gebhart/patrepeval huggingface dataset:
Pulse irradiation of low-power laser stimulates bone nodule formation. (2001)

Although low-power laser irradiation provides many anabolic effects such as acceleration of bone formation, the effects of different pulse frequencies used during laser irradiation on bone formation have not been elucidated. Osteoblastic cells isolated from fetal rat calvariae were irradiated once with a low-power Ga-Al-As laser (830 nm, 500 mW) in two different irradiation modes; continuous irradiation (CI), and 1 Hz pulsed irradiation (PI). We then investigated the effects on cellular proliferation, bone nodule formation, alkaline phosphatase (ALP) activity, and ALP gene expression. Laser irradiation in both groups significantly stimulated cellular proliferation, bone nodule formation, ALP activity, and ALP gene expression, as compared with the nonirradiation group. Notably, PI markedly stimulated these factors, when compared with the CI group. Since 1 Hz pulsed laser irradiation significantly stimulates bone formation in vitro, it is most likely that pulse frequency is an important factor affecting biological responses in bone formation.
A Haptic Back Display for Attentional and Directional Cueing (2003)

We have been developing a haptic back display using a 3-by-3 tactor array. This paper reports two studies that investigated the use of such a display for delivering attention- and direction-related information to its user. The first study measured the effectiveness of haptic cues in redirecting an observer's visual spatial attention. The observer was first tapped on the back, and then asked to detect a change between two similar visual scenes. We found that reaction time decreased by an average of 41% when the location of the tactor coincided with the quadrant of the visual scene where a change occurred. We also found that reaction time increased by an average of 19% when the locations of the tapping and visual change did not coincide. Such a haptic attentional cueing system can be beneficial to a user who must attend to information in small areas within a large and complex visual display (e.g. an aircraft cockpit). In the second study, sequenced pulses were employed to impart directional information. We found that native and minimally-trained observers were able to discern the directions of a set of horizontal, vertical and diagonal directional lines with an overall accuracy of 81%. Means of improving the overall accuracy were suggested and tested. These directional lines can be applied to a haptic navigation guidance or situation awareness system.
Isolation of a preadipocyte cell line from rat bone marrow and differentiation to adipocytes (1995)

A unique population of rat adipocyte precursor cells was derived from normal rat bone marrow. The epitheloid-like preadipocytes were isolated from a mixed culture of bone marrow cells by a combination of differential trypsinization, enrichment by Ficoll gradient centrifugation, and differential seeding. This cell line, designated RBM-Ad, can be fully differentiated into multilocular adipocytes morphologically resembling brown adipose tissue. No changes in the differentiation pattern are observed during propagation of these cells, and they have been successfully carried and differentiated up to passage 49. Histological staining of differentiated cells with Sudan black, Sudan IV, and oil red O indicates the presence of lipids in intracellular vesicles. The nonselective beta-adrenergic agonist isoproterenol stimulates adenylyl cyclase activity in both preadipocytes and differentiated adipocytes. In contrast, BRL-37344, a beta 3-adrenergic receptor-specific agonist, stimulates adenylyl cyclase activity and glycerol release in differentiated adipocytes, but not preadipocytes. In addition, differentiated adipocytes contain messenger RNA encoding the brown adipose-specific protein, thermogenin. Thus, this rat preadipocyte cell line can be differentiated into adipocytes that histologically and functionally resemble brown adipose tissue.
The chronic mild stress (CMS) model of depression: History, evaluation and usage (2016)

