gebhart/patrepeval huggingface dataset:
Sequence-specific endonucleolytic cleavage and protection of mRNA in Xenopus and Drosophila. (1993)

Previously, a small region of the 3'-untranslated region (3' UTR) of Xlhbox2B mRNA was shown to be sufficient for sequence-specific endonucleolytic cleavage after injection into Xenopus oocytes. Here, we report an in vitro RNA degradation reaction that mimics the in vivo result accurately. The reaction also reveals that oocytes contain a sequence-specific RNA-binding factor that inhibits the endoribonuclease. These opposing activities may be regulated during Xenopus oogenesis. Partial purification shows that the endonuclease does not require translation or ribosomes and does not resemble previously described RNA processing complexes. We have isolated another Xenopus cDNA, Xoo1, that contains a long, repetitive destabilizing element similar to the one in Xlhbox2B. Based on a comparison of these natural destabilizing sequences and in vitro mutagenesis experiments, we find that a single destabilizing site is, at most, 19 bases in length and that the endonuclease and protective factor recognition sites may be overlapping subsets of this sequence. Finally, we show that Drosophila embryos contain similar activities, each of which can use Xenopus recognition sites. This level of conservation suggests an important biological function for this system of post-transcriptional regulation.
First record of chirping cisticola Cisticola pipiens from Burundi (1994)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Purification of a Chlamydia Trachomatis-Specific Antigen by Immunoadsorption with Monospecific Antibody (1977)

Abstract This study describes the isolation and partial characterization of a Chlamydia trachomatis specific antigen. A species-specific antigen of C. trachomatis (antigen-0.65) was identified by two-dimensional immunoelectrophoresis. Antiserum specific for antigen-0.65 was prepared in rabbits by immunizing with agarose-gel precipitates excised from two-dimensional immunoelectrophorograms. Purified γ-globulins from antigen-0.65 specific serum were coupled to the N-hydroxysuccinimide ester derivative of agarose which was then used for the immunoadsorbent purification of antigen-0.65 from Triton X-100 solubilized lymphogranuloma venereum (L2/434/Bu) organisms. The isolated antigen was immunochemically pure when tested against rabbit antiserum prepared to LGV-434 organisms by using rocket and two-dimensional immunoelectrophoresis. Antigenicity was destroyed by protease treatment and heating at 56°C for 30 min, but the antigen was stable to ribonuclease, deoxyribonuclease, periodate oxidation and pH extremes of 2.2 and 10.6. Polyacrylamide gel electrophoresis of purified antigen showed a major protein band with an apparent m.w. of 155,000.
A Convenient Synthesis of Phosphorines and Phospholidins by Lawesson′s Reagent and Microwave Irradiation. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
The use of IP-anycast for building efficient multicast trees (2003)

In this paper, we show that substantial improvement in multicast performance and reliability can be achieved by regarding a multicast group as a network region and using anycast to access it along the shortest path. We introduce the anycast-based tree (ABT), a novel architecture for building efficient shared multicast trees. ABT is a non-core tree; thus, it does not suffer from the traditional problems exhibited by core-based trees, such as traffic concentration or poor core placement. Moreover, ABT exhibits greater robustness and lower bandwidth consumption than other shared muiticast trees. Our simulation shows that ABT reduces traffic concentration by 60% and decreases average bandwidth consumption by 25%. In addition, the paper extends the core based tree multicast routing protocol with an ABT mode. The result is a new intra-domain protocol, called ACBT, that conserves the desirable features of the original protocol while reducing bandwidth consumption and alleviating traffic concentration.
T21/DP107, A Synthetic Leucine Zipper-Like Domain of the HIV-1 Envelope gp41, Attracts and Activates Human Phagocytes by Using G-Protein-Coupled Formyl Peptide Receptors (1999)

