gebhart/patrepeval huggingface dataset:
The effect of including Lactobacillus reuteri KUB-AC5 during post-hatch feeding on the growth and ileum microbiota of broiler chickens (2011)

The probiotic strain Lactobacillus reuteri KUB-AC5, which was originally isolated from chicken intestine, was fed to newborn broiler chicks for the first week post-hatch. The growth and ileum microbiota of the chickens were carefully monitored for 6 wk. The inclusion of 5 log cfu/g of feed statistically increased the BW gain in the first week compared with that of the control group, but this effect did not continue thereafter. Significant effects on host feed consumption and the feed-to-growth conversion ratio were not detected. The total amount and composition of ileum bacteria were investigated by quantitative PCR and pyrosequencing of the 16S rRNA gene (rDNA), respectively, and were compared between the control and the probiotic-treated groups. The amount of total bacterial 16S rDNA in ileum samples at d 42 was 5 times higher in the probiotic group than in the control, whereas no significant difference was observed at d 21. A composition analysis revealed the establishment of lactobacilli-enriched microbiota in the probiotic-treated chickens at d 42. At this point, the population level and species diversity of lactobacilli were significantly enhanced compared with those of the control group. In addition, Actinobacteria, mainly genera Corynebacterium and Dietzia, were also statistically higher in the probiotic group. However, Proteobacteria, including those of the family Campylobacterales and some other nonbeneficial bacterial groups, were decreased in the probiotic group at the growing stage. Therefore, with probiotic supplementation, it was demonstrated that Lactobacillus reuteri KUB-AC5 in the early post-hatching period had a delayed effect on ileum microbiota, which resulted in the enrichment of potentially beneficial lactobacilli and the suppression of Proteobacteria, including nonbeneficial bacterial groups.
Abnormal cholesterol biosynthesis in the Smith-Lemli-Opitz syndrome. (1996)

The Smith-Lemli-Opitz syndrome is caused by an inherited defect in 7-dehydrocholesterol-delta7-reductase, the enzyme that catalyzes the last reaction in cholesterol biosynthesis, the conversion of 7-dehydrocholesterol to cholesterol. As a result, deficient cholesterol is produced and the precursor 7-dehydrocholesterol and derivatives (8-dehydrocholesterol and 19-nor-5,7,9(10)-cholestatrien-3 beta-ol) accumulate. Tissues (especially brain) deprived of cholesterol, or because of the deposited sterol precursors and derivatives, develop abnormally and function poorly. Replacement with dietary cholesterol may help correct the biochemical defects and improve symptoms.
Digital microfluidics: a versatile tool for applications in chemistry, biology and medicine (2012)

Digital microfluidics (DMF) has recently emerged as a popular technology for a wide range of applications. In DMF, nanoliter to microliter droplets containing samples and reagents can be manipulated to carry out a range of discrete fluidic operations simply by applying a series of electrical potentials to an array of patterned electrodes coated with a hydrophobic insulator. DMF is distinct from microchannel-based fluidics as it allows for precise control over multiple reagent phases (liquids and solids) in heterogeneous systems with no need for complex networks of connections, microvalves, or pumps. In this review, we discuss the most recent developments in this technology with particular attention to the potential benefits and outstanding challenges for applications in chemistry, biology, and medicine.
Apheresis of low molecular weight protein fraction and the onset of labor. (1990)

In our study, we subjected six (6) pregnant goats of known gestational age to whole blood ultrapheresis using an extracorporeal circuit. The serum fraction removed was replaced with equal volume of the same material prepared from non-gravid goats. The serum fraction removed was identified as to content of clinically measurable parameters and plotted as permeability coefficient compared with molecular weight. The goats were observed to enter the first stage of labor as a consequence of this form of apheresis and to deliver normal products of conception. No clinically significant deleterious effects on the goats were observed. There was no evidence of complement activation, nonspecific heparin effect, or endotoxin effect. We consider the possibility that soluble mediators of immune suppression may play a role in the maintenance of pregnancy and that the onset of the first stage of labor may be an immunologic event.
Posttranscriptional regulation of the zinc finger-encoding EGR-1 gene by granulocyte-macrophage colony-stimulating factor in human U-937 monocytic leukemia cells: involvement of a pertussis toxin-sensitive G protein. (1991)

