gebhart/patrepeval huggingface dataset:
Characterization of an 80-Kilodalton Bull Sperm Protein Identified as PH-201 (2001)

This paper presents the partial characterization and the identification of an 80-kDa protein detected in bull spermatozoa using a monoclonal antibody directed against a 16-amino acid long peptide from the N-terminal domain of the protooncogene p60(src) from the Rous Sarcoma Virus When subjected to two-dimensional electrophoresis, this 80-kDa protein migrated as several isoforms, with an isoelectric point ranging from 7.4 to 8.2. Amino acid sequence analysis of a peptide obtained following trypsin digestion of the bull sperm protein showed homology to the PH-20/hyaluronidase precursor sperm protein. As for PH-20, this bull sperm 80-kDa protein is located at the plasma membrane surface in the postacrosomal region of the head. An increased immunolabeling in the anterior head region of fixed/permeabilized spermatozoa was observed when these cells were incubated under capacitating conditions, whereas most sperm cells challenged with the calcium ionophore A23187 to acrosome react lost their labeling almost completely. As for the PH-20 protein, the 80-kDa bull sperm protein possesses a hyaluronidase activity that is higher at pH 7.0 than at pH 4.0 in an in-gel assay. Unlike what has been observed in the guinea pig, mouse, and human PH-20, this 80-kDa protein was not released from the surface of bull spermatozoa by treatment with phosphatidylinositol-specific phospholipase C or with trypsin. However, this protein was not sedimented by a 100,000 x g centrifugation after nitrogen cavitation, which suggests that the 80-kDa protein is loosely attached to the sperm membrane by a yet-unknown mechanism. These results suggest that the 80-kDa bull sperm protein shares many homologies with the sperm PH-20 protein reported in the literature and, most likely, is the bull sperm homologue of the PH-20.
Highly Conserved Regions of Influenza A Virus Polymerase Gene Segments Are Critical for Efficient Viral RNA Packaging (2007)

The genome of the influenza A virus is composed of eight different segments of negative-sense RNA. These eight segments are incorporated into budding virions in an equimolar ratio through a mechanism that is not fully understood. Two different models have been proposed for packaging the viral ribonucleoproteins into newly assembling virus particles: the random-incorporation model and the selective-incorporation model. In the last few years, increasing evidence from many different laboratories that supports the selective-incorporation model has been accumulated. In particular, different groups have shown that some large viral RNA regions within the coding sequences at both the 5' and 3' ends of almost every segment are sufficient for packaging foreign RNA sequences. If the packaging regions are crucial for the viability of the virus, we would expect them to be conserved. Using large-scale analysis of influenza A virus sequences, we developed a method of identifying conserved RNA regions whose conservation cannot be explained by population structure or amino acid conservation. Interestingly, the conserved sequences are located within the regions identified as important for efficient packaging. By utilizing influenza virus reverse genetics, we have rescued mutant viruses containing synonymous mutations within these highly conserved regions. Packaging of viral RNAs in these viruses was analyzed by reverse transcription using a universal primer and quantitative PCR for individual segments. Employing this approach, we have identified regions in the polymerase gene segments that, if mutated, result in reductions of more than 90% in the packaging of that particular polymerase viral RNA. Reductions in the level of packaging of a polymerase viral RNA frequently resulted in reductions of other viral RNAs as well, and the results form a pattern of hierarchy of segment interactions. This work provides further evidence for a selective packaging mechanism for influenza A viruses, demonstrating that these highly conserved regions are important for efficient packaging.
At what level of collective equipoise does a clinical trial become ethical? (1991)

It has often been argued that if a clinician cannot decide which of two treatments to offer, a trial may be ethical, but it is unethical if she/he has a preference. Since individual clinicians usually have a preference, most trials could be judged unethical according to this line of argument. A recent important article in the New England Journal of Medicine argued that individual preferences are not as important as the collective uncertainty of informed clinicians. If clinicians are equally divided, there is a state of collective equipoise and a trial is ethical. However, clinicians will seldom be exactly equally divided. We conducted an ethometric study to find out how much collective equipoise can be disturbed before the potential subjects in a trial think that it is unethical. Half of our subjects perceived a trial as unethical when equipoise was disturbed beyond 70:30. In other words, when 70 per cent of experts favour one treatment, 50 per cent of subjects would prefer that treatment to be administered rather than subjected to critical assessment. When equipoise is disturbed beyond 80:20, less than 3 per cent of subjects would consider human trials morally justifiable.
Cancer Gene Therapy (2003)