A leucine zipper-like domain, T21/DP107, located in the amino terminus of the ectodomain of gp41, is crucial to the formation of fusogenic configuration of the HIV-1 envelope protein gp41. We report that the synthetic T21/DP107 segment is a potent stimulant of migration and calcium mobilization in human monocytes and neutrophils. The activity of T21/DP107 on phagocytes was pertussis toxin-sensitive, suggesting this peptide uses Gi-coupled seven-transmembrane receptor(s). Since the bacterial chemotactic peptide fMLP partially desensitized the calcium-mobilizing activity of T21/DP107 in phagocytes, we postulated that T21/DP107 might preferentially use a lower affinity fMLP receptor. By using cells transfected to express cloned prototype chemotactic N-formyl peptide receptor (FPR) or its variant, FPR-like 1 (FPRL1), we demonstrate that T21/DP107 activates both receptors but has a much higher efficacy for FPRL1. In addition, T21/DP107 at nM concentrations induced migration of FPRL1-transfected human embryonic kidney 293 cells. In contrast, fMLP did not induce significant chemotaxis of the same cells at a concentration as high as 50 microM. Although a lipid metabolite, lipoxin A4, was a high-affinity ligand for FPRL1, it was not reported to induce Ca2+ mobilization or chemotaxis in FPRL1-transfected cells. Therefore, T21/DP107 is a first chemotactic peptide agonist identified thus far for FPRL1. Our results suggest that this peptide domain of the HIV-1 gp41 may have the potential to activate host innate immune response by interacting with FPR and FPRL1 on phagocytes.
Behavior classification and image processing for biorobot-rat interaction (2017)

In this paper, we focus on rat's behavior classification for biorobot-rat interaction. The automatic behavior analysis and classification of laboratory rats can effectively improve the adaptivity of interaction between rat-like robot and biological rats. Basic image processing algorithm as Labeling and Contour Finding were employed to extract feature parameters (body length, body area, body radius, rotational angle, and ellipticity) of rat's actions. These feature parameters are integrated as the input feature vector of CNN (Convolutional Neural Network) and SVM (Support Vector Machine) training system respectively. Preliminary experiment result shows that the grooming, rotating, crouching and rearing actions could be recognized with extremely high rate (more than 90%) by both CNN and SVM. Furthermore, CNN provides better recognition rate and SVM provides less computational cost.
DaliLite workbench for protein structure comparison (2000)

DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.
Silicon solar cells from transition metal doped Czochralski and web crystals (1976)

The influence of metallic impurities on solar cell characteristics has been examined to establish the cost sensitive purity versus performance trade-offs. Solar cells were fabricated on 2 to 4 ohm-cm p-type substrates obtained by Czochralski and dendritic web growth processes. Controlled amounts of metallic impurities were introduced into the melt during growth and included Fe, Cr, Mn, Ni, Cu, Ti, V, Zr, Mg, Zn, and Al. Impurity concentrations in the crystals were determined using emission and mass spectrographic techniques and in some cases by neutron activation analysis. The solar cells were characterized by means of a computer program to curve-fit measured voltage-current data. The principal effect of the added impurities is a degradation of lifetime and diffusion length.
Real-Time High Resolution Digital Video for Range and Training Applications (2001)

International Telemetering Conference Proceedings / October 22-25, 2001 / Riviera Hotel and Convention Center, Las Vegas, Nevada
Activity of the yeast MNN1 α-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases (1998)

A wide diversity of biological molecules are modified by the addition of sugar residues, and a large number of glycosyltransferases have been identified that are responsible for these reactions. Despite catalyzing closely related reactions, many of these transferases show little apparent sequence homology. By comparing two apparently unrelated families of yeast Golgi mannosyltransferases, a short motif containing two aspartate residues was observed that was conserved in both groups of proteins. Mutagenesis of one of the members of these families, the alpha-1, 3-mannosyltransferase Mnn1p, showed that altering either of these aspartates eliminates all enzymatic activity. These changes do not appear to affect the overall folding and assembly of Mnn1p. A similar aspartate-containing sequence was found to be conserved in a diverse range of other glycosyltransferase families, much more frequently than would be expected by chance, suggesting that it is a feature of the catalytic site, or an element of a structural fold, shared by many glycosyltransferases.
Atomic-Scale Electron-Beam Sculpting of Near-Defect-Free Graphene Nanostructures (2011)