The EGR-1 gene is an immediate early response gene encoding a zinc finger DNA-binding protein. The present studies have examined the regulation of EGR-1 gene expression in human U-937 monocytic leukemia cells treated with granulocyte-macrophage colony-stimulating factor (GM-CSF). The results demonstrate that GM-CSF rapidly and transiently increases EGR-1 gene expression in U-937 cells. Similar findings were obtained in GM-CSF-treated human monocytes. We also show that the regulation of EGR-1 expression by GM-CSF is a pertussis toxin-sensitive event. The results of nuclear run-on assays further demonstrate that the EGR-1 gene is constitutively transcribed in untreated U-937 cells and that GM-CSF has little effect on this rate of transcription. Inhibition of protein synthesis with cycloheximide also had no detectable effect on EGR-1 gene transcription but was associated with superinduction of EGR-1 mRNA levels in GM-CSF-treated cells. Moreover, the half-life of GM-CSF-induced EGR-1 transcripts was prolonged from 33 to 70 min following inhibition of protein synthesis. Taken together, the results indicate that GM-CSF activates signaling pathways which regulate EGR-1 gene expression through a pertussis toxin-sensitive G protein and that these events increase EGR-1 mRNA levels by a posttranscriptional mechanism. This GM-CSF-dependent regulation of EGR-1 expression may provide a mechanism for transducing signals to the nucleus that are involved in the control of gene transcription.
An L1-like molecule, the 8D9 antigen, is a potent substrate for neurite extension. (1987)

The 8D9 antigen, a cell surface protein isolated from chicken brain that is related to the L1 class of cell adhesion molecules, is shown to contain an activity that promotes the attachment of neurons and the outgrowth of neurites from chicken tecta and mouse cerebellum. When purified 8D9 antigen is attached to a nitrocellulose-coated substrate, neurons rapidly attach and extend unfasciculated neurites. Little or no attachment of astroglia, oligodendroglia, and fibroblast-like cells to the 8D9 antigen is observed. We propose that a function of the 8D9 antigen is that of a neurite extension-promoting substrate in axon fascicles and in regeneration of peripheral nerves.
Resonance Energy Transfer: Methods and Applications (1994)

Resonance energy transfer is widely used in studies of biomolecular structure and dynamics. It provides information about distances on the order of 10 to 100 A and is thus suitable for investigating spatial relationships of interest in biochemistry. The information available from energy transfer studies has been enhanced by the advances in instrumental methods and procedures of data analysis related to fluorescence decay studies. Some practical aspects of the method are reviewed. These include sample preparation, Förster type distance determination, methods of detecting energy transfer and calculating transfer efficiency, time-resolved measurements, and data analysis. Applications of resonance energy transfer, including qualitative measurements as well as microscopy, average distance estimation, and distance distribution analysis, are surveyed.
Decreasing the spectral radius of a graph by link removals (2011)

The decrease of the spectral radius, an important characterizer of network dynamics, by removing links is investigated. The minimization of the spectral radius by removing m links is shown to be an NP-complete problem, which suggests considering heuristic strategies. Several greedy strategies are compared, and several bounds on the decrease of the spectral radius are derived. The strategy that removes that link l=i~j with largest product (x(1))(i)(x(1))(j) of the components of the eigenvector x(1) belonging to the largest adjacency eigenvalue is shown to be superior to other strategies in most cases. Furthermore, a scaling law where the decrease in spectral radius is inversely proportional to the number of nodes N in the graph is deduced. Another sublinear scaling law of the decrease in spectral radius versus the number m of removed links is conjectured.
Structure and function of the influenza virus genome (1983)

