gebhart/patrepeval huggingface dataset:
Mesenchymal Stem Cells (MSC) Derived from Induced Pluripotent Stem Cells (iPSC) Equivalent to Adipose-Derived MSC in Promoting Intestinal Healing and Microbiome Normalization in Mouse Inflammatory Bowel Disease Model (2018)

Cellular therapy with allogeneic or autologous mesenchymal stem cells (MSC) has emerged as a promising new therapeutic strategy for managing inflammatory bowel disease (IBD). However, MSC therapy ideally requires a convenient and relatively homogenous cell source (typically bone marrow or adipose tissues) and the ability to generate cells with stable phenotype and function. An alternative means of generating allogeneic MSC is to derive them from induced pluripotent stem cells (iPSC), which could in theory provide an indefinite supply of MSC with well-defined phenotype and function. Therefore, we compared the effectiveness of iPSC-derived MSC (iMSC) and adipose-derived MSC (adMSC) in a mouse model of IBD (dextran sodium sulfate-induced colitis), and investigated mechanisms of intestinal protection. We found that iMSC were equivalent to adMSC in terms of significantly improving clinical abnormalities in treated mice and reducing lesion scores and inflammation in the gut. Administration of iMSC also stimulated significant intestinal epithelial cell proliferation, increased in the numbers of Lgr5+ intestinal stem cells, and increased intestinal angiogenesis. In addition, the microbiome alterations present in mice with colitis were partially restored to resemble those of healthy mice following treatment with iMSC or adMSC. Thus, iMSC administration improved overall intestinal health and healing with equivalent potency to treatment with adMSC. This therefore is the first report of the effectiveness of iMSC in the treatment of IBD, along with a description of unique mechanisms of action with respect to intestinal healing and microbiome restoration. Stem Cells Translational Medicine 2018;7:456-467.
Implementation of multi-axis smart driver system via EtherCAT network based on IEC61800 standard (2011)

Industrial network, often referred to as fieldbus, becomes an indispensable component for intelligent manufacturing systems. Thus, in order to satisfy the real-time requirements of field devices such as sensros, actuators, and controllers, numerous fieldbus protocols have been developed. But, the application of fieldbus has been limited due to the high cost of hardware and the difficulty in interfacing with multi-vendor products. Recently, the EtherCAT protocol becomes a very promising alternative for real-time industrial application due to the elimination of uncertainties in Ethernet. This paper focuses on the development of the real-time EtherCAT network for multi-axis smart driver. And IEC 61800 standard is being adapted to connect with products at driver manufacturers. In addition, this paper presents performance evaluation of the synchronization on the experimental EtherCAT test-bed with 6-axis smart driver and data mapping using IEC 61800 power driver system standard.
A pivotal role of FOS-mediated BECN1/Beclin 1 upregulation in dopamine D2 and D3 receptor agonist-induced autophagy activation (2015)

Autophagy dysfunction is implicated in the pathogenesis of Parkinson disease (PD). BECN1/Beclin 1 acts as a critical regulator of autophagy and other cellular processes; yet, little is known about the function and regulation of BECN1 in PD. In this study, we report that dopamine D2 and D3 receptor (DRD2 and DRD3) activation by pramipexole and quinpirole could enhance BECN1 transcription and promote autophagy activation in several cell lines, including PC12, MES23.5 and differentiated SH-SY5Y cells, and also in tyrosine hydroxylase positive primary midbrain neurons. Moreover, we identified a novel FOS (FBJ murine osteosarcoma viral oncogene homolog) binding sequence (5'-TGCCTCA-3') in the rat and human Becn1/BECN1 promoter and uncovered an essential role of FOS binding in the enhancement of Becn1 transcription in PC12 cells in response to the dopamine agonist(s). In addition, we demonstrated a critical role of intracellular Ca<sup>2+</sup> elevation, followed by the enhanced phosphorylation of CAMK4 (calcium/calmodulin-dependent protein kinase IV) and CREB (cAMP responsive element binding protein) in the increases of FOS expression and autophagy activity. More importantly, pramipexole treatment ameliorated the SNCA/α-synuclein accumulation in rotenone-treated PC12 cells that overexpress wild-type or A53T mutant SNCA by promoting autophagy flux. This effect was also demonstrated in the substantia nigra and the striatum of SNCA<sup>A53T</sup> transgenic mice. The inhibition of SNCA accumulation by pramipexole was attenuated by cotreatment with the DRD2 and DRD3 antagonists and Becn1 siRNAs. Thus, our findings suggest that DRD2 and DRD3 agonist(s) may induce autophagy activation via a BECN1-dependent pathway and have the potential to reduce SNCA accumulation in PD.
Isolation and Characterization of Rice MADS Box Gene Homologues and Their RFLP Mapping (1999)