Now 30 years old, the chronic mild stress (CMS) model of depression has been used in >1300 published studies, with a year-on-year increase rising to >200 papers in 2015. Data from a survey of users show that while a variety of names are in use (chronic mild/unpredictable/varied stress), these describe essentially the same procedure. This paper provides an update on the validity and reliability of the CMS model, and reviews recent data on the neurobiological basis of CMS effects and the mechanisms of antidepressant action: the volume of this research may be unique in providing a comprehensive account of antidepressant action within a single model. Also discussed is the use of CMS in drug discovery, with particular reference to hippocampal and extra-hippocampal targets. The high translational potential of the CMS model means that the neurobiological mechanisms described may be of particular relevance to human depression and mechanisms of clinical antidepressant action.
Alkylation of Amino Acids and Glutathione in Water by o-Quinone Methide. Reactivity and Selectivity (2000)

o-Quinone methide (1) has been produced in water both thermally and photochemically from (2-hydroxybenzyl)trimethylammonium iodide (2). Michael addition reactions of 1 to various amines, and sulfides, including amino acids and glutathione have been carried out, obtaining alkylated adducts (3-16) in fairly good to quantitative yields. The reaction rate and selectivity of 1 toward nitrogen and sulfur nucleophiles, in competition with the hydration reaction, have been investigated at different pH by laser flash photolysis technique. The observed reactivity spans 7 orders of magnitude on passing from water (kNu = 5.8 M-1 s-1) to the most reactive nucleophile (2.8 x 10(8) M-1 s-1, 2-mercaptoethanol under alkaline conditions). These are the first direct reaction rate measurements of nucleophilic addition to the parent o-quinone methide (1). Competition experiments provided strong kinetic support to the involvement of free 1 as an intermediate in both thermal and photochemical reactions. Furthermore, several alkylation adducts regenerate 1 either by heating (9, 10, 13, and 14) or by irradiation (9, 11-13, 16). Such a thermal and photochemical reversibility of the alkylation process opens a new perspective for the use and application of such adducts as o-QM molecular carriers.
GeneSilico protein structure prediction meta-server (2003)

Rigorous assessments of protein structure prediction have demonstrated that fold recognition methods can identify remote similarities between proteins when standard sequence search methods fail. It has been shown that the accuracy of predictions is improved when refined multiple sequence alignments are used instead of single sequences and if different methods are combined to generate a consensus model. There are several meta-servers available that integrate protein structure predictions performed by various methods, but they do not allow for submission of user-defined multiple sequence alignments and they seldom offer confidentiality of the results. We developed a novel WWW gateway for protein structure prediction, which combines the useful features of other meta-servers available, but with much greater flexibility of the input. The user may submit an amino acid sequence or a multiple sequence alignment to a set of methods for primary, secondary and tertiary structure prediction. Fold-recognition results (target-template alignments) are converted into full-atom 3D models and the quality of these models is uniformly assessed. A consensus between different FR methods is also inferred. The results are conveniently presented on-line on a single web page over a secure, password-protected connection. The GeneSilico protein structure prediction meta-server is freely available for academic users at http://genesilico.pl/meta.
Can high performance software DSM systems designed with InfiniBand features benefit from PCI-Express? (2005)

The performance of software distributed shared memory systems has traditionally been lower than other programming models primarily because of overhead in the coherency protocol, communication bottlenecks and slow networks. Software DSMs have benefited from interconnection technologies like Myrinet, InfiniBand and Quadrics, which offer low latency and high bandwidth communication. Additionally, some of their features like RDMA and atomic operations have been used to implement some portions of the software DSM protocols directly, further reducing overhead. Such network aware protocols are dependent on characteristics of these networks. The performance of the networks is in turn dependent on the system architecture, specially the I/O bus. PCI-Express the successor to the PCI-X architecture, offers improved latency and bandwidth characteristics. In this paper, we evaluate the impact of using an improved bus technology like PCI-Express, on the performance of software DSM protocols, which use the network features of InfiniBand. We can see a reduction in application execution time of up to 13% at four nodes, when PCI-Express is used instead of PCI-X.
SPK1 Is an Essential S-Phase-Specific Gene of Saccharomyces cerevisiae That Encodes a Nuclear Serine/Threonine/Tyrosine Kinase (1993)