Research Article| May 01 1983 Structure and function of the influenza virus genome J W McCauley; J W McCauley Search for other works by this author on: This Site PubMed Google Scholar B W J Mahy B W J Mahy Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1983) 211 (2): 281–294. https://doi.org/10.1042/bj2110281 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation J W McCauley, B W J Mahy; Structure and function of the influenza virus genome. Biochem J 1 May 1983; 211 (2): 281–294. doi: https://doi.org/10.1042/bj2110281 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search © 1983 London: The Biochemical Society1983 Article PDF first page preview Close Modal You do not currently have access to this content.
Diagnosis of Herpes Simplex Virus Infections in the Clinical Laboratory by LightCycler PCR (2000)

Herpes simplex virus (HSV) causes several clinical manifestations in both normal and immunocompromised hosts; this agent is the most frequently detected virus in diagnostic laboratories. Recovery of the virus in cell culture is considered the "gold standard" for detection of this virus from sources other than cerebrospinal fluid. LightCycler is a newly developed, commercially available system designed to rapidly perform PCR, with real-time detection of PCR products by a fluorescence resonance energy transfer assay. We compared the detection of HSV for 200 specimens (number of genital specimens, 160; number of dermal specimens, 38; number of ocular specimens, 2) by shell vial cell cultures (MRC-5) and by LightCycler PCR. Of a total of 88 (44%) HSV strains detected, 69 (78%) were detected by both shell vial cell cultures and LightCycler PCR (DNA polymerase target). A total of 19 (22%) specimens were detected exclusively by LightCycler PCR. No specimens were positive by the shell vial assay only. All 19 discrepant samples had HSV DNA detected by an independent PCR directed to the thymidine kinase gene of the virus. The melting curve analysis feature of the LightCycler instrument identified identical genotype results for HSV type 1 (HSV-1) and HSV-2 from 84 of 88 (96%) positive samples. Specimens can be extracted, target HSV DNA can be amplified, and HSV PCR products can be identified by genotype within 2 h after receipt of specimen into the laboratory. The increased level of accurate identification (all 88 positive samples) compared with that of shell vial cell culture (69 of 88 samples identified as positive) and the agreement of LightCycler PCR results with all shell vial positive results indicate the potential for routine implementation of this technology for laboratory diagnosis of HSV infections.
The sulfur cycle in a permanently meromictic haloalkaline lake (2006)

Soap Lake is a haloalkaline lake located in central Washington. This lake is a remnant of the Missoula flood events that created the landscape of western Montana, the southeastern portion of Washington state, and much of Oregon. It is 15,000 - 20,000 years old, and has maintained a stable meromixis for the last 10,000 years. This carbonate lake is characterized by a brackish mixolimnion, and a monimolimnion with a salinity of ~14%. The pH of both layers of the lake is approximately 10. Both layers also have a high concentration of dissolved sulfate, with the mineral mirabilite (Na<sub>2</sub>SO<sub>4</sub>•10H<sub>2</sub>O) found in the monimolimnion sediments. Sulfide concentrations in the monimolimnion exceed 100 mM. As part of the mission of the NSF Soap Lake Microbial Observatory, microorganisms involved in the sulfur cycle in this lake were studied in terms of their diversity and function. High rates of sulfate reduction were measured in both layers of the lake, with new species of sulfate-reducing bacteria seen in both areas. A particularly novel psychrophilic sulfur oxidizer was isolated from the monimolimnion. This organism has the ability to induce the formation of mirabilite, which was assumed to be an abiotically deposited evaporite mineral. This is the first evidence for a biogenic origin of this mineral. This leads to the possibility that related sulfate minerals, such as those reported on the Mars surface, may have a biogenic origin.
A Comparison of Eubacterial and Archaeal Structure-specific 5′-Exonucleases (1999)