Cancer gene therapy is the transfer of genetic material to the cells of an individual with the goal of eradicating cancer cells, both in the primary tumor and metastases. Cancer gene therapy strategies exploit our expanding knowledge of the genetic basis of cancer, thereby allowing rationally targeted interventions at the molecular level. The successful implementation of cancer gene therapy in the clinic awaits the development of vectors capable of specific and efficient gene delivery to cancer cells. The first clinical applications of cancer gene therapy are likely to be in combination with conventional therapies, such as radiotherapy and immunotherapy.
Evaluation of Biodistribution and Safety of Adenovirus Vectors Containing Group B Fibers After Intravenous Injection into Baboons (2005)

Vectors containing group B adenovirus (Ad) fibers are able to efficiently transduce gene therapy targets that are refractory to infection with standard Ad serotype 5 (Ad5) vectors, including malignant tumor cells, hematopoietic stem cells, and dendritic cells. Preliminary studies in mice indicate that, after intravenous injection, B-group fiber-containing Ads do not efficiently transduce most organs and cause less acute toxicity than Ad5 vectors. However, biodistribution and safety studies in mice are of limited value because the mouse analog of the B-group Ad receptor, CD46, is expressed only in the testis, whereas in humans, CD46 is expressed on all nucleated cells. Unlike mice, baboons have CD46 expression patterns and levels that closely mimic those in humans. We conducted a biodistribution and toxicity study of group B Ad fiber-containing vectors in baboons. Animals received phosphate-buffered saline, Ad5-bGal (a first-generation Ad5 vector), or B-group fiber-containing Ads (Ad5/35-bGal and Ad5/11-bGal) at a dose of 2 x 10(12) VP/kg, and vector biodistribution and safety was analyzed over 3 days. The amount of Ad5/35-bGal and Ad5/11-bGal vector genomes was in most tissues one to three orders of magnitude below that of Ad5. Significant Ad5/35- and Ad5/11-mediated transgene (beta-galactosidase) expression was seen only in the marginal zone of splenic follicles. Compared with the animal that received Ad5-bGal, all animals injected with B-group fiber-containing Ad vectors had lower elevations in serum proinflammatory cytokine levels. Gross and histopathology were normal in animals that received B-group Ad fiber-containing Ads, in contrast to the Ad5-infused animal, which showed widespread endothelial damage and inflammation. In a further study, a chimeric Ad5/35 vector carrying proapoptotic TRAIL and Ad E1A genes under tumor-specific regulation was well tolerated in a 30-day toxicity study. No major clinical, serologic, or pathologic abnormalities were noticed in this animal.
Lipid Composition of Commercial Bakers’ Yeasts Having Different Freeze-tolerance in Frozen Dough (1996)

The lipid composition of some commercial bakers' yeasts having different freeze-sensitivity in frozen dough was investigated to clarify the correlation between their lipid composition and freeze-tolerance. The total lipid content including neutral lipid, free fatty acid, sterol, and phospholipid ranged between 23.0 to 32.2 mg/100 mg protein of the yeasts tested. Phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and phosphatidylserine were the main phospholipids found in all yeast strains, but no distinct difference in these components between freeze-tolerant and freeze-sensitive strains was observed. Palmitoleic (C16:1), oleic (C18:1), palmitic (16:0), and stearic (C18:0) acids were the major fatty acids present in total lipid and phospholipid, and unsaturation indices of fatty acid in these lipid components were almost equal by the strains. The molar ratios of sterol to phospholipid of freeze-sensitive strains were higher than those of freeze-tolerant strains. The difference in the sterol-phospholipid ratio that influences the fluidity of plasma membranes in yeast cells was supposed to reflect the difference in freeze-sensitivity of bakers' yeast.
A Silicon-Strip Detector for Photon-Counting Spectral CT: Energy Resolution From 40 keV to 120 keV (2014)

