gebhart/patrepeval huggingface dataset:
Genome Diversity of Spore-Forming <i>Firmicutes</i> (2013)

Formation of heat-resistant endospores is a specific property of the members of the phylum Firmicutes (low-G+C Gram-positive bacteria). It is found in representatives of four different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, and Negativicutes, which all encode similar sets of core sporulation proteins. Each of these classes also includes non-spore-forming organisms that sometimes belong to the same genus or even species as their spore-forming relatives. This chapter reviews the diversity of the members of phylum Firmicutes, its current taxonomy, and the status of genome-sequencing projects for various subgroups within the phylum. It also discusses the evolution of the Firmicutes from their apparently spore-forming common ancestor and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, ruminococci) in the course of their adaptation to the saprophytic lifestyle in a nutrient-rich environment. It argues that the systematics of Firmicutes is a rapidly developing area of research that benefits from the evolutionary approaches to the ever-increasing amount of genomic and phenotypic data and allows arranging these data into a common framework.
Effect of solder reflow temperature profile on plastic package delamination (2002)

The major cause of IC package failure mechanisms such as delamination, cracking or popcorning is package saturation with moisture and subsequent exposure to high temperature during solder reflow. Different PCB reflow methods and temperature profiles are an important factor affecting this type of failure mechanism. A series of tests were carried out using three plastic packages, PBGA, TQFP and PQFP, as test vehicles in order to optimize the process conditions, material compatibility and reliability. Tests were carried out to assess the impact of different reflow methods and temperature profiles. The reflow methods tested were vapour phase reflow and convection reflow, and nine reflow temperature profiles were studied. The profile variations were ramp rate, preheat time, dwell time and peak temperature. The study also included JEDEC standard vapor phase and convection reflow temperature profiles. Package interfacial integrity was examined by SAM with C-SAM and THRU-scan/sup TM/ methods, after JEDEC moisture preconditioning, followed by delamination (popcorn) performance and compared for the influence of different reflow methods/temperature profiles. The results show that the severity of plastic package cracking and delamination can be highly dependent on solder reflow parameters. The dominant reflow factor is total heat energy applied to the package throughout the reflow time. The higher the temperature and the longer the dwell time, the more likely a package is to crack if the moisture level inside the package is nearly at, or above the critical level.
Effects of Fixative and Fixation Time for Quantitative Computerized Image Analysis of Immunohistochemical Staining (1999)

Fixation time plays a more critical role in quantitative computerized immunohistochemistry than in routine qualitative studies. This study assessed the significance of fixation time in methanol-Carnoy solution (MC) and 10% neutral buffered formalin (NBF) relative to computerized quantitation of immunohistochemical staining with 2 different antibodies.Normal skin specimens were fixed in NBF or MC solution for times ranging from 4 hr to 1 week. Paraffin sections were stained immunohistochemically with a polyclonal antibody for transforming growth factor-β (TGF-β) or a monoclonal antibody for thrombomodulin (TM). Extracellular matrix-associated TGF-β immunoreactivity and TM-positive vessels were identified and assessed with quantitative computerized image analysis.For both fixatives and antibodies, staining was superior in specimens fixed for 24 hr. TGF-β and TM stainings were stronger and more specific in MC-fixed tissues than in NBF-fixed tissues. We concluded that 24 hr in NBF and MC is the optimal fixation time for quantitative image analysis. MC is superior to NBF for immunohistochemical staining of TGF-β and TM. (The J Histotechnol 22:109, 1999)
Evaluation of Protease Inhibitors in Pacific Whiting Surimi (1994)

Bovine plasma powder, whey protein concentrate and would potato powder were compared with purified bovine serum albumin, chicken egg albumin and a-lactalbumin as protease inhibitors in Pacific whiting surimi. Spectrophotometric and sodium dodecyl sulfate gel electrophoretic analyses demonstrated that the extent of proteolysis in samples containing the purified albumins was, in all cases, equal to the control. The same test also showed that at equal concentrations, whole plasma powder was a more effective inhibitor of proteolysis than whey protein concentrate or potato powder. However, electrophortic gels and punch test scores indicated that at higher concentrations, whey protein concentrate and potato powder could substitute for plasma powder in directly heat set gels, but not in suwari gels.
Regulation of Angiotensin II-induced Phosphorylation of STAT3 in Vascular Smooth Muscle Cells (1999)

