of both methods, which can be used for industrial process monitoring and chemical quality control applications, are discussed, and have been used in several research projects of BSc students within their degree course of bio- and nano-technologies of our University of Applied Sciences.
Long-wave infrared nBn photodetectors based on InAs/InAsSb type-II superlattices (2012)

Long-wave infrared InAs/InAsSb type-II superlattice nBn photodetectors are demonstrated on GaSb substrates. The typical device consists of a 2.2 μm thick absorber layer and has a 50% cutoff wavelength of 13.2 μm, a measured dark current density of 5 × 10−4 A/cm2 at 77 K under a bias of −0.3 V, a peak responsivity of 0.24 A/W at 12 μm, and a maximum resistance-area product of 300 Ω cm2 at 77 K. The calculated generation-recombination noise limited specific detectivity (D*) and experimentally measured D* at 12 μm and 77 K are 1 × 1010 cm Hz1/2/W and 1 × 108 cm Hz1/2/W, respectively.
Sequence Matching and Learning in Anomaly Detection for Computer Security (1997)

Two problems of importance in computer security are to 1) detect the presence of an intruder masquerading as the valid user and 2) detect the perpetration of abusive actions on the part of an otherwise innocuous user. We havedeveloped an approach to these problems that examines sequences of user actions (UNIX commands) to classify behavior as normal or anomalous. In this paper we explore the matching function needed to compare a current behavioral sequence to a historical pro le. We discuss the di culties of performing matching in human-generated data and show that exact string matching is insu cient to this domain. We demonstrate a number of partial matching functions and examine their behavior on user command data. In particular, we explore two methods for weighting scores by adjacency of matches as well as two growth functions (polynomial and exponential) for scoring similarities. We nd, empirically, that the optimal similarity measure is user dependant but that measures based on the assumption of causal linkage between user commands are superior for this domain.
A system for typesetting mathematics (1975)

This paper describes the design and implementation of a system for typesetting mathematics. The language has been designed to be easy to learn and to use by people (for example, secretaries and mathematical typists) who know neither mathematics nor typesetting. Experience indicates that the language can be learned in an hour or so, for it has few rules and fewer exceptions. For typical expressions, the size and font changes, positioning, line drawing, and the like necessary to print according to mathematical conventions are all done automatically. For example, the input sum from i=0 to infinity x sub i = pi over 2 produces ∑ ∞ i =0 x i = π/2 The syntax of the language is specified by a small context-free grammar; a compiler-compiler is used to make a compiler that translates this language into typesetting commands. Output may be produced on either a phototypesetter or on a terminal with forward and reverse half-line motions. The system interfaces directly with text formatting programs, so mixtures of text and mathematics may be handled simply. This paper was typeset by the authors using the system described.
Accumulation ofPlasmodium berghei-Infected Red Blood Cells in the Brain Is Crucial for the Development of Cerebral Malaria in Mice (2010)

Cerebral malaria is the most severe complication of human infection with Plasmodium falciparum. It was shown that Plasmodium berghei ANKA-induced cerebral malaria was prevented in 100% of mice depleted of CD8+ T cells 1 day prior to the development of neurological signs. However, the importance of parasites in the brains of these mice was never clearly investigated. Moreover, the relevance of this model to human cerebral malaria has been questioned many times, especially concerning the relative importance of leukocytes versus parasitized erythrocytes sequestered in the brain. Here, we show that mice protected from cerebral malaria by CD8+ T-cell depletion have significantly fewer parasites in the brain. Treatment of infected mice with an antimalarial drug 15 to 20 h prior to the estimated time of death also protected mice from cerebral malaria without altering the number of CD8+ T cells in the brain. These mice subsequently developed cerebral malaria with parasitized red blood cells in the brain. Our results clearly demonstrated that sequestration of CD8+ T cells in the brain is not sufficient for the development of cerebral malaria in C57BL/6 mice but that the concomitant presence of parasitized red blood cells is crucial for the onset of pathology. Importantly, these results also demonstrated that the experimental cerebral malaria model shares many features with human pathology and might be a relevant model to study its pathogenesis.
A modified distortion metric for audio coding (2009)

Current audio coding standards employ the modified discrete cosine transform (MDCT) where overlapped frames of audio are windowed and transformed to the frequency domain. Encoding parameters are chosen so as to minimize a distortion measure subject to a rate constraint. At the decoder, inverse transformation involves additional windowing and overlap-add of frames. An analysis of the time domain error in the reconstructed frame reveals that distortion metrics based solely on the MDCT domain error are in fact unable to capture the effects of windowing and overlap-add at the decoder. The main contribution of this paper is a modified distortion metric that does capture these effects via modified discrete sine transform analysis. When incorporated into an Advanced Audio Coder the proposed distortion metric significantly improves subjective quality of reconstructed audio.
Scaffold Attachment Regions Increase Reporter Gene Expression in Stably Transformed Plant Cells (1993)