SPK1 was originally discovered in an immunoscreen for tyrosine-protein kinases in Saccharomyces cerevisiae. We have used biochemical and genetic techniques to investigate the function of this gene and its encoded protein. Hybridization of an SPK1 probe to an ordered genomic library showed that SPK1 is adjacent to PEP4 (chromosome XVI L). Sporulation of spk1/+ heterozygotes gave rise to spk1 spores that grew into microcolonies but could not be further propagated. These colonies were greatly enriched for budded cells, especially those with large buds. Similarly, eviction of CEN plasmids bearing SPK1 from cells with a chromosomal SPK1 disruption yielded viable cells with only low frequency. Spk1 protein was identified by immunoprecipitation and immunoblotting. It was associated with protein-Ser, Thr, and Tyr kinase activity in immune complex kinase assays. Spk1 was localized to the nucleus by immunofluorescence. The nucleotide sequence of the SPK1 5' noncoding region revealed that SPK1 contains two MluI cell cycle box elements. These elements confer S-phase-specific transcription to many genes involved in DNA synthesis. Northern (RNA) blotting of synchronized cells verified that the SPK1 transcript is coregulated with other MluI box-regulated genes. The SPK1 upstream region also includes a domain highly homologous to sequences involved in induction of RAD2 and other excision repair genes by agents that induce DNA damage. spk1 strains were hypersensitive to UV irradiation. Taken together, these findings indicate that SPK1 is a dual-specificity (Ser/Thr and Tyr) protein kinase that is essential for viability. The cell cycle-dependent transcription, presence of DNA damage-related sequences, requirement for UV resistance, and nuclear localization of Spk1 all link this gene to a crucial S-phase-specific role, probably as a positive regulator of DNA synthesis.
Antiviral agents and human viral diseases. (1997)

Part 1 Basic biology - drug development: virus replication - target functions and events for virus-specific inhibitors pathogenesis of viral infection preclinical evaluation of antiviral agents - in vitro and animal testing clinical drug development - human pharmacology, safety, and tolerance trials. Part 2 Laboratory diagnosis/clinical trials: laboratory diagnosis of viral infections clinical trials methodology and statistical evaluation major ocular viral infections Varicella-Zoster virus infections herpes simplex virus infections human papilloma viruses and interferon therapy respiratory viruses infections viral infections of the gastrointestinal tract antiviral therapy of viral hepatitis viral infections of the central nervous system chronic interuterine and perinatal infections HIV and other human herpesvirus type 6 infections cytomegalovirus and the immunocompromised patient hantaviruses and other RNA haemorrhagic, encephalitic, and febrile disease viruses. Part 3 Prevention: immunization against viral diseases.
Uptake of HIV and latex particles by fresh and cultured dendritic cells and monocytes (2001)

Blood dendritic cells (DC) efficiently carry HIV-1 and transmit infection to CD4+ T cells in the absence of productive infection of the APC. Fluorescent latex beads were used to define the endocytic pathways that may contribute to this non-infectious pathway of virus carriage. Beads between 14 nm and 2300 nm in diameter were taken up by uncultured blood DC, but uptake of beads larger than 280 nm was much reduced in the DC compared to monocytes. After culture, there was a reduction in bead carriage in DC compared to monocytes. In the DC, beads were found as small aggregates in class II containing compartments or as single beads just below the cell surface. Beads accumulated in monocytes as aggregates in class II negative compartments. Bead recycling occurred in DC, but not in the fresh or cultured monocytes. Electron microscopy of HIV-1-pulsed DC cultured with CD4+ T cells showed accumulation of apoptotic debris and virions within endosomes in the DC. The peripheral location and recycling of endocytosed material in DC provides a pathway for virion transfer from DC to T cells that does not occur in monocytes.
Shan‐and‐Chen‐type multiphase lattice Boltzmann study of viscous coupling effects for two‐phase flow in porous media (2008)