Ligand binding to the angiotensin II (Ang II) AT1 receptor on vascular smooth muscle cells (VSMCs) activates the Janus-activated kinase (JAK)/signal transducers and activators of transcription (STAT) pathway. We have shown previously that the JAK2 tyrosine kinase and the Src family p59 Fyn tyrosine kinase are required for Ang II-induced STAT1 tyrosine phosphorylation in VSMCs. The mitogen-activated protein kinase phosphatase, MKP-1, is required for STAT1 tyrosine dephosphorylation. In the present study, using specific enzyme inhibitors and antisense oligonucleotides, we show that Ang II-induced tyrosine phosphorylation and nuclear translocation of STAT3 in VSMCs is mediated by p60 c-Src, whereas tyrosine dephosphorylation is mediated by calcineurin. Calcineurin is activated in response to Ang II stimulation of VSMCs and is translocated to the nucleus. In addition, we show that Ang II-induced serine phosphorylation of STAT3 in VSMCs is mediated by mitogen-activated protein kinase and that dephosphorylation is mediated by protein phosphatase 2A (PP2A). PP2A translocates to the nucleus in response to Ang II stimulation of VSMCs and forms a complex with STAT3 in an Ang II-dependent manner.
BIOETHANOL AND BIOBUTANOL PRODUCTION WITH CLOSTRIDIUM CARBOXIDIVORANS, CLOSTRIDIUM BEIJERINCKII, AND CO-CULTURE FROM BIOMASS: CARBON DIOXIDE/HYDROGEN GAS VS. GLUCOSE FERMENTATION (2017)

Clostridium carboxidivorans (NCIMB 15243) is a well-known acetogenic bacterium with the capability to produce acetyl-CoA and subsequently biofuel products such as ethanol and butanol from waste gas such as CO2 and H2 [1,4,5] .To be more specific, C. carboxidivorans can utilize CO2 and H2 via the reductive acetyl-CoA or Wood-Ljungdahl pathway to produce organic acids, such as acetate and butyrate, and alcohols, such as ethanol and butanol [1,4] .Clostridium beijerinckii (NCIMB 8052) produces CO2 and H2 as waste products from converting pyruvate into acetyl-CoA [2,3] .Because these two different Clostridium strains use two different, but very similar, metabolic pathways that rely on two different substrates to produce ethanol and butanol, both individual strain and co-cultured fermentative profiles were studied in autotrophic fermentation with CO2/H2 and heterotrophic fermentation with glucose as carbon and energy source.During both fermentations, initial medium pH values of 6.1 and 7.1 were studied for optimal ethanol and butanol production without any pH adjustments during glucose and CO2/H2 gas fermentations.Both fermentations were performed in serum bottles containing 50 ml of CGM medium.All serum bottles were incubated in a shaking incubator with agitation at 150 rpm at 25 o C or 37 o C. We observed that more acids and alcohols were produced with the higher initial pH of 7.1 in glucose and CO2/H2 gas fermentations.To explore the effect of temperature shift on alcohol production, serum bottles were incubated in 37 o C shaker for the first 24 hours then in 25 o C shaker for the iii rest of fermentation.During the glucose fermentation, two co-culture batches were able to produce significant amount of butanol by utilizing temperature shift technique.Since we have observed that C. carboxidivorans can more effectively convert CO2 into ethanol rather than butanol, we also examined the effect of co-culturing it with C. beijerinckii in gas fermentation.Co-culture batches were able to boost butanol productivity in CO2/H2 gas fermentation by converting acetyl-CoA produced by C. carboxidivorans prior to the second inoculation of C. beijerinckii at 37 o C. Max Productivity [mg/(L*hr)] Max Prod.Time (hr) C.C-Glu7.1A 0.055 192 0.050 0.004 1.246 24 C.C-Glu7.1B 0.013 48 0.013 0.001 0.263 48 C.C-Glu6.1A 0.000 -0.000 0.000 -C.C-Glu6.1B0.000 -0.000 0.000 -Table 6. Butanol production profile for C. carboxidivorans in CO2/H2 gas fermentation at T:37 C Batch Name Max Conc.(g/L) Max Conc.Time (hr) Conc.Avg for stationary (g/L) Max Productivity [mg/(L*hr)] Max Prod.Time (hr) C.C-Gas7.1A 0.022 192 0.015 0.008 0.13 24 C.C-Gas7.1B 0.023 264 0.017 0.004 0.17 72 C.C-Gas6.1A 0.000 -0.000 0 -C.C-Gas6.1B0.
Agents of the "suis-ide diseases" of swine: Actinobacillus suis, Haemophilus parasuis, and Streptococcus suis. (1999)