The 5'-exonuclease domains of the DNA polymerase I proteins of Eubacteria and the FEN1 proteins of Eukarya and Archaea are members of a family of structure-specific 5'-exonucleases with similar function but limited sequence similarity. Their physiological role is to remove the displaced 5' strands created by DNA polymerase during displacement synthesis, thereby creating a substrate for DNA ligase. In this paper, we define the substrate requirements for the 5'-exonuclease enzymes from Thermus aquaticus, Thermus thermophilus, Archaeoglobus fulgidus, Pyrococcus furiosus, Methanococcus jannaschii, and Methanobacterium thermoautotrophicum. The optimal substrate of these enzymes resembles DNA undergoing strand displacement synthesis and consists of a bifurcated downstream duplex with a directly abutted upstream duplex that overlaps the downstream duplex by one base pair. That single base of overlap causes the enzymes to leave a nick after cleavage and to cleave several orders of magnitude faster than a substrate that lacks overlap. The downstream duplex needs to be 10 base pairs long or greater for most of the enzymes to cut efficiently. The upstream duplex needs to be only 2 or 3 base pairs long for most enzymes, and there appears to be interaction with the last base of the primer strand. Overall, the enzymes display very similar substrate specificities, despite their limited level of sequence similarity.
Differences in the pattern of hippocampal neuronal loss in normal ageing and Alzheimer's disease (1994)

The distinction between the neurodegenerative changes that accompany normal ageing and those that characterise Alzheimer's disease is not clear. The resolution of this issue has important implications for the design of therapeutic and investigative strategies. To this end we have used modern stereological techniques to compare the regional pattern of neuronal cell loss in the hippocampus related to normal ageing to that associated with Alzheimer's disease. The loss related to normal ageing was evaluated from estimates of the total number of neurons in each of the major hippocampal subdivisions of 45 normal ageing subjects who ranged in age from 13 to 101 years. The Alzheimer's disease related losses were evaluated from similar data obtained from 7 cases of Alzheimer's disease and 14 age matched controls. Qualitative differences were observed in the regional patterns of neuronal loss related to normal ageing and Alzheimer's disease. The most distinctive Alzheimer's disease related neuron loss was seen in the CA1 region of the hippocampus. In the normal ageing group there was almost no neuron loss in this region (final neuron count in the CA1 region: 4.40 x 10(6) neurons for the Alzheimer's disease group vs 14.08 x 10(6) neurons in the normal ageing group). It is concluded that the neurodegenerative processes associated with normal ageing and with Alzheimer's disease are qualitatively different and that Alzheimer's disease is not accelerated by ageing but is a distinct pathological process.
Techniques for information retrieval from speech messages (1991)

• The goalin speech-message information retrieval is to categorize an input speech utterance according to a predefined notion ofa topic, or message class. The components ofa speech-message information-retrieval system include an acoustic front end that provides an incomplete transcription ofa spoken message, and a message classifier that interprets the incomplete transcription and classifies the message according to message category. The techniques and experiments described in this paper concern the integration ofthese components, and represent the first demonstration ofa complete system that accepts speech messages as input and produces an estimated message class as output. The promising results obtained in information retrieval on conversational speech messages demonstrate the feasibility ofthe technology. THE GOAL IN SPEECH-.MESSAGE information retrieval is similar to that of the more well-known. problem ofinformation retrieval from text documents. Text-based information-retrieval systems sort large collections of documents according to predefined relevance classes. This discipline is a mature area ofresearch with a number of well-known document-retrieval systems already in existence. Speech-message information retrieval is a relatively new area, and work in this area is motivated by the rapid proliferation ofspeech-messaging and speech-storage technology in the home and office. A good example is the widespread application of large speech-mail and speech-messaging systems that can be accessed over telephone lines. The potential length and number of speech messages in these systems make exhaustive user review ofall messages in a speech mailbox difficult. In such a system, speech-message information retrieval could automatically categorize speech messages by context to facilitate user review. Another application would be to classifY incoming customer telephone calls automatically and route them to the appropriate customer service areas [1]. Unlike information-retrieval systems designed for text messages, the speech-message information-retrieval system illustrated in Figure 1 relies on a limited-vocabulary acoustic front end that provides only an incomplete transcription of a spoken message. The second stage of the system is a message classifier that must interpret the incomplete transcription and classifY the message
Spectral redemption in clustering sparse networks (2013)

