gebhart/patrepeval huggingface dataset:
Trigger factor is induced upon cold shock and enhances viability of Escherichia coli at low temperatures (1997)

Trigger factor (TF) in Escherichia coli is a molecular chaperone with remarkable properties: it has prolyl-isomerase activity, associates with nascent polypeptides on ribosomes, binds to GroEL, enhances GroEL's affinity for unfolded proteins, and promotes degradation of certain polypeptides. Because the latter effects appeared larger at 20 degrees C, we studied the influence of temperature on TF expression. Unlike most chaperones (e.g., GroEL), which are heat-shock proteins (hsps), TF levels increased progressively as growth temperature decreased from 42 degrees C to 16 degrees C and even rose in cells stored at 4 degrees C. Upon temperature downshift from 37 degrees C to 10 degrees C or exposure to chloramphenicol, TF synthesis was induced, like that of many cold-shock proteins. We therefore tested if TF expression might be important for viability at low temperatures. When stored at 4 degrees C, E. coli lose viability at exponential rates. Cells with reduced TF content die faster, while cells overexpressing TF showed greater viability. Although TF overproduction protected against cold, it reduced viability at 50 degrees C, while TF deficiency enhanced viability at this temperature. By contrast, overproduction of GroEL/ES, or hsps generally, while protective against high temperatures, reduced viability at 4 degrees C, which may explain why expression of hsps is suppressed in the cold. Thus, TF represents an example of an E. coli protein which protects cells against low temperatures. Moreover, the differential induction of TF at low temperatures and hsps at high temperatures appears to provide selective protection against these opposite thermal extremes.
Basic matrixes for the matrix-assisted laser desorption/ionization mass spectrometry of proteins and oligonucleotides (1993)

In order to examine the importance of pH in the matrix-assisted laser desorption/ionization (MALDI) analysis of proteins and oligonucleotides, 37 highly substituted pyrimidine, pyridine, and benzene derivatives containing basic amino groups were screened as potential matrices. Several of these compounds were useful for the preparation and analysis of samples under neutral and basic pH conditions. The matrix, 2-amino-4-methyl-5-nitropyridine, gave good results with small proteins (up to approximately 12,000 Da). The best results with oligonucleotides were obtained with 2-amino-5-nitropyridine, which was a useful matrix for the analysis of mixed-base oligonucleotides smaller than 20 nucleotides in length and homopolymers of thymidine. In general, oligonucleotide analysis using basic matrices was found to be subject to similar constraints of size and base composition that hold when acidic matrices are used. A major advantage of these newly discovered matrix materials over the more commonly used acidic matrices is that they extend the utility of MALDI to the analysis of acid-sensitive species.
Nematic polar anchoring strength measured by electric field techniques (1999)

We analyze the high-electric-field technique designed by Yokoyama and van Sprang [J. Appl. Phys. 57, 4520 (1985)] to determine the polar anchoring coefficient W of a nematic liquid crystal-solid substrate. The technique implies simultaneous measurement of the optical phase retardation and capacitance as functions of the applied voltage well above the threshold of the Frederiks transition. We develop a generalized model that allows for the determination of W for tilted director orientation. Furthermore, the model results in a new high-field technique, (referred to as the RV technique), based on the measurement of retardation versus applied voltage. W is determined from a simple linear fit over a well-specified voltage window. No capacitance measurements are needed to determine W when the dielectric constants of the liquid crystal are known. We analyze the validity of the Yokoyama–van Sprang (YvS) and RV techniques and show that experimental data in real cells often do not follow the theoretical curves. The reason is that the director distribution is inhomogeneous in the plane of the bounding plates, while the theory assumes that the director is not distorted in this plane. This discrepancy can greatly modify the fitted value of 1/W, and even change its sign, thus making the determination of W meaningless. We suggest a protocol that allows one to check if the cell can be used to measure W by the YvS or RV techniques. The protocol establishes new criteria that were absent in the original YvS procedure. The results are compared with other data on W, obtained by a threshold-field technique for the same nematic-substrate pair.
Effects of platelet-derived growth factor, vitamin D and parathyroid hormone on osteoblasts derived from cancer patients on chronic bisphosphonate therapy (2009)

