gebhart/patrepeval huggingface dataset:
The Molecular Evolution of terminal ear1, a Regulatory Gene in the Genus Zea (1999)

Nucleotide diversity in the terminal ear1 (te1) gene, a regulatory locus hypothesized to be involved in the morphological evolution of maize (Zea mays ssp. mays), was investigated for evidence of past selection. Nucleotide polymorphism in a 1.4-kb region of te1 was analyzed for a sample of 26 sequences isolated from 12 maize lines, five populations of the maize progenitor, Z. mays ssp. parviglumis, six other Zea populations, and two Tripsacum species. Although nucleotide diversity in te1 in maize is reduced relative to ssp. parviglumis, phylogenetic and statistical analyses of the pattern of polymorphism among these sequences provided no evidence of past selection, indicating that the region of the gene studied was probably not involved in maize evolution. The level of reduction in genetic diversity in te1 in maize relative to its progenitor is comparable to that found in previous reports for isozymes and other neutrally evolving maize genes and is consistent with a genome-wide reduction of genetic diversity resulting from a domestication bottleneck. An estimate of the age (1.2-1.4 million yr) of the maize gene pool based on te1 is roughly consistent with previous estimates based on other neutral genes, but may be biased by the apparently slow synonymous substitution rate at te1.
The three major types of CRISPR‐Cas systems function independently in CRISPR RNA biogenesis in Streptococcus thermophilus (2014)

CRISPR-Cas systems are small RNA-based immune systems that protect prokaryotes from invaders such as viruses and plasmids. We have investigated the features and biogenesis of the CRISPR (cr)RNAs in Streptococcus thermophilus (Sth) strain DGCC7710, which possesses four different CRISPR-Cas systems including representatives from the three major types of CRISPR-Cas systems. Our results indicate that the crRNAs from each CRISPR locus are specifically processed into divergent crRNA species by Cas proteins (and non-coding RNAs) associated with the respective locus. We find that the Csm Type III-A and Cse Type I-E crRNAs are specifically processed by Cas6 and Cse3 (Cas6e), respectively, and retain an 8-nucleotide CRISPR repeat sequence tag 5' of the invader-targeting sequence. The Cse Type I-E crRNAs also retain a 21-nucleotide 3' repeat tag. The crRNAs from the two Csn Type II-A systems in Sth consist of a 5'-truncated targeting sequence and a 3' tag; however, these are distinct in size between the two. Moreover, the Csn1 (Cas9) protein associated with one Csn locus functions specifically in the production of crRNAs from that locus. Our findings indicate that multiple CRISPR-Cas systems can function independently in crRNA biogenesis within a given organism - an important consideration in engineering coexisting CRISPR-Cas pathways.
A study of nitrogen oxide containing vasodilators on guinea pig trachea, a nonvascular smooth muscle (1985)

1. Sodium nitroprusside, sodium nitrite and papaverine produced concentration-dependent relaxation of guinea-pig isolated tracheal chain preparations contracted with KCI (20 mM), but had no effect on the resting tone of the preparation.

2. Methemoglobin and methylene blue known inhibitors of cGMP accumulation rightward shifts of concentration curves of sodium nitroprusside and sodium nitrite.

3. Neither methemoglobin nor methylene blue modified the papaverine-induced relaxation.

4. It is concluded that sodium nitroprusside and sodium nitrite induced relaxation of the guinea-pig trachea may be partly due to their cGMP elevating action. Papaverine induced relaxation seems to be totally independent of cGMP action.
Killing cancer cells by poly‐drug elevation of ceramide levels (2001)

Many papers have shown that sphingolipids control the balance in cells between growth and proliferation, and cell death by apoptosis. Sphingosine-1-phosphate (Sph1P) and glucosylceramide (GlcCer) induce proliferation processes, and ceramide (Cer), a metabolic intermediate between the two, induces apoptosis. In cancers, the balance seems to have come undone and it should be possible to kill the cells by enhancing the processes that lead to ceramide accumulation. The two control systems are intertwined, modulated by a variety of agents affecting the activities of the enzymes in Cer-GlcCer-Sph1P interdependence. It is proposed that successful cancer chemotherapy requires the use of many agents to elevate ceramide levels adequately. This review updates current knowledge of sphingolipid metabolism and some of the evidence showing that ceramide plays a causal role in apoptosis induction, as well as a chemotherapeutic agent.
Surgical Resection of Hepatocellular Carcinoma (1996)