Spectral algorithms are classic approaches to clustering and community detection in networks. However, for sparse networks the standard versions of these algorithms are suboptimal, in some cases completely failing to detect communities even when other algorithms such as belief propagation can do so. Here, we present a class of spectral algorithms based on a nonbacktracking walk on the directed edges of the graph. The spectrum of this operator is much better-behaved than that of the adjacency matrix or other commonly used matrices, maintaining a strong separation between the bulk eigenvalues and the eigenvalues relevant to community structure even in the sparse case. We show that our algorithm is optimal for graphs generated by the stochastic block model, detecting communities all of the way down to the theoretical limit. We also show the spectrum of the nonbacktracking operator for some real-world networks, illustrating its advantages over traditional spectral clustering.
Comparative Characterization of a Wild Type and Transmembrane Domain-Deleted Fatty Acid Amide Hydrolase:  Identification of the Transmembrane Domain as a Site for Oligomerization (1998)

Fatty acid amide hydrolase (FAAH) is an integral membrane protein responsible for the hydrolysis of a number of primary and secondary fatty acid amides, including the neuromodulatory compounds anandamide and oleamide. Analysis of FAAH's primary sequence reveals the presence of a single predicted transmembrane domain at the extreme N-terminus of the enzyme. A mutant form of the rat FAAH protein lacking this N-terminal transmembrane domain (DeltaTM-FAAH) was generated and, like wild type FAAH (WT-FAAH), was found to be tightly associated with membranes when expressed in COS-7 cells. Recombinant forms of WT- and DeltaTM-FAAH expressed and purified from Escherichia coli exhibited essentially identical enzymatic properties which were also similar to those of the native enzyme from rat liver. Analysis of the oligomerization states of WT- and DeltaTM-FAAH by chemical cross-linking, sedimentation velocity analytical ultracentrifugation, and size exclusion chromatography indicated that both enzymes were oligomeric when membrane-bound and after solubilization. However, WT-FAAH consistently behaved as a larger oligomer than DeltaTM-FAAH. Additionally, SDS-PAGE analysis of the recombinant proteins identified the presence of SDS-resistant oligomers for WT-FAAH, but not for DeltaTM-FAAH. Self-association through FAAH's transmembrane domain was further demonstrated by a FAAH transmembrane domain-GST fusion protein which formed SDS-resistant dimers and large oligomeric assemblies in solution.
Leukocyte-endothelial cell recognition: evidence of a common molecular mechanism shared by neutrophils, lymphocytes, and other leukocytes. (1987)

The interaction of leukocytes with endothelial cells is intrinsic to the process of leukocyte extravasation, whether during the entry of blood polymorphonuclear leukocytes and monocytes into sites of acute and chronic inflammation, or during the homing of lymphocytes to lymphoid organs. A lymphocyte surface glycoprotein, defined by monoclonal antibody MEL-14, has been described that appears to mediate lymphocyte recognition of postcapillary venules in peripheral lymph nodes, and to control the migration of lymphocytes from the blood into these lymphoid organs. We now report that the antigenic determinant recognized by MEL-14 is present at high levels on other leukocytes as well, including neutrophils, monocytes, and eosinophils; and we demonstrate involvement of the MEL-14 antigen in neutrophil-endothelial cell interactions. MEL-14 immunoprecipitates a neutrophil surface protein of Mr approximately 100,000, similar in m.w. to the 80,000 to 90,000 dalton lymphocyte surface MEL-14 antigen, and it blocks the interaction of neutrophils with endothelial cells in an in vitro model of adhesion to postcapillary venules in lymph node frozen sections. Neutrophil binding to lymph node venules is also inhibited by PPME, a mannose-6-phosphate-rich yeast polysaccharide that is thought to mimic the endothelial cell ligand for the MEL-14-defined lymphocyte receptor. Interestingly, neither MEL-14 nor PPME exhibit a major effect on neutrophil binding to postcapillary venules in Peyer's patches, suggesting that as for lymphocytes, the neutrophil MEL-14 antigen is involved in recognition of tissue-specific endothelial determinants. Finally, we show that MEL-14 inhibits the capacity of neutrophils to migrate from the blood into sites of acute inflammation in the skin. These observations lead us to propose that receptors for tissue-specific endothelial determinants are utilized by neutrophils and lymphocytes and probably other leukocytes during the physiologic process of leukocyte extravasation in vivo.