Bisphosphonates consist of a family of pyrophosphate analogues that are currently being used to treat metastatic bone diseases as well as systemic bone diseases such as osteoporosis. There is accumulating evidence suggesting that patients treated with these bisphosphonates can develop, particularly with invasive dental procedures, osteonecrosis of the jaw. This present study investigated the ability of osteoblastic cells obtained from the alveolar bone of patients on long term intravenous bisphosphonate therapy to respond to agents normally involved in bone regulation and repair. The effects of platelet-derived growth factor-BB (PDGF-BB), 1,25-dihydroxycholecalciferol [1,25(OH)2VitaminD3] and parathyroid hormone (PTH) on basic parameters of cell viability, proliferation, and differentiation were studied. Osteoblastic cells from a diagnosed necrotic alveolar bone specimen obtained with consent from a multiple myeloma female patient, and a non-necrotic sample from a breast cancer female patient both on chronic bisphosphonate therapy (zolendronic acid) were successfully cultured. Cells from an alveolar bone specimen obtained from a female donor with no known medical conditions were also studied for comparative responses. The cells were exposed to 1,25(OH)2D3, PDGF, or PTH under various incubation conditions. The osteoblastic cell differentiation marker, alkaline phosphatase activity, was assayed using a biochemical analysis. Cell viability was assessed with an MTT assay which measures mitochondrial activity and cell proliferation with a tritiated thymidine assay. This study on osteoblastic cells grown from a necrotic alveolar bone from a multiple myeloma patient and a non-necrotic sample from a breast cancer patient, both on long term bisphosphonate treatment, suggests that viable cells from the bone are responsive to agents such as PTH, PDGF and 1,25(OH)2D3 with changes in alkaline phosphatase activity, proliferation and viability suggestive of normal osteoblastic cell responses observed in cultures from a donor of the same gender and age, but not on bisphosphonate treatment. This work provides a rationale for clinical studies to further assess whether the osteonecrosis that sometimes develops in patients treated with bisphosphonates, can be controlled or prevented by close attention to the levels of bone/calcium regulatory agents and/or, in some cases, therapeutic intervention with PDGF to restore regenerative processes that may be compromised at the necrotic site.
Detained introns are a novel, widespread class of post-transcriptionally spliced introns (2015)

Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as "detained" introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs-including those in Mdm4, a negative regulator of p53-was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.
Nucleosome‐restricted antibodies are detected before anti‐dsdna and/or antihistone antibodies in serum of mrl‐mp lpr/lpr and +/+ mice, and are present in kidney eluates of lupus mice with proteinuria (1994)

Our findings support the notion that nucleosomes play a major role in the emergence of antinuclear autoantibodies and that antinucleosome antibodies might be involved in the nephritogenic process in murine lupus.
Synthesis of selenocysteine peptides and their oxidation to diselenide‐bridged compounds (1997)

Using the Fmoc/tBu protection scheme and the p-methoxybenzyl derivative of selenocysteine, the synthesis of related peptides in the selenol-protected form could be optimized by operating the coupling steps in the absence of auxiliary bases and by reducing the piperidine treatment to the minimum time required for quantitative Fmoc cleavage. Under these conditions, β-elimination of the p-methoxybenzylselenol as the main side reaction of these syntheses, as well as epimerization of the protected selenocysteine, was largely suppressed. Conversion of the selenol- and thiol-protected bis-selenocysteine and selenocysteine, cysteine peptides into the related cyclic monomeric forms by iodine-mediated oxidation failed since a complex mixture of compounds was produced. Cleavage of the selenoether bond with mercuric acetate was found to proceed smoothly, but displacement of the heavy metal ions by treatment with excesses of thiols or hydrogen sulphide was unsuccessful since a stable Hg2+ diselenide complex was obtained. However, oxidation was achieved in good yields by the dimethylsulphoxide/trifluoroacetic acid procedure and the peptides were then used for determining the redox potential of the diselenide and selenide/sulphide bridge, respectively. © 1997 European Peptide Society and John Wiley & Sons, Ltd.
Cloning PCR Products: An Overview (2003)

A successful cloning of polymerase chain reaction (PCR)-derived DNA fragment is a key step for further analysis of the amplified DNAs, though it is often a difficult task. Many cloning methods have been established; various commercial cloning kits are also available. These methods can be separated into two groups: ligation-dependent cloning and ligation-independent cloning. The former is used more widely than the latter. According to DNA ends, the existing ligation-dependent cloning methods for PCR products can be further divided into three types: blunt-end cloning, sticky-end cloning, and T-A cloning.
Escape from Flatland: Increasing Saturation as an Approach to Improving Clinical Success (2009)