In recent years, Actinobacillus suis, Haemophilus parasuis, and Streptococcus suis have emerged as important pathogens of swine, particularly in high health status herds. Their association with a wide range of serious clinical conditions and has given rise to the moniker "suis-ide diseases." These organisms are early colonizers and, for that reason, are difficult to control by management procedures such as segregated early weaning. Vaccination, serodiagnostic testing, and even serotyping are complicated by the presence of multiple serotypes, cross-reactive antigens, and the absence of clear markers for virulence. In this review, we discuss our current understanding of the pathogenesis, epidemiology, and management of the causative agents of the "suis-ide diseases" of swine.
Prediction of B‐cell Linear Epitopes with a Combination of Support Vector Machine Classification and Amino Acid Propensity Identification (2011)

Epitopes are antigenic determinants that are useful because they induce B-cell antibody production and stimulate T-cell activation. Bioinformatics can enable rapid, efficient prediction of potential epitopes. Here, we designed a novel B-cell linear epitope prediction system called LEPS, Linear Epitope Prediction by Propensities and Support Vector Machine, that combined physico-chemical propensity identification and support vector machine (SVM) classification. We tested the LEPS on four datasets: AntiJen, HIV, a newly generated PC, and AHP, a combination of these three datasets. Peptides with globally or locally high physicochemical propensities were first identified as primitive linear epitope (LE) candidates. Then, candidates were classified with the SVM based on the unique features of amino acid segments. This reduced the number of predicted epitopes and enhanced the positive prediction value (PPV). Compared to four other well-known LE prediction systems, the LEPS achieved the highest accuracy (72.52%), specificity (84.22%), PPV (32.07%), and Matthews' correlation coefficient (10.36%).
NEW ANTIVIRAL ANTIBIOTICS; XANTHOCILLIN X MONO- AND DIMETHYLETHER, AND METHOXY- XANTHOCILLIN X DIMETHYLETHER. I (1968)

The production, isolation, chemical and physical characteristics and biological properties of the new antiviral antibiotics, xanthocillin X mono- and dimethylether, and methoxy-xanthocillin X dimethylether are described. They were produced by two strains of Aspergillus sp. isolated from soil samples. The active principles were extracted from the mycelium, and isolated as yellowish crystals. They were identified as derivatives of xanthocillin X by physical methods. All three were effective against Newcastle disease, vaccinia and herpes simplex viruses in plate assays, and all inhibited the growth of Bacillus subtilis.
Melbourne's road strategy - the outcome of METRAS (1987)

In September 1983, the then Minister of Transport announced the coinmencement of a strategic study of Melbourne's arterial road network - the Metropolitan Arterial Road Access Study (METRAS). The Study was carried out by a small Study Team in the Ministry of Transport (MoT), with assistance from and in consultation with the Road Construction Authority (RCA) and the Road Traffic Authority (RTA).
Phase-amplitude coupling in human scalp EEG during NREM sleep (2015)