Thirty-five MADS box gene homologues were identified through a large-scale cDNA analysis in rice. Based on the nucleotide sequences of the 3'-untranslated region, these clones were classified into 11 independent species. Seven species were found to be new among the rice MADS box gene family, and the other 4 corresponded to the previously reported OsMADS1, OsMADS2, OsMADS4, and OsMADS5. The full nucleotide sequences of the 7 new species were determined. Each clone encoded a deduced protein of 164-267 amino acids. The K-domain of the MADS protein was conserved in all clones though with lower degree in clone S10304. Reverse transcription PCR analysis showed that clones E31254 and E31864 were expressed mainly in panicles. Dendrogram analysis suggested that E31254 and E31864 are close to Arabidopsis AGL9 and AP1, respectively. Restriction fragment length polymorphism (RFLP) linkage mapping revealed that the rice MADS box gene homologues reported here are not clustered but are located throughout the genome. The locus of E31864 on the RFLP map was closely linked to the long sterile lemma gene, g-1.
Mechanism of intramolecular activation of pepsinogen. Evidence for an intermediate delta and the involvement of the active site of pepsin in the intramolecular activation of pepsinogen. (1976)

Intramolecular pepsinogen activation is inhibited either by pepstatin, a potent pepsin inhibitor, or by purified globin from hemoglobin, a good pepsin substrate. Also, pepsinogen at pH 2 can be bound to a pepstatin-Sepharose column and recovered as native zymogen upon elution in pH 8 buffer. Kinetic studies of the globin inhibition of pepsinogen activation show that globin binds to a pepsinogen intermediate. This interaction gives rise to competitive inhibition of intramolecular pepsinogen activation. The evidence presented in this paper suggests that pepsinogen is converted rapidly upon acidification to the pepsinogen intermediate delta. In the absence of an inhibitor, the intermediate undergoes conformational change to bind the activation peptide portion of this same pepsinogen molecule in the active center to form an intramolecular enzyme-substrate complex (intermediate theta). This is followed by the intramolecular hydrolysis of the peptide bond between residues 44 and 45 of the pepsinogen molecule and the dissociation of the activation peptide from the pepsin. Intermediate delta apparently does not activate another pepsinogen molecule via an intermolecular process. Neither does intermediate delta hydrolyze globin substrate.
Sending a personalized advertisement to loyal customers in the ubiquitous environment (2016)

In this paper, we propose an approach combining behavioral and targeting techniques for a better reaction of the customer with a star product using a personalized ubiquitous advertisement. We use the clustering to study the customers behavior. In order to validate our approach, we develop a prototype to send a personalized advertisement to loyal customers in an ubiquitous environment. Each target receives the advertising according his degree of loyalty obtained by the behavioral analysis.
Experiences with evaluating network QoS for IP telephony (2003)

Successful deployment of networked multimedia applications such as IP telephony depends on the performance of the underlying data network. QoS requirements of these applications are different from those of traditional data applications. For example, while IP telephony is very sensitive to delay and jitter, traditional data applications are more tolerant of these performance metrics. Consequently, assessing a network to determine whether it can accommodate the stringent QoS requirements of IP telephony becomes critical. We describe a technique for evaluating a network for IP telephony readiness. Our technique relies on the data collection and analysis support of our prototype tool, ExamiNet/spl trade/. It automatically discovers the topology of a given network and collects and integrates network device performance and voice quality metrics. We report the results of assessing the IP telephony readiness of a real network of 31 network devices (routers/switches) and 23 hosts via ExamiNet/spl trade/. Our evaluation identified links in the network that were over utilized to the point at which they could not handle IP telephony.
Physics driven reduced order model for real time blood flow simulations (2019)