In order to harvest the many promising properties of graphene in (electronic) applications, a technique is required to cut, shape, or sculpt the material on the nanoscale without inducing damage to its atomic structure, as this drastically influences the electronic properties of the nanostructure. Here, we reveal a temperature-dependent self-repair mechanism that allows near-damage-free atomic-scale sculpting of graphene using a focused electron beam. We demonstrate that by sculpting at temperatures above 600 °C, an intrinsic self-repair mechanism keeps the graphene in a single-crystalline state during cutting, even though the electron beam induces considerable damage. Self-repair is mediated by mobile carbon ad-atoms that constantly repair the defects caused by the electron beam. Our technique allows reproducible fabrication and simultaneous imaging of single-crystalline free-standing nanoribbons, nanotubes, nanopores, and single carbon chains.
Detection and characterization of carcinoma cells in the blood (1998)

A highly sensitive assay combining immunomagnetic enrichment with multiparameter flow cytometric and immunocytochemical analysis has been developed to detect, enumerate, and characterize carcinoma cells in the blood. The assay can detect one epithelial cell or less in 1 ml of blood. Peripheral blood (10-20 ml) from 30 patients with carcinoma of the breast, from 3 patients with prostate cancer, and from 13 controls was examined by flow cytometry for the presence of circulating epithelial cells defined as nucleic acid+, CD45(-), and cytokeratin+. Highly significant differences in the number of circulating epithelial cells were found between normal controls and patients with cancer including 17 with organ-confined disease. To determine whether the circulating epithelial cells in the cancer patients were neoplastic cells, cytospin preparations were made after immunomagnetic enrichment and were analyzed. Epithelial cells from patients with breast cancer generally stained with mAbs against cytokeratin and 3 of 5 for mucin-1. In contrast, no cells that stained for these antigens were observed in the blood from normal controls. The morphology of the stained cells was consistent with that of neoplastic cells. Of 8 patients with breast cancer followed for 1-10 months, there was a good correlation between changes in the level of tumor cells in the blood with both treatment with chemotherapy and clinical status. The present assay may be helpful in early detection, in monitoring disease, and in prognostication.
Etifoxine stimulates allopregnanolone synthesis in the spinal cord to produce analgesia in experimental mononeuropathy (2013)

This preclinical study shows that stimulating the production of endogenous analgesics such as 3αNS represents an interesting strategy to reduce neuropathic pain symptoms. Since EFX is already prescribed as an anxiolytic in several countries, a translation to the human clinic needs to be rapidly evaluated.
Design, Synthesis, and Biological Activity of Peptides which Release Growth Hormone in Vitro* (1981)

Experimental observations showed that the analogs [D-Trp2]- and [D-Phe2]methionine enkephalin amide were weakly active in releasing GH from rat pituitary in vitro. These observations were used to design more active GH-releasing factors. Conformational energy calculations were carried out, and energetically favored conformations of these polypeptides were found. Structural similarities as well as structural differences between active and inactive analogs were examined, and new sequences were predicted. Progressively more active analogs were designed, then synthesized, and tested. This cycle of steps was repeated, each time using structural and chemical concepts as design guides, until a series of very active analogs resulted. The most active analog to date, Tyr-D-Trp-Ala-Trp-D-Phe-NH2, was shown to release GH in vitro at 10-30 ng/ml medium, which is approximately 10(3) times more active than the two starting enkephalin-based analogs. From the structure-activity data, a mechanism for binding at the receptors is formulated, and a comparison is made between the structural relationships of the GH-releasing peptide analogs and the GH inhibitor, somatostatin.
The Neurologic Effects of Thiopental Therapy Following Experimental Cardiac Arrest in Cats (1982)