BACKGROUND: Surgical management of hepatocellular carcinoma is challenging. Advances in patient selection and operative techniques are taking place in various parts of the world. METHODS: The literature on diagnosis, evaluation, and surgical treatment of hepatocellular carcinoma is reviewed and combined with the extensive clinical experience of the authors. RESULTS: While alpha-fetoprotein levels often are elevated in patients with large hepatocellular tumors, a combination of hepatic arteriography and Lipiodol computed tomography is the most sensitive imaging approach. An indocyanine green retention of more than 14% at 15 minutes predicts a poor outcome from surgery. Intraoperative ultrasound and ultrasonic dissector assist surgery. One-, three-, and five-year survival rates of 68%, 44%, and 35%, respectively, have been reported. CONCLUSIONS: Methods to diagnose and assess the suitability of patients with hepatocellular carcinoma for surgical resection are now available, and operative and postoperative care has improved. Surgery remains the "gold standard" to which other treatments can be compared.
Blocking the tunnel: engineering of Candida rugosa lipase mutants with short chain length specificity (2002)

The molecular basis of chain length specificity of Candida rugosa lipase 1 was investigated by molecular modeling and site-directed mutagenesis. The synthetic lip1 gene and the lipase mutants were expressed in Pichia pastoris and assayed for their chain length specificity in single substrate assays using triglycerides as well as in a competitive substrate assay using a randomized oil. Mutation of amino acids at different locations inside the tunnel (P246F, L413F, L410W, L410F/S300E, L410F/S365L) resulted in mutants with a different chain length specificity. Mutants P246F and L413F have a strong preference for short chain lengths whereas substrates longer than C10 are hardly hydrolyzed. Increasing the bulkiness of the amino acid at position 410 led to mutants that show a strong discrimination of chain lengths longer than C14. The results obtained can be explained by a simple mechanical model: the activity for a fatty acid sharply decreases as it becomes long enough to reach the mutated site. In contrast, a mutation at the entrance of the tunnel (L304F) has a strong impact on C4 and C6 substrates. This mutant is nevertheless capable of hydrolyzing chain lengths longer than C8.
131I-Tositumomab Radioimmunotherapy: Initial Tumor Dose–Response Results Using 3-Dimensional Dosimetry Including Radiobiologic Modeling (2010)

Improved dose-response correlations were demonstrated when EUD incorporating the cold antibody effect was used instead of the conventionally used mean tumor-absorbed dose. This work demonstrates the importance of 3D calculation and radiobiologic modeling when estimating absorbed dose for correlation with outcome.
Equilibrium Phase Behavior of a Continuous-Space Microphase Former (2016)

Periodic microphases universally emerge in systems for which short-range interparticle attraction is frustrated by long-range repulsion. The morphological richness of these phases makes them desirable material targets, but our relatively coarse understanding of even simple models hinders controlling their assembly. We report here the solution of the equilibrium phase behavior of a microscopic microphase former through specialized Monte Carlo simulations. The results for cluster crystal, cylindrical, double gyroid, and lamellar ordering qualitatively agree with a Landau-type free energy description and reveal the nontrivial interplay between cluster, gel, and microphase formation.
Pore distribution changes of calcium‐based sorbents reacting with sulfur dioxide (1987)

Abstract Changes in the pore structure of calcium oxide sorbents derived from calcium carbonate (c‐CaO) and calcium hydroxide (h‐CaO) reacting with sulfur dioxide are determined. Results show that the pore shape of c‐CaO approximates a cylinder while that of h‐CaO appears to be slit‐ or platelike. The pore volume of c‐CaO is located in much smaller pores than that of h‐CaO when compared on the basis of an equivalent pore shape model. The effect of sintering was to reduce surface area through coalescence of smaller pores, while only minor effects were observed upon pore volume and conversion from calcium oxide to calcium sulfate. Both sorbents expand to allow greater reaction than is possible given the initial porosity and formation of a larger volume product. The h‐CaO reacts to higher levels of conversion than the c‐CaO because the pore shape of the h‐CaO allows for greater particle expansion and, therefore, reaction beyond the limits of the initial porosity.
Automatic Detection of Region of Interest Based on Object Tracking in Neurosurgical Video (2005)