We are developing a segmented silicon-strip detector for spectral computed tomography. The detector operates in photon-counting mode and allows pulse-height discrimination with 8 adjustable energy bins. In this work, we determine the energy resolution of a detector module using monoenergetic x-rays from 40 keV to 120 keV, provided at the European Synchrotron Radiation Facility, Grenoble. For each incident x-ray energy, pulse height spectra at different input photon fluxes are obtained. We investigate changes of the energy resolution due to charge sharing between pixels and pulse pileup. The different incident energies are used to channel-wise calibrate the pulse-height response in terms of signal gain and offset and to probe the homogeneity of the detector module. The detector shows a linear pulse-height response in the energy range from 40 keV to 120 keV. The gain variation among the channels is below 4%, whereas the variation of the offsets is on the order of 1 keV. We find an absolute energy resolution ( σE) that degrades from 1.5 keV to 1.9 keV with increasing x-ray energy from 40 keV to 100 keV. With increasing input count rate, σE degrades by approximately 4 ·10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> keV Mcps <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , which is, within error bars, the same for the different energies. The effect of charge sharing on the width of the response peak is found to be negligible.
Where Is the Anterior Temporal Lobe and What Does It Do? (2013)

The anterior temporal lobe (ATL) is thought to be critical for semantic memory–our knowledge of objects, people, words, and facts. However, there is substantial disagreement over the precise role of the ATL in semantic memory, and there is considerable variability in the anatomic findings that
Role of CD1d-Restricted NKT Cells in Microbial Immunity (2003)

The discovery that T cells recognize lipid and glycolipid molecules presented by CD1 proteins has greatly expanded the number of potential microbial antigens targeted by the immune system following infection. The ability of CD1d-restricted NKT cells to activate innate and adaptive immune responses has led to the idea that these cells can modulate immunity to infectious agents. In addition, CD1d-restricted NKT cells may directly contribute to host resistance as they express a variety of effector molecules that could mediate an antimicrobial effect. Although much has been learned about CD1d-restricted NKT cells through the use of the synthetic antigen α-galactosylceramide (αGalCer), the field has been hampered by the paucity of information about the physiological self and microbial lipid antigens that can be presented by CD1d. Here we review the literature stating that CD1d-restricted NKT cells contribute to host defense against microbial pathogens.
762. Successful Use of Out-of-Frame Exon 2 Skipping Induces IRES-Driven Expression of the N-Truncated Dystrophin Isoform: Promising Approach for Treating Other 5’ Dystrophin Mutations (2014)

Nicolas Wein,1 Adeline Vulin,1 Maria S. Falzanaro,2 Cristina Al-Khalili Szigyarto,3 Baijayanta Maiti,4 Andrew Findlay,1 Kristin N. Heller,1 Mathias Uhlen,3 Baskar Bakthavachalu,5 Sonia Messina,6 Giuseppe L. Vita,6 Francesca Gualandi,2 Steve D. Wilton,7 Lin Yang,8 Diane M. Dunn,9 Daniel Schoenberg,5 Robert B. Weiss,9 Michael T. Howard,9 Alessandra Ferlini,2 Kevin M. Flanigan.1
Interleukin-12- and Gamma Interferon-Dependent Protection against Malaria Conferred by CpG Oligodeoxynucleotide in Mice (2001)

ABSTRACT Unmethylated CpG dinucleotides in bacterial DNA or synthetic oligodeoxynucleotides (ODNs) cause B-cell proliferation and immunoglobulin secretion, monocyte cytokine secretion, and activation of natural killer (NK) cell lytic activity and gamma interferon (IFN-γ) secretion in vivo and in vitro. The potent Th1-like immune activation by CpG ODNs suggests a possible utility for enhancing innate immunity against infectious pathogens. We therefore investigated whether the innate immune response could protect against malaria. Treatment of mice with CpG ODN 1826 (TCCATGA CG TTCCTGA CG TT, with the CpG dinucleotides underlined) or 1585 (ggGGTCAA CG TTGAgggggG, with g representing diester linkages and phosphorothioate linkages being to the right of lowercase letters) in the absence of antigen 1 to 2 days prior to challenge with Plasmodium yoelii sporozoites conferred sterile protection against infection. A higher level of protection was consistently induced by CpG ODN 1826 compared with CpG ODN 1585. The protective effects of both CpG ODNs were dependent on interleukin-12, as well as IFN-γ. Moreover, CD8 + T cells (but not CD4 + T cells), NK cells, and nitric oxide were implicated in the CpG ODN 1585-induced protection. These data establish that the protective mechanism induced by administration of CpG ODN 1585 in the absence of parasite antigen is similar in nature to the mechanism induced by immunization with radiation-attenuated P. yoelii sporozoites or with plasmid DNA encoding preerythrocytic-stage P. yoelii antigens. We were unable to confirm whether CD8 + T cells, NK cells, or nitric oxide were required for the CpG ODN 1826-induced protection, but this may reflect differences in the potency of the ODNs rather than a real difference in the mechanism of action of the two ODNs. This is the first report that stimulation of the innate immune system by CpG immunostimulatory motifs can confer sterile protection against malaria.
Sutterella wadsworthensis gen. nov., sp. nov., Bile-Resistant Microaerophilic Campylobacter gracilis-Like Clinical Isolates (1996)