The medicinal chemistry community has become increasingly aware of the value of tracking calculated physical properties such as molecular weight, topological polar surface area, rotatable bonds, and hydrogen bond donors and acceptors. We hypothesized that the shift to high-throughput synthetic practices over the past decade may be another factor that may predispose molecules to fail by steering discovery efforts toward achiral, aromatic compounds. We have proposed two simple and interpretable measures of the complexity of molecules prepared as potential drug candidates. The first is carbon bond saturation as defined by fraction sp(3) (Fsp(3)) where Fsp(3) = (number of sp(3) hybridized carbons/total carbon count). The second is simply whether a chiral carbon exists in the molecule. We demonstrate that both complexity (as measured by Fsp(3)) and the presence of chiral centers correlate with success as compounds transition from discovery, through clinical testing, to drugs. In an attempt to explain these observations, we further demonstrate that saturation correlates with solubility, an experimental physical property important to success in the drug discovery setting.
Realtime MPEG video via software decompression on a PA-RISC processor (2002)

This paper describes the first software implementation of an MPEG video decoder that runs at realtime rates of 30 frames per second, on a general purpose microprocessor. Previously, realtime MPEG decoding could only be achieved by using special-purpose MPEG or video chips, with "programmability" either nonexistent or limited to low-level firmware. In this paper, we describe how synergistic software and hardware optimizations allow us to implement realtime, high-fidelity MPEG video and audio decompression in a software video player written in C, running on a PA-RISC microprocessor in the entry-level HP712 workstations. The PA-7100LC microprocessor described here is a fully-compliant PA-RISC 1.1 general purpose processor with a few generic instructions added to speedup parallel arithmetic on subword (16-bit) data.
Evidence for cancer stem cells contributing to the pathogenesis of ovarian cancer (2010)

Ovarian cancer represents the most lethal gynecologic malignancy, primarily due to a lack of early detection, which results in most patients being diagnosed at an advanced stage of disease. Though the ovarian surface epithelium is thought to provide the primary site of tumorigenesis, the exact etiology of the various tumor types associated with this disease remain undefined. Recent evidence suggests that ovarian tumors, like other solid tumors, contain distinct populations of cells that are responsible for tumor initiation, maintenance and growth. These specialized cells, termed cancer stem cells, display some of the hallmarks of normal stem cells and are thought to evade current chemotherapeutic strategies, resulting in an increased risk of recurrence. Here we review evidence for the existence of cancer stem cells in ovarian malignancies and their contribution to the pathology of this disease, critically evaluate the methods used for ovarian cancer stem cell definition and isolation, and discuss their clinical relevance.
TH‐B‐224C‐01: Permanent Prostate Brachytherapy Using Plastic Palladium‐103 Seeds (2006)

Purpose: A new model of palladium‐103 (Pd‐103) seeds with plastic encapsulation (OptiSeed 103 Model 1032P, International Brachytherapy, Norcross, Georgia) is commercially available. The abstract reports the investigation of using the plastic Pd‐103 seeds in prostate brachytherapy. Method and Materials: The RTOG criteria were adopted in patient selection. A real‐time transrectal‐ultrasound (TRUS) guided transperineal implant technique was employed. A Foley catheter was used to localize the urethra. The seed placement followed a modified uniform loading protocol. At the completion of an implant, TRUS images were recorded. Post CT dosimetry was accomplished in the patient's 30‐day follow‐up visit and a seed migration survey was also performed. Results: Three prostate cancer patients underwent the Pd‐103 seed implantation. 386 loose seeds with total activity of 656.1 U were implanted. The patients tolerated the procedure. No abnormal symptoms have been reported in the first half‐year follow‐up, except the detection of 3 migrated seeds to the lungs in a patient. The seed appearances in the pelvic radiographs and CT images were similar to that of the metallic seeds. A significant seed enhancement was observed in the post‐implant TRUS images. Phantom studies showed similar results. A post plan for each patient was generated on the post‐implant TRUS images where 97% of the seeds were identified with confidence. The patterns of the seed distribution in the TRUS and CT images were similar although the GTVs were different due to implant edema. Conclusion: Regarding the dosimetry and implant process, there are no differences between the plastic and metallic seeds. A superior property of the plastic seeds is its appearance in TRUS images. The seed distribution can be immediately displayed in the TRUS images at the completion of an implant. Cold spots can be identified in real time and additional seeds may be added so as to improve the implant quality.
Molecular cloning of a transcription factor, AGP/EBP, that belongs to members of the C/EBP family. (1990)