Automatic detection of region of interest (ROIs) in a complex image or video, such as an angiogram or endoscopic neurosurgery video, is a critical task in many medical image and video processing applications. In this paper, we present a new method that addresses several challenges in automatic detection of ROI of neurosurgical video for ROI coding which is used for neurophysiological intraoperative monitoring (IOM) system. This method is based on an object tracking technique with multivariate density estimation theory, combined with the shape information of the object. By defining the ROIs for neurosurgical video, this method produces a smooth and convex emphasis region within which surgical procedures are performed. A large bandwidth budget is assigned within the ROI to archive high-fidelity Internet transmission. Outside the ROI, a small bandwidth budget is allocated to efficiently utilize the bandwidth resource. We believe this method also can be used to image-guiduance surgery (IGS) systems to track the positions of surgical instruments in the physical space occupied by the patient after some improvement.
The Mitochondrial RNA Ligase from Leishmania tarentolae Can Join RNA Molecules Bridged by a Complementary RNA (1999)

A biochemical characterization was performed with a partially purified RNA ligase from isolated mitochondria of Leishmania tarentolae. This ligase has a K(m) of 25 +/- 0.75 nM and a V(max) of 1.0 x 10(-4) +/- 2.4 x 10(-4) nmol/min when ligating a nicked double-stranded RNA substrate. Ligation was negatively affected by a gap between the donor and acceptor nucleotides. The catalytic efficiency of the circularization of a single-stranded substrate was 5-fold less than that of the ligation of a nicked substrate. These properties of the mitochondrial RNA ligase are consistent with an expected in vivo role in the process of uridine insertion/deletion RNA editing, in which the mRNA cleavage fragments are bridged by a cognate guide RNA.
Synergismus von Interferon β-1b und Fumarsäure? (2009)

Synergistische Effekte von Interferon β-1b und Fumarsäure könnten im vorliegenden Fall einer 46-jährigen Patientin mit sekundär-progredienter Multipler Sklerose (MS) und überlagernden Schüben vorliegen. Aufgrund eines Erythema nodosum nimmt die Patientin seit 8 Monaten zusätzlich zur vorbestehenden Interferon-β-1b-Medikation niedrig dosiert Dimethylfumarat (Fumaderm initial®) (90 mg / d) ein. Unter der Kombinationstherapie kam es bei zuvor hoher überlagernder Schubaktivität – 5 Schübe in den letzten 3 Jahren – bislang zu keinem weiteren Schub. Auch eine weitere Behinderungsprogredienz war nicht zu beobachten (EDSS konstant 5,5). Da die von der Patientin eingenommene Fumarsäuredosis deutlich unter den in vorausgegangenen klinischen Studien als wirksam erachteten Dosierungen liegt, muss ein synergistischer Effekt mit der vorbestehenden Interferon-β-1b-Therapie diskutiert werden.
Long-Term Treatment of Osteopetrosis with Recombinant Human Interferon Gamma (1995)

Long-term therapy with interferon gamma in patients with osteopetrosis increases bone resorption and hematopoiesis and improves leukocyte function.
Technique and Results of Linear Ablation at the Mitral Isthmus (2004)

Catheter ablation of the mitral isthmus results consistently in demonstrable conduction block and is associated with a high cure rate for paroxysmal AF.
Roles of the heat shock transcription factors in regulation of the heat shock response and beyond (2001)

The heat shock response, characterized by increased expression of heat shock proteins (Hsps) is induced by exposure of cells and tissues to extreme conditions that cause acute or chronic stress. Hsps function as molecular chaperones in regulating cellular homeostasis and promoting survival. If the stress is too severe, a signal that leads to programmed cell death, apoptosis, is activated, thereby providing a finely tuned balance between survival and death. In addition to extracellular stimuli, several nonstressful conditions induce Hsps during normal cellular growth and development. The enhanced heat shock gene expression in response to various stimuli is regulated by heat shock transcription factors (HSFs). After the discovery of the family of HSFs (i.e., murine and human HSF1, 2, and 4 and a unique avian HSF3), the functional relevance of distinct HSFs is now emerging. HSF1, an HSF prototype, and HSF3 are responsible for heat-induced Hsp expression, whereas HSF2 is refractory to classical stressors. HSF4 is expressed in a tissue-specific manner; similar to HSF1 and HSF2, alternatively spliced isoforms add further complexity to its regulation. Recently developed powerful genetic models have provided evidence for both cooperative and specific functions of HSFs that expand beyond the heat shock response. Certain specialized functions of HSFs may even include regulation of novel target genes in response to distinct stimuli.
Iterative fractionation of recycling receptors from lysosomally destined ligands in an early sorting endosome. (1989)