Campylobacter gracilis (formerly Bacteroides gracilis) is an asaccharolytic, nitrate-positive, urease-negative organism that requires formate and fumarate or hydrogen as a growth additive and may pit agar media. Clinical isolates that were obtained primarily from appendiceal and peritoneal fluid specimens and initially were identified in our laboratory as B. gracilis were later found to include "unusual" strains that could be distinguished by biochemical and genetic criteria. These unusual C. gracilis strains were bile resistant, could not reduce tetrazolium chloride under aerobic conditions if formate and fumarate were added to the medium, and could grow in the presence of 2 or 6% oxygen if no blood was added to the medium. C. gracilis, other campylobacters, and the unusual strains produced distinctive dehydrogenase patterns when gels were incubated anaerobically. A cellular fatty acid analysis revealed that the cluster formed by the unusual organisms was distinct from the (separate) clusters formed by C. gracilis, Bacteroides ureolyticus, and other Campylobacter species. 16S rRNA sequence data indicated that these organisms are not related phylogenetically to either C. gracilis or other Campylobacter species; the most closely related taxa as determined by rRNA sequence analysis were unrelated aerobes (members of the genera Bordetella, Alcaligenes, Rhodocyclus, and Comamonas). DNA homology data confirmed that these taxa are separate groups. Our data indicate that the unusual organisms are members of a new genus and new species, for which we propose the name Sutterella wadsworthensis. The type strain of S. wadsworthensis is strain WAL 9799 (= ATCC 51579).
Isotope dilution--mass spectrometric quantification of specific proteins: model application with apolipoprotein A-I (1996)

An enzymatic hydrolysis isotope dilution-mass spectrometric method was developed for reference quantification of specific proteins. The analytical procedure involved measuring a reproducibly hydrolyzed peptide (serving as the primary standard) unique to a specific protein. This new mass spectrometric method was evaluated by assessing the concentration of apolipoprotein (apo) A-I in the European Community Bureau of Reference (BCR) lyophilized Certified Reference Material (CRM 393). We used the method to make 96 measurements (4 replicate analyses of 4 enzymatic digests of 6 vials of BCR-CRM 393), which gave an average total protein mass of 1.048 mg (+/- 1.0% at 99% confidence limits). The total overall analytical CV was 3.95%. The results of this evaluation of our model approach to determine the concentration of a specific protein in a purified preparation demonstrated that our new mass spectrometric method can be used to measure apolipoproteins and other specific proteins without the use of epitopic immunoassay methods.
Identification and characterization of genes differentially expressed in meningiomas. (1993)

Meningiomas are common tumours derived from the thin membrane that surrounds the brain and spinal cord. Currently, the molecular mechanisms responsible for the initiation and progression of these tumors are largely unknown. Toward the elucidation of such mechanisms, we have formulated an experimental design utilizing the technique of subtractive hybridization that is aimed at identifying the changes in gene expression between intracranial meningiomas and their normal precursor cells, leptomeningeal cells. We report here the identification and initial characterization of three genes whose expression is altered or aberrant in meningioma cell lines and tumours relative to cultures of normal leptomeningeal cells. Complementary DNA probes from one of these genes detect transcripts of altered size in several meningiomas relative to normal leptomeningeal cells. Another of these genes demonstrates decreased expression in meningiomas and in tumours associated with the disorder neurofibromatosis 2. A third gene isolated by this procedure is differentially expressed in both meningiomas and breast carcinomas. Therefore, the decreased expression of these genes may play roles in growth-regulatory pathways that are abrogated not only in meningiomas, but in other tumor types as well.
Growth characteristics of uniaxial InGaN/GaN MQW/n-GaN nanowires on Si(111) using MOCVD (2012)