George C. Allen, Gerald E. Hall, Jr., Lisa C. Childs, Arthur K. Weissinger, Steven Spiker, William F. Thompson, Scaffold Attachment Regions Increase Reporter Gene Expression in Stably Transformed Plant Cells, The Plant Cell, Vol. 5, No. 6 (Jun., 1993), pp. 603-613
A New Human Somatic Stem Cell from Placental Cord Blood with Intrinsic Pluripotent Differentiation Potential (2004)

Here a new, intrinsically pluripotent, CD45-negative population from human cord blood, termed unrestricted somatic stem cells (USSCs) is described. This rare population grows adherently and can be expanded to 10(15) cells without losing pluripotency. In vitro USSCs showed homogeneous differentiation into osteoblasts, chondroblasts, adipocytes, and hematopoietic and neural cells including astrocytes and neurons that express neurofilament, sodium channel protein, and various neurotransmitter phenotypes. Stereotactic implantation of USSCs into intact adult rat brain revealed that human Tau-positive cells persisted for up to 3 mo and showed migratory activity and a typical neuron-like morphology. In vivo differentiation of USSCs along mesodermal and endodermal pathways was demonstrated in animal models. Bony reconstitution was observed after transplantation of USSC-loaded calcium phosphate cylinders in nude rat femurs. Chondrogenesis occurred after transplanting cell-loaded gelfoam sponges into nude mice. Transplantation of USSCs in a noninjury model, the preimmune fetal sheep, resulted in up to 5% human hematopoietic engraftment. More than 20% albumin-producing human parenchymal hepatic cells with absence of cell fusion and substantial numbers of human cardiomyocytes in both atria and ventricles of the sheep heart were detected many months after USSC transplantation. No tumor formation was observed in any of these animals.
Purification of Enterocytozoon bieneusi Spores from Stool Specimens by Gradient and Cell Sorting Techniques (2004)

A three-step method for the purification of Enterocytozoon bieneusi spores from stool specimens was developed. The primary process of purification of the spores from bacterial contaminants involved Percoll gradient centrifugation followed by additional separation using cesium chloride density gradient centrifugation. The cesium chloride-isolated spores were further purified using a flow cytometer with cell sorting capabilities. Sorting was performed without the use of antibodies, fluorochromes, or dyes, leaving the sorted spores in their native state, which appears to be less destructive for spores. When quantified by flow cytometry using tubes with known numbers of highly fluorescent polystyrene beads, the sorted material showed a slight decrease in light scatter characteristics compared with the slightly larger Encephalitozoon species spores. Although the overall recovery of the E. bieneusi spores was low, calcofluor and Gram chromotrope staining, indirect immunofluorescence assay, and transmission electron microscopy revealed that the sorted material was highly purified and contained large numbers of E. bieneusi spores and relatively few bacteria and other debris. The sorted material appeared to be sufficiently pure and could be used for in vitro culture and for the development of a variety of diagnostic reagents as well as in studying the genome of E. bieneusi and host-parasite interactions.
Clinical Characteristics of Patients With Anti-Jo-1 Antibodies (2009)

Mileti, Linda M. MD; Strek, Mary E. MD; Niewold, Timothy B.; Curran, James J. MD; Sweiss, Nadera J. MD Author Information
Cell Biology of the Neurovascular Unit: Implications for Drug Delivery Across the Blood–Brain Barrier (2005)

The central nervous system (CNS) neurovascular unit is a dynamic structure consisting of vascular endothelial cells, pericytes, and closely juxtaposed astrocytes and neurons. Contact and communication events between cells of the neurovascular unit regulate CNS development, modulate cerebral blood flow, and influence permeability properties of the blood-brain barrier. Dysregulation of proper neurovascular unit function is linked to many common human CNS pathologies, making it a target for a variety of neurotherapeutic interventions. Furthermore, manipulation of the neurovascular unit to enhance the delivery of drugs to the CNS is an active area of interest. In this review I summarize current data concerning the cell and molecular biology of the neurovascular unit. Additionally, I suggest how manipulation of novel protein components of the neurovascular unit may enhance delivery of neurotherapeutic drugs across the blood-brain barrier.