Abstract In this paper, the Shan–Chen‐type (SC) multiphase lattice Boltzmann model was used to study the viscous coupling effects for immiscible two‐phase flow in porous media. In the model, any typical equation of state can be incorporated and different contact angles of the gas–liquid interface at a solid wall can be obtained easily through adjusting the ‘density of wall’ (Benzi et al ., Phys. Rev. E 2006; 74 (2):021509). The viscous coupling effects due to capillary number, the viscosity ratio and the wetting angle were investigated. The two‐phase flows with density ratio as high as 56 in porous media were simulated. For different viscosity ratios and wettability, two‐phase flow patterns and relative‐permeability curves as a function of wetting saturation were obtained. It is observed that when the wetting phase is less viscous and covers the solid surface, the relative permeability of the non‐wetting phase may be greater than unity. Here, the SC model is demonstrated as a suitable tool to study the immiscible two‐phase flow in porous media because it is simple, easy to get the desired contact angle and able to simulate immiscible phase flow with high‐density ratio. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Influence of CpG Methylation and Target Spacing on V(D)J Recombination in a Transgenic Substrate (1993)

We have previously described a line of transgenic mice with multiple head-to-tail copies of an artificial V-J recombination substrate and have shown that the methylation of this transgene is under the control of a dominant strain-specific modifier gene, Ssm-1. When the transgene array is highly methylated, no recombination is detectable, but when it is unmethylated, V-J joining is seen in the spleen, bone marrow, lymph nodes, and Peyer's patches but not in the thymus or nonlymphoid tissues, including brain tissue. Strikingly, in mice with partially methylated transgene arrays, rearrangement preferentially occurs in hypomethylated copies. Therefore, V-J recombination is negatively correlated with methylated DNA sequences. In addition, it appears that recombination occurs randomly between any two recombination signal sequences within the transgene array. This lack of target preference in an unselectable array of identical targets rules out simple mechanisms of one-dimensional tracking of a V(D)J recombinase complex.
Constructing Multigenome Views of Whole Microbial Genomes (1998)

We have designed and implemented a system to carry out cross-genome comparisons of open reading frames (ORFs) from multiple genomes. This implementation includes a genome profiling system that allows us to explore pairwise comparisons at different levels of match similarity and ask biologically motivated queries involving number and identity of ORFs, their function, functional category, distribution in genomes or in biological domains, and statistics on their matches and match families. This analysis required precise definition of new classification terms and concepts. We define the terms genomic signature, summary signature, biologic domain signature, domain class, match level, match family, and extended match family, then use these terms to define concepts, including genomically universal proteins and proteins characteristics of sets of genomes. We initiate an analysis based on automated FASTA (Pearson, 1996) comparison of 22,419 conceptually translated protein sequences from nine microbial genomes.
Vaccination of mice with a soluble protein fraction of Mycobacterium leprae provides consistent and long-term protection against M. leprae infection (1992)

Groups of BALB/c mice were vaccinated intradermally with either Freund's incomplete adjuvant (FIA) alone, 10(7) heat-killed Mycobacterium leprae organisms in FIA, or a number of fractions of M. leprae containing soluble and/or cell wall components. At 1, 3, 6, 9, and 12 months later, vaccinated mice were challenged in the right hind footpad with 5,000 live M. leprae organisms, and vaccine protection was assessed 6 to 8 months later, at the peak of M. leprae multiplication in the negative control (FIA alone), by the two-sample rank-sum test. In these studies, a cell wall fraction rich in peptidoglycan was consistently ineffective. Both heat-killed M. leprae and a fraction containing cell wall and fixed proteins generally protected when the interval between vaccination and challenge was 1 or 3 months but not subsequently. On the other hand, soluble proteins of M. leprae alone or in combination (with cell wall fractions) consistently (14 of 14 instances) afforded highly significant protection (P less than or equal to 0.01) at all challenge intervals up to 1 year after vaccination. These results suggest that the soluble protein fraction of M. leprae offers promise for a vaccine against leprosy.
Learning outcomes, course features and learning factors of WBI client learning courses (2004)