Slow oscillations and spindle waves are dominant electroencephalographic (EEG) rhythms during non-rapid-eye-movement (NREM) sleep that have been demonstrated to be associated with various brain functionalities. Previous studies have demonstrated that thalamus originated spindle waves are regulated by cortically generated slow oscillations through cortico-cortical and cortico-thalamic connections. To investigate the changes of coupling between slow oscillations and higher rhythms during different NREM sleep stages, we analyzed scalp EEG data measured from two bipolar electrodes (Fpz-Cz and Pz-Oz) in 15 healthy adults, with accompanying expert annotations of sleep stages. A normalized modulation index (MI) of statistical significance was used to measure the phase-amplitude interaction between phase of slow oscillations (0.1-1.5 Hz) and amplitude of spindle waves (12-16 Hz). It is found that the normalized MI increased from NREM1 to NREM4 for both anterior and posterior channels, and statistically significant coupling occurs in slow wave sleep (p<;0.05). Further, the coupling strength is correlated with the power of slow oscillations [Spearman correlation coefficient r=0.79 (Fpz-Cz) and 0.61 (Pz-Oz)], which might contribute to the dominant role of slow oscillations in the neuronal modulation mechanism.
The Chameleon: A Pervasive Grid Security Architecture (2007)

The convergence between Grid and Pervasive computing environments lead to the Pervasive Grids paradigm. This new paradigm gives birth to some new security challenges related to adhoc authentication and privacy protection. In distributed systems, and especially in pervasive grid environments, the users usually face difficulties to obtain permissions to use the resources from the sites they visit. Either they have an account locally, or they can show a certificate obtained beforehand that gives them the access. Problems arise when they arrive in an unknown environment, which is likely to occur in a pervasive grid environment. Ideally, they would like to present only the needed credentials to access the resources. In this paper, we propose the Chameleon architecture based on a trust model for authentication and access control that allows nomadic users to roam from site to site and to gain access to surrounding/remote resources wrt her status in her home site and to the local policy of the site where she is standing. The Chameleon permits users to access pervasive grid resources and to implement adhoc interactions through the local grid site.
Automation of data collection for PWAS-based structural health monitoring (2005)

Crack detection with piezoelectric wafer active sensors (PWAS) is emerging as an effective and powerful technique in structural health monitoring (SHM). Because of the piezoelectric properties of the PWAS, they act as both transmitters and receivers of guided Lamb waves for such applications. With arrays of PWAS attached to the structure, excitation signals are sent to one of the PWAS and wave signals from the structure are received at all the PWAS. The signals are analyzed to detect the position of cracks. One important issue associated with the PWAS-assisted SHM is the connectivity between the PWAS arrays and the measurement instruments. An automatic signal collection unit is necessary to send the excitation signals to PWAS and acquire the response signal from another PWAS. Such a program-controlled switching unit can quickly and precisely execute the data collection in a way which is more efficient and reliable than the manual switching operations. In this paper, we present an innovative design of a LabVIEW controlled automatic signal collection unit (ASCU) for PWAS-assisted SHM. The hardware circuit construction and the control LabVIEW program are discussed. As a conduit between the phase array of PWAS and the signal instruments (signal generators, oscilloscopes etc.), the ASCU provides a convenient way to switch excitation and echo signals automatically to the selected PWAS transducers with the help of GUI in the LabVIEW control program. The control program is easy to implement and can be integrated into an upper level program that executes the whole task of signal acquisition and analysis. Because of the concise design of the hardware, the ASCU concept of the auto signal switch has been extended to other application cases such as the electromechanical (E/M) impedance measurement for SHM.
A network of growing relationships (2000)

About the Staff Exchange Program. Come to learn, stay to teach. Boot camp for brains. Conference highlights, May 10-12, 2000. Fast forward with Samsung. Alumnus heads up partnership group, Jean-Marie Yamine. Concluding his assignment (Richard Stern). Let the conference commence. Sharing people and knowledge through partnership. Five years and counting. Entrance to a global community, by Network World Fusion. Pushing the envelope of postal services, Jurgen Lohmeyer. How a relationship grew. Waving a network of CDF partnerships, by Markus Repnik. Seizing the future at the UBA, by Mansur Muhtar. A local government with a global perspective, by Robyn Renneberg. Moving on, moving in. Share pays dividends.
Pyridinoline, a Mature Collagen Cross-Link, in Fibrotic Livers from Schistosoma mansoni-Infected Mice (1992)

International audience
Collaborative Group Memory: Processes, Performance, and Techniques for Improvement (2010)