A C/EBP-like transcription factor, AGP/EBP, that binds to three distinct motifs in the 5'-flanking region of alpha 1-acid glycoprotein gene (AGP) has been identified. Here we report the cloning and properties of cDNA corresponding to mouse AGP/EBP. AGP/EBP and C/EBP share 87% amino acid sequence homology in the "leucine zipper" and its associated DNA-binding domains, while their sequences outside these domains and the sizes of their mRNAs are different. Unlike the limited expression of C/EBP in tissues and cells, AGP/EBP appears to be ubiquitously expressed in tissues like lung, spleen, kidney, heart, testis, and liver and cell lines like p388D1, 129P (hepatoma cell line of C3H/HeJ), FO (mouse myeloma), and L929. Antibody against cloned and expressed AGP/EBP which was raised in rabbits could recognize AGP/EBP from nuclear extract of a number of cells and tissues. On the basis of our findings about the structural relationship and the similarity of motif recognition, we propose that a family of C/EBP-like transcription factors exists.
Synthetic Messenger RNA and Cell Metabolism Modulation (2013)

Synthetic mRNA is an attractive tool for mammalian cell reprogramming that can be used in basic research, as well as in clinical applications. Present mRNA in vitro synthesis is a rather simple proced
An Essential Role for BAFF in the Normal Development of B Cells Through a BCMA-Independent Pathway (2001)

The B cell activating factor BAFF (BlyS/TALL-1/zTNF4) is a tumor necrosis factor (TNF)-related ligand that promotes B cell survival and binds to three receptors (BCMA, TACI, and the recently described BAFF-R). Here we report an absolute requirement for BAFF in normal B cell development. Examination of secondary lymphoid organs from BAFF-deficient mice revealed an almost complete loss of follicular and marginal zone B lymphocytes. In contrast, mice lacking BCMA had normal-appearing B lymphocyte compartments. BAFF therefore plays a crucial role in B cell development and can function through receptors other than BCMA.
Systematic review and meta-analysis: Multi-strain probiotics as adjunct therapy forHelicobacter pylorieradication and prevention of adverse events (2015)

Our meta-analysis found adjunctive use of some multi-strain probiotics may improve H. pylori eradication rates and prevent the development of adverse events and antibiotic-associated diarrhea, but not all mixtures were effective.
Optically active phthalocyanines and their circular dichroism (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOptically active phthalocyanines and their circular dichroismNagao Kobayashi, Yayoi Kobayashi, and Tetsuo OsaCite this: J. Am. Chem. Soc. 1993, 115, 23, 10994–10995Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ja00076a069https://doi.org/10.1021/ja00076a069research-articleACS PublicationsRequest reuse permissionsArticle Views428Altmetric-Citations64LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Directing cell migration with asymmetric micropatterns (2005)

This report shows that the direction of polarization of attached mammalian cells determines the direction in which they move. Surfaces micropatterned with appropriately functionalized self-assembled monolayers constrain individual cells to asymmetric geometries (for example, a teardrop); these geometries polarize the morphology of the cell. After electrochemical desorption of the self-assembled monolayers removes these constraints and allows the cells to move across the surface, they move toward their blunt ends.
Reverse engineering to the architectural level (1995)

Article Free AccessReverse engineering to the architectural level Authors: David R. Harris The MITRE Corporation, 202 Burlington Road, Bedford, MA The MITRE Corporation, 202 Burlington Road, Bedford, MAView Profile , Howard B. Reubenstein GTE Laboratories, 40 Sylvan Road, Waltham, MA GTE Laboratories, 40 Sylvan Road, Waltham, MAView Profile , Alexander S. Yeh The MITRE Corporation, 202 Burlington Road, Bedford, MA The MITRE Corporation, 202 Burlington Road, Bedford, MAView Profile Authors Info & Claims ICSE '95: Proceedings of the 17th international conference on Software engineeringApril 1995Pages 186–195https://doi.org/10.1145/225014.225032Published:23 April 1995Publication History 64citation960DownloadsMetricsTotal Citations64Total Downloads960Last 12 Months41Last 6 weeks12 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Aspirin (2000)

alicylates, in the form of willow bark, were used as an analgesic during the time of Hippocrates, and their antipyretic effects have been recognized for more than 200 years. 1Acetylsalicylic acid, or aspirin, was introduced in the late 1890s 2 and has been used to treat a variety of inflammatory conditions; however, the antiplatelet activity of this agent was not recognized until almost 70 years later. 3Recent advances in our understanding of the central role of platelets in the pathophysiology of cardiovascular disease have spurred in-depth investigations into the mechanisms of action of aspirin and the clinical utility of this agent in the treatment of common cardiovascular disorders.
Voxel-based analysis of PET amyloid ligand [ 11 C]PIB uptake in Alzheimer disease (2006)

Voxel-based analysis revealed widespread distribution of increased [(11)C]PIB uptake in Alzheimer disease (AD). These findings are in accordance with the distribution and phases of amyloid pathology in AD, previously documented in postmortem studies.