To study the fusion and separation of endocytic compartments, we have used digital image analysis to quantify the accumulation of fluorescent ligands in endosomes during continuous endocytosis for periods of 1-20 min. Fluorescently labeled transferrin (Tf) and low density lipoproteins (LDL) were used as markers of recycling receptors and lysosomally directed ligands respectively. By measuring the intensity of individual endosomes, we found that the amount of LDL per endosome increases 30-40-fold between 1 and 10 min and then plateaus. In contrast, the amount of Tf per endosome reaches a steady state within 2 min at a level that is only three to four times that at 1 min. We used pulse-chase double label methods to demonstrate that Tf cycles through the compartment in which the LDL accumulates. When both Tf and LDL are added to cells simultaneously for 2 min, nearly all endosomes contain both labels. With 2-4 min further incubation in the absence of external ligands, LDL-containing compartments become depleted of Tf as Tf is directed to para-Golgi recycling endosomes. However, if Tf is added to the medium 2-4 min after a pulse with LDL, most of the LDL-containing endosomes become labeled with Tf. The data indicate that at least 30-40 endocytic vesicles containing both Tf and LDL fuse with an endosomal compartment over a period of 5-10 min. LDL accumulates within this compartment and Tf is simultaneously removed. Simple mathematical models suggest that this type of iterative fractionation can lead to very high efficiency sorting.
Human immunodeficiency virus type 1 gp120 C5 region mimics the HLA class I α1 peptide‐binding domain (1993)

Molecular mimicry of major histocompatibility (MHC) antigens by viral glycoproteins has been suggested as one of the possible mechanisms of induction of an autoimmune response by human immunodeficiency viruses. A monoclonal antibody (M38) was previously shown to bind to both human immunodeficiency virus type 1 (HIV-1) gp120 and beta-2 microglobulin-free HLA class I heavy chains encoded by an HLA C allele. Using HLA C recombinant proteins and synthetic peptides, the M38 class I binding site was mapped to a stretch of 44 amino acids of the alpha 1 domain. The amino acid residues recognized are clustered in two non-contiguous regions at positions 66-69 (KYKR) and 79-82 (RKLR) shared by almost all HLA C alleles. On HIV-1 gp120, M38 binds to two non-contiguous sequences (KYK and KAKR) at positions 490-492 and 505-508 located at the edges of a large hydrophobic region that is apparently involved in binding the transmembrane glycoprotein gp41. The C-terminal gp120 M38-reactive region (KAKR) lies within the immunodominant sequence APTKAKRRVVQREKR, against which the majority of HIV-infected individuals produce antibodies. The results indicate that a functionally important region of HIV-1 gp120 shares similar amino acid sequence motifs with the antigen recognition site of most HLA class I C alleles. The molecular mimicry may be the basis for autoimmune responses in HIV infection.
The YadA Protein ofYersinia pseudotuberculosisMediates High-Efficiency Uptake into Human Cells under Environmental Conditions in Which Invasin Is Repressed (2002)