Abstract Groups are often asked to perform important tasks that require them to remember and report accurate information. A review of research on memory processes in groups suggests that collaboration enhances select performance outcomes. Collaboration allows group members to pool their memories and correct one another’s memory errors. Nonetheless, there are opportunities for improvement in the memory performance of collaborative groups. Collaborative groups typically do not recall as much information as the same number of individuals working alone and sometimes fail to correct the memory errors of their members. In this article, we integrate research findings to present an account of collaborative group memory processes and performance. We present a cognitive‐social‐motivational framework for viewing collaborative group memory processes, emphasize the value of collaboration on memory tasks, and suggest ways in which collaborative group memory performance may be improved.
Transfer and Expression of Plasmids Containing Human Cytomegalovirus Immediate‐Early Gene 1 Promoter‐Enhancer Sequences in Eukaryotic and Prokaryotic Cells (1988)

The human cytomegalovirus immediate-early gene region 1 promoter-enhancer is active in bacteria and in many mammalian cells. Recombinant plasmids containing portions of this DNA can be used to promote the expression of foreign proteins in many cells. In this communication, we report the optimal conditions for transfer of plasmid DNA to cells by electroporation and the transient expression assays which document the activity of different promoter constructions. The observed activity of the human cytomegalovirus promoter is more than 100-fold higher than the activity of the early promoter of SV40.
Significant entry of tubocurarine into the brain of rats by adsorption to polysorbate 80–coated polybutylcyanoacrylate nanoparticles: An<i>in situ</i>brain perfusion study (1998)

The possibility of using polysorbate 80-coated polybutylcyanoacrylate nanoparticles to deliver low molecular polar hydrophilic drugs to the CNS has been studied. Tubocurarine (a quaternary ammonium salt) does not penetrate the normal intact blood-brain barrier. However, the injection of this drug directly into the cerebral ventricles of the brain provokes the development of epileptiform seizures as assessed by electroencephalogram (EEG). An in situ perfused rat brain technique was used as an experimental technique together with a simultaneous recording of the EEG. Nanoparticles were prepared by butylcyanoacrylate polymerization in an acidic medium. Fifteen minutes after the introduction of tubocurarine-loaded polysorbate 80-coated nanoparticles into the perfusate, epileptiform spikes in the EEG appeared. Intraventricular injection of tubocurarine caused the appearance of the EEG seizures 5 min after administration. Neither tubocurarine solution nor tubocurarine-loaded nanoparticles without polysorbate 80 or a mixture of polysorbate 80 and tubocurarine were able to influence the EEG. Thus only the loading of tubocurarine onto the polysorbate 80-coated nanoparticles appears to enable the transport of this quaternary ammonium compound through the blood-brain barrier.
Epigenetic Landscape during Coronavirus Infection (2017)

Coronaviruses (CoV) comprise a large group of emerging human and animal pathogens, including the highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) strains. The molecular mechanisms regulating emerging coronavirus pathogenesis are complex and include virus-host interactions associated with entry, replication, egress and innate immune control. Epigenetics research investigates the genetic and non-genetic factors that regulate phenotypic variation, usually caused by external and environmental factors that alter host expression patterns and performance without any change in the underlying genotype. Epigenetic modifications, such as histone modifications, DNA methylation, chromatin remodeling, and non-coding RNAs, function as important regulators that remodel host chromatin, altering host expression patterns and networks in a highly flexible manner. For most of the past two and a half decades, research has focused on the molecular mechanisms by which RNA viruses antagonize the signaling and sensing components that regulate induction of the host innate immune and antiviral defense programs upon infection. More recently, a growing body of evidence supports the hypothesis that viruses, even lytic RNA viruses that replicate in the cytoplasm, have developed intricate, highly evolved, and well-coordinated processes that are designed to regulate the host epigenome, and control host innate immune antiviral defense processes, thereby promoting robust virus replication and pathogenesis. In this article, we discuss the strategies that are used to evaluate the mechanisms by which viruses regulate the host epigenome, especially focusing on highly pathogenic respiratory RNA virus infections as a model. By combining measures of epigenome reorganization with RNA and proteomic datasets, we articulate a spatial-temporal data integration approach to identify regulatory genomic clusters and regions that play a crucial role in the host's innate immune response, thereby defining a new viral antagonism mechanism following emerging coronavirus infection.