This report reviews the learning outcomes of these courses, describes the course features and instructional practices used in these courses, and explores course features or factors that were associated with participant learning in these courses. It uses participant test scores at the beginning and at the end of the course, course information from a survey filled by the course Task Team Leaders (TTLs), and data from WBI Client Registration System.
Lesion genesis in a subset of patients with multiple sclerosis: a role for innate immunity? (2007)

Lesions obtained early in the course of multiple sclerosis (MS) have been studied immunocytochemically, and compared with the early stages of the experimental lesion induced in rats by the intraspinal injection of lipopolysaccharide. Large hemispheric or double hemispheric sections were examined from patients who had died in the course of acute or early relapsing multiple sclerosis. In MS patients exhibiting hypoxia-like lesions [Pattern III; Lucchinetti et al. Ann Neurol (2000) 47: 707-17], focal areas in the white matter showed mild oedema, microglial activation and mild axonal injury in the absence of overt demyelination. In such lesions T-cell infiltration was mild and restricted to the perivascular space. Myeloperoxidase and the inducible form of nitric oxide synthase were expressed primarily by microglia, and the activated form of these cells was associated with extracellular deposition of precipitated fibrin. In addition, these lesions showed up-regulation of proteins involved in tissue preconditioning. When active demyelination started, lesions were associated with massive T-cell infiltration and microglia and macrophages expressed all activation markers studied. Similar tissue alterations were found in rats in the pre-demyelinating stage of lesions induced by the focal injection of bacterial lipopolysaccharide into the spinal white matter. We suggest that the areas of microglial activation represent an early stage of tissue injury, which precedes the formation of hypoxia-like demyelinated plaques. The findings indicate that mechanisms associated with innate immunity may play a role in the formation of hypoxia-like demyelinating lesions in MS.
Wavelet transform for Shah convolution velocity measurements of single particles and solutes in a microfluidic chip (2001)

Wavelet transform analysis is applied to determine the speed of fluorescent polystyrene microspheres and fluorescent solutes in a microchip. The data analysed consist of the periodical signal (Shah convolution) obtained when fluorescent particles or solute plugs move in a channel that is covered with a chromium grid pattern. This setup converts velocity into a (fluorescence emission) frequency, and previous analyses therefore used Fourier transform to extract the frequency information. In this paper it is shown that wavelet transform has some advantages over Fourier transform. With wavelet transform, time information can be obtained in addition to frequency information. Thus the speed of individual particles was determined together with their moments of appearance and disappearance in the system. With solutes small changes of velocity during the analysis were detected, and an improvement in peak frequency resolution was obtained.
The Islamic Challenge (1996)

Within an hour of King Hussein's speech relinquishing the Hashemite claim of sovereignty over the West Bank, Israeli intelligence officers accompanied by police and soldiers drove from the Russian compound, its walls looped with concertina wire, to Faisal Husayni's home and ultimately to the Arab Studies Center, Husayni's research organization. Husayni's staff, who were still in the office, were used to such surprise visits. The Israelis had repeatedly closed the center, claiming its real function was to coordinate PLO activities in the West Bank and Gaza.
Where big data meets linked data: Applying standard data models to environmental data streams (2016)

In August 2015, a new seafloor observatory was deployed in Galway Bay, Ireland. The sensors on the observatory platform are connected by fibre-optic cable to a shore station, where a broadband connection allows data transfer to the Marine Institute's data centre. This setup involved the development of a new data acquisition system which takes advantage of open source streaming data solutions developed in response to the Big Data paradigm, in particular the Velocity aspect. This activity merges concepts from the arenas of both Big Data and Internet of Things where data standardisation is not normally considered. This paper considers the architecture implemented to stream marine data from instrument to end user and offers suggestions on how to standardise these data streams.