To define the utility of high-dose barbiturate therapy following an episode of complete global cerebral ischemia, we investigate the effects of 60 mg/kg of thiopental given to cats five minutes after resuscitation from 12, 14, or 16 min of electrically induced ventricular fibrillation (VF). All aspects of the arrest, resuscitation, with post-arrest care were carefully controlled, with the EEG becoming isoelectric 20-25 s after the onset mean resuscitation time of 2.5 +/- 0.2 (SEM) min. For any given duration of VF, there were no differences (control vs thiopental) in any pre- or post-arrest parameters (blood pressure, blood gases, electrolytes, etc.) A total of 68 resuscitated cats were entered into various treatment and control groups, and all but one group received 20-24 h of post-resuscitation paralysis, mechanical ventilation, and ICU support before being extubated. Cats received an additional six days of aggressive nursing care, and daily examinations were performed with the assignment of a neurologic deficit score (NDS) between 0 (normal) and (brain dead). Autopsies were performed to determine the cause of death in animals which died before the end of the seven-day observation period. The early post-arrest period was marked by the occurrence of repetitive, rhythmic bursts of high-frequency electroencephalographic (EEG) activity (? seizures) in 38 per cent of control animals (16/42, all arrest times combined). Ten of these animals died as a result of severe neurologic injuries. By contrast, only 12 per cent of treated cats (3/26) developed similar EEG patterns (P less than 0.05) and there were no neurologic deaths in the thiopental groups. The differences in the incidence of neurologic deaths (control vs. thiopental) was significant (P less than 0.02). The change in overall mortality did not quite reach significance (36 per cent vs. 21 per cent), and treatment had no effect on the incidence of deaths due to cardiovascular causes (e.g., myocardial infarctions). In spite of the effects on mortality, treatment had no effect on the neurologic function of survivors (assessed by NDS). These findings suggest that thiopental improved survival rates by suppressing an unusual post-arrest EEG pattern (? anticonvulsant effect), but had no additional cerebral protective effects.
Promoter analysis in living zebrafish embryos identifies a cis-acting motif required for neuronal expression of GATA-2 (1997)

We have used zebrafish embryos to dissect the promoter activity of a gene with a complex expression pattern during embryogenesis. GATA-2 is a transcription factor required for hematopoiesis and is dynamically expressed in hematopoietic tissues and in the central nervous system. Using constructs containing zebrafish GATA-2 genomic flanking sequences and the green fluorescent protein (GFP) reporter gene, we demonstrate that distinct regulatory domains are required for hematopoietic, enveloping layer (EVL), and neuronal expression of GATA-2. During gastrulation, GFP expression is confined to the ventral ectoderm and lateral mesoderm and is lacking in the dorsal shield. Cells derived from the regions expressing GFP give rise to hematopoietic progenitors, EVL cells, and neurons. Deletion analysis of the 7.3-kb GATA-2 promoter region revealed that a 1.1-kb DNA sequence is critical for expression of GATA-2 in neurons. Fine mapping revealed that a 31-bp region is required for neuron enhancer activity, and mutagenesis showed that the DNA motif CCCTCCT is essential for GATA-2 promoter activity in the central nervous system of zebrafish. Our use of zebrafish embryos can be exploited as a whole animal system for the dissection of any developmentally regulated vertebrate promoter.
Posttraumatic Stress Disorder in Migraine (2009)

The frequency of PTSD in migraineurs, whether episodic or chronic, is higher than the historically reported prevalence of PTSD in the general population. In addition, in the subset of migraineurs with depression, PTSD frequency is greater in CDH sufferers than in episodic migraineurs. Finally, the presence of PTSD is independently associated with greater headache-related disability in migraineurs.
New Trifluoromethylated Pyridazines by Reductive Cyclization of Vinyldiazomethanes Bearing a Carbonyl Group (1995)

The synthesis of new vinyldiazomethanes from ethyl 2-diazo-4,4,4-trifluoroacetoacetate and Wittig or Horner-Emmons-Wadsworth (HEW) reagents is described. Vinyldiazomethanes which have a double bond bearing a carbonyl group undergo reductive cyclization in the presence of triphenylphosphine providing a new route to the pyridazine chemistry.
Restored glial glutamate transporter EAAT2 function as a potential therapeutic approach for Alzheimer’s disease (2015)