We report on the growth of the uniaxial InGaN/GaN multiple quantum well (MQW) on n-GaN nanowires (NWs) on Si(111) substrates by dynamically adjusting the growth parameters using the pulsed flow metalorganic chemical vapor deposition (MOCVD) technique. We carried out a two-step growth process to grow the uniaxial InGaN/GaN MQW/n-GaN NWs structure. In the first step, the n-GaN NWs were grown at 950 °C and in the second stage, we suitably decreased the growth temperature to 630 and 710 °C, respectively, to grow InGaN/GaN MQW NWs. The surface morphology, structural and optical characterization of the grown InGaN/GaN MQW/n-GaN NWs were studied by field-emission scanning electron microscopy (FE-SEM), high-resolution transmission electron microscopy (HR-TEM), X-ray diffraction (XRD), photoluminescence (PL) and cathodoluminescence (CL) measurements. The CL spectrum recorded on an individual InGaN/GaN MQW/n-GaN NW is dominated by the band-edge emission at 366.7 and 413.5 nm corresponding to n-GaN and MQW structures, respectively. The resultant NWs were found to be free of strain. These results indicate that the pulsed MOCVD technique is an effective method to grow uniaxial InGaN/GaN MQW on n-GaN NWs which is advantageous to other growth techniques. These kinds of uniaxial NWs are promising to allow flat band quantum structures that are shown to improve the efficiency of light-emitting diodes.
Injection technique 1: administering drugs via the intramuscular route (2018)

This article has been double-blind peer reviewedAbstractThe intramuscular route allows for rapid absorption of drugs into the circulation. Using the correct injection technique and selecting the correct site will minimise the risk of complications.
Prospective Estimation of Recombination Signal Efficiency and Identification of Functional Cryptic Signals in the Genome by Statistical Modeling (2003)

The recombination signals (RS) that guide V(D)J recombination are phylogenetically conserved but retain a surprising degree of sequence variability, especially in the nonamer and spacer. To characterize RS variability, we computed the position-wise information, a measure correlated with sequence conservation, for each nucleotide position in an RS alignment and demonstrate that most position-wise information is present in the RS heptamers and nonamers. We have previously demonstrated significant correlations between RS positions and here show that statistical models of the correlation structure that underlies RS variability efficiently identify physiologic and cryptic RS and accurately predict the recombination efficiencies of natural and synthetic RS. In scans of mouse and human genomes, these models identify a highly conserved family of repetitive DNA as an unexpected source of frequent, cryptic RS that rearrange both in extrachromosomal substrates and in their genomic context.
An alternatively spliced miniexon alters the subcellular fate of the human asialoglycoprotein receptor H2 subunit. Endoplasmic reticulum retention and degradation or cell surface expression. (1991)

Two types of cDNAs encoding the H2 subunit of the human asialoglycoprotein receptor had been cloned, differing only by the presence (H2a) or absence (H2b) of a segment of 15 base pairs (bp), encoding five amino acids (Glu-Gly-His-Arg-Gly) immediately carboxylterminal (exoplasmic) to the single membrane-spanning segment. We have cloned and sequenced this region of the H2 gene and showed that the two H2 forms are alternatively spliced variants differing in the presence of a 15-bp miniexon. Both H2 messenger RNAs were found in HepG2 cells, H2b accounting for about 92% of the H2 mRNAs. When expressed in NIH 3T3 cells without the H1 receptor subunit, the two-variant polypeptides exhibit different subcellular fates. H2a is completely retained in and degraded in the endoplasmic reticulum or a related pre-Golgi compartment. In contrast a substantial amount of H2b is processed by Golgi enzymes and reaches the cell surface. Thus, the sole difference determining the subcellular localization of the two forms if the five-amino acid insert in H2a. When a virion-packaged retroviral vector containing H2a cDNA infected 3T3 cells, 70% of the resulting clones expressed H2b and 30% H2a. Thus the 15-bp H2a miniexon can be spliced out, at least during the retrovirus life cycle.