The YadA protein is a major adhesin of Yersinia pseudotuberculosis that promotes tight adhesion to mammalian cells by binding to extracellular matrix proteins. In this study, we first addressed the possibility of competitive interference of YadA and the major invasive factor invasin and found that expression of YadA in the presence of invasin affected neither the export nor the function of invasin in the outer membrane. Furthermore, expression of YadA promoted both bacterial adhesion and high-efficiency invasion entirely independently of invasin. Antibodies against fibronectin and beta(1) integrins blocked invasion, indicating that invasion occurs via extracellular-matrix-dependent bridging between YadA and the host cell beta(1) integrin receptors. Inhibitor studies also demonstrated that tyrosine and Ser/Thr kinases, as well as phosphatidylinositol 3-kinase, are involved in the uptake process. Further expression studies revealed that yadA is regulated in response to several environmental parameters, including temperature, ion and nutrient concentrations, and the bacterial growth phase. In complex medium, YadA production was generally repressed but could be induced by addition of Mg(2+). Maximal expression of yadA was obtained in exponential-phase cells grown in minimal medium at 37 degrees C, conditions under which the invasin gene is repressed. These results suggest that YadA of Y. pseudotuberculosis constitutes another independent high-level uptake pathway that might complement other cell entry mechanisms (e.g., invasin) at certain sites or stages during the infection process.
A Novel Phorbol Ester from Excoecaria agallocha (1995)

The novel phorbol ester 12-deoxyphorbol 13-(3E,5E-decadienoate) [1] was isolated as the anti-HIV principle of Excoecaria agallocha leaves and stems collected in northwest Australia. The structure was determined by spectral means. Compound 1 was also a potent displacer of [3H]-phorbol dibutyrate from rat brain membranes.
Kinetics of association of serine proteinases with native and oxidized alpha-1-proteinase inhibitor and alpha-1-antichymotrypsin. (1980)

The association rate constants for the interaction of alpha-1-proteinase inhibitor, oxidized alpha-1-proteinase inhibitor, and alpha-1-antichymotrypsin with several mammalian serine proteinases have been determined. The results indicate that leukocyte elastase reacts more rapidly with alpha-1-proteinase inhibitor than any other proteinase tested, while leukocyte cathepsin G shows the strongest association with alpha-1-antichymotrypsin. Oxidation of the critical methionine residue of alpha-1-proteinase inhibitor reduces the association with leukocyte elastase by a factor of more than 2000 and also lowers the association with all of the other enzymes tested with the exception of chymotrypsin. Significantly, oxidation completely abolishes any interaction of alpha-1-proteinase inhibitor with porcine elastase, human plasmin or human thrombin. These data support previous results (Johnson, D., and Travis, J. (1979) J. Biol. Chem. 254, 4022-4026) which indicated that oxidation of human alpha-1-proteinase inhibitor in vivo could reduce the effectiveness of this inhibitor in controlling proteolysis. In the lung, in particular, oxidizing agents of both chemical and biological sources could, indirectly, augment elastolysis in this tissue, resulting in the development of pulmonary emphysema.
Staining of Tissue Sections for Electron Microscopy with Heavy Metals (1958)

Heavy metals may be incorporated from solution into tissue sections for electron microscopy. The resulting increase in density of the tissue provides greatly enhanced contrast with minimal distortion. Relative densities of various structures are found to depend on the heavy metal ions present and on the conditions of staining. Certain hitherto unobserved details are revealed and some sort of specificity exists, although the factors involved are not yet understood.
MIMIC: Using passive network measurements to estimate HTTP-based adaptive video QoE metrics (2017)

HTTP-based Adaptive Streaming (HAS) has seen a major growth in the cellular networks. As a key application and network demand driver, user-perceived Quality of Experience (QoE) of video streaming contributes to the overall user satisfaction. Therefore, it becomes critical for the cellular network operators to understand the QoE of video streams. It can help with long-term network planning and provisioning and QoE-aware traffic management. However, tracking QoE is challenging as network operators do not have direct access to the video streaming apps, user devices or servers. In this paper, we provide a methodology that uses passive network measurements of unencrypted HAS video streams to estimate three key video QoE metrics - average bitrate, re-buffering ratio and bitrate switches. Our approach relies on the semantics of HAS to model a video session on the client. We first develop and validate our methodology through controlled experiments in the lab. Then, we conduct a large-scale validation of our approach using network data from a major cellular operator and ground truth QoE metrics from a large video service. We accurately predict the value of average bitrate within a relative error of 10% for 70%-90% of video sessions and re-buffering ratio within 1 percentage point for 65-90% of sessions. We further quantify the network overhead due to video chunk replacement and observe that a significant number of sessions have a high overhead of 20% or more. Finally, we highlight several challenges with video QoE metrics estimation in a large-scale monitoring system.
ChemInform Abstract: The Multi‐Component Reactions and Their Libraries ‐ Progress in Organic Chemistry and Applications (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.