Glutamatergic systems play a critical role in cognitive functions and are known to be defective in Alzheimer's disease (AD) patients. Previous literature has indicated that glial glutamate transporter EAAT2 plays an essential role in cognitive functions and that loss of EAAT2 protein is a common phenomenon observed in AD patients and animal models. In the current study, we investigated whether restored EAAT2 protein and function could benefit cognitive functions and pathology in APPSw,Ind mice, an animal model of AD. A transgenic mouse approach via crossing EAAT2 transgenic mice with APPSw,Ind. mice and a pharmacological approach using a novel EAAT2 translational activator, LDN/OSU-0212320, were conducted. Findings from both approaches demonstrated that restored EAAT2 protein function significantly improved cognitive functions, restored synaptic integrity, and reduced amyloid plaques. Importantly, the observed benefits were sustained one month after compound treatment cessation, suggesting that EAAT2 is a potential disease modifier with therapeutic potential for AD.
Two-dimensional Arrangement of Vertically Oriented Cylindrical Domains of Diblock Copolymers using Graphoepitaxy with Artificial Guiding Pattern Layout (2007)

In this paper, we demonstrate that a two-dimensional arrangement of vertical cylindrical domains of asymmetric poly(styrene-b-methyl methacrylate) (PSt-b-PMMA) is achieved by graphoepitaxy using a resist pattern as the guide for alignment. The key to success is the combination of the neutralization of a bottom surface and the introduction of a two-dimensional hydrophilic guiding pattern, which leads to vertical orientation and lateral arrangement of cylindrical domains, respectively.
Reactions in the diene series : condensationof isoprene with aniline and phenol (1955)

G. R. Clemo and N. D. Ghatge, J. Chem. Soc., 1955, 4347 DOI: 10.1039/JR9550004347
Association of clinical benefit rate (CBR) with survival: A pooled-analysis of metastatic breast cancer (MBC) trials submitted to the U.S. Food and Drug Administration (FDA). (2016)

e18091 Background: CBR is commonly used as one the secondary endpoints in many cancer clinical trials. There are no comprehensive analyses to demonstrate that CBR adds to the value of the conventional time-to-event efficacy endpoints of progression-free and overall survival (PFS and OS) in clinical trials, and to date, CBR data are not reported in the clinical studies section of the U.S. package inserts for products approved for the treatment of MBC. We conducted a pooled analysis of data from MBC trials submitted to the FDA to understand the association of CBR with PFS and OS. In this analysis, CBR is defined as the percentage of patients with MBC who have achieved complete response, partial response or stable disease ≥ 6 months. Methods: We identified 13 trials of experimental agents with 10,263 patients submitted for treatment of MBC in initial or supplemental New Drug or Biologics License Applications since 2005. Criteria for inclusion of the trials in this analysis were: randomized, active-controlled, multicenter. The estimated PFS hazard ratio (HR) and OS HR versus the estimated odds ratio (OR) of CBR on the log-scale was calculated. Weighted least square regression analyses (weight equal to the number of patients) were performed on log-transformed effects. Responder analysis was performed to compare PFS and OS between patients with and without CBR, irrespective of the treatment assignment. Hazard ratios and 95% confidence intervals of PFS and OS were calculated from stratified Cox regression models with study as a stratification factor. Results: In trial level analysis, there was a moderate association between PFS HR and CBR OR (R2 = 0.52) and little to no association between OS HR and CBR OR (R2 = 0.01). Based on the responder analysis, in the patient level, the CBR was positively associated with PFS (HR = 0.078, 95% CI: 0.073, 0.084) and OS (HR = 0.32, 95% CI: 0.301, 0.340). Conclusions: There was a moderate association between CBR and PFS. An association between CBR and OS was not established. There is insufficient evidence to add CBR in product labeling if PFS and/or OS are reported.
Regulated transcription of Clostridium difficile toxin genes (1998)

The Clostridium difficile toxA and toxB genes, encoding cytotoxic and enterotoxic proteins responsible for antibiotic-associated colitis and pseudomembranous colitis, were shown to be transcribed both from gene-specific promoters and from promoters of upstream genes. However, the gene-specific transcripts represented the majority of tox gene mRNAs. The 5' ends of these mRNAs were shown to correspond to DNA sequences that had promoter activity when fused to the Escherichia coli beta-glucuronidase (gusA) gene and introduced into C. perfringens. The appearance of tox mRNA in C. difficile was repressed during exponential growth phase but increased substantially as cells entered stationary phase. When glucose or other rapidly metabolizable sugars were present in the medium, the stationary phase-associated induction was inhibited, indicating that the toxin genes are subject to a form of catabolite repression. This glucose effect was general to many toxinogenic strains having varying levels of toxin production.