Predictive modeling of blood flow and pressure have numerous applications ranging from non-invasive assessment of functional significance of disease to planning invasive procedures. While several such predictive modeling techniques have been proposed, their use in the clinic has been limited due in part to the significant time required to perform virtual interventions and compute the resultant changes in hemodynamic conditions. We propose a fast hemodynamic assessment method based on first constructing an exploration space of geometries, tailored to each patient, and subsequently building a physics driven reduced order model in this space. We demonstrate that this method can predict fractional flow reserve derived from coronary computed tomography angiography in response to changes to a patient-specific lumen geometry in real time while achieving high accuracy when compared to computational fluid dynamics simulations. We validated this method on over 1300 patients that received a coronary CT scan and demonstrated a correlation coefficient of 0.98 with an error of 0.005 +- 0.015 (95% confidence interval: (-0.020, 0.031)) as compared to three-dimensional blood flow calculations.
Interactions between the 2.4 and 4.2 regions of  S, the stress-specific   factor of Escherichia coli, and the -10 and -35 promoter elements (2004)

The sigmas subunit of Escherichia coli RNA polymerase holoenzyme (EsigmaS) is a key factor of gene expression upon entry into stationary phase and in stressful conditions. The selectivity of promoter recognition by EsigmaS and the housekeeping Esigma70 is as yet not clearly understood. We used a genetic approach to investigate the interaction of sigmaS with its target promoters. Starting with down-promoter variants of a sigmaS promoter target, osmEp, altered in the -10 or -35 elements, we isolated mutant forms of sigmaS suppressing the promoter defects. The activity of these suppressors on variants of osmEp and ficp, another target of sigmaS, indicated that sigmaS is able to interact with the same key features within a promoter sequence as sigma70. Indeed, (i) sigmaS can recognize the -35 element of some but not all its target promoters, through interactions with its 4.2 region; and (ii) amino acids within the 2.4 region participate in the recognition of the -10 element. More specifically, residues Q152 and E155 contribute to the strong preference of sigmaS for a C in position -13 and residue R299 can interact with the -31 nucleotide in the -35 element of the target promoters.
Effects of a Novel Compound (AL 721) on HTLV-III Infectivity in Vitro (1985)

This letter reports the results of a study indicating that AL 721 a lipid compound with a demonstrated ability to extract cholesterol from cellular membranes inhibits human T-lymphotropic virus type III (HTLV-III) infection of human peripheral-blood lymphocytes or an immortalized helper T-cell line (H9). When H9 cells were incubated with HTLV-III for 4 days reductions were detected in cell numbers and there were significant levels of reverse transciptase p15 and p24. After H9 cells were infected with HTLV-III in the presence of AL 721 there was a reduction in viral infectivity. The median dose for this effect was 100 mcg/ml of AL 721. It is not clear whether the virucidal effects of AL 721 are due to its actions on the retroviral envelope or on the host cell membrane. In preliminary clinical trials with elderly human subjects daily oral doses of AL 721 over a 6-week period restored diminished lymphocyte proliferative capacity and were well tolerated. AL 721 is considered a promising new candidate for investigation in the treatment of acquired immunodeficiency syndrome (AIDS) especially since it does not produce the side effects that are associated with reverse transcriptase inhibitors.
Bilevel rendition method for documents including gray‐scale and bilevel image (1985)

Abstract The demand of facsimile transmission of printed matter as well as photographs is becoming strong daily as the variety of information is increasing. The disadvantage of the previous methods is that the character quality is deteriorated because in the case of artificial half‐tone reproduction using black and white recording, the resolution is sacrificed and tonal reproduction is performed. In this paper, a method to solve this problem is reported in which each block consisting of multiple picture elements is distinguished as bilevel region or gray‐scale region, and the processing suitable to each region is performed. This paper also describes the results of computer simulation obtained by applying this method to reproduce the characters and photographs. Moreover, the case of gray‐scale region lying inside the character region is discussed and it is shown that a simple region correction method is very effective.
The dog-eaters of bali (1991)

Presentation d'un groupe de Balinais d'un village de Klungkung (Bali), mangeurs de chien, et vivant d'equarissage, de mendicite et de detroussement de cadavres (lors des exhumations precedant les cremations). Ces activites hautement impures selon la societe balinaise sont cependant tolerees par le reste du village
Distributed wireless communication system: a new architecture for future public wireless access (2003)

The distributed wireless communication system (DWCS) is a new architecture for a wireless access system with distributed antennas, distributed processors, and distributed control. With distributed antennas, the system capacity can be expanded through dense frequency reuse, and the transmission power can be greatly decreased. With distributed processors control, the system works like a software or network radio, so different standards can coexist, and the system capacity can be increased by coprocessing of signals to and from multiple antennas.
Fluorescent staphylococci as microbeads (1989)

Fixed bacteria of the protein A-rich Cowan I Staphylococcus strain were labelled with fluorescein isothiocyanate and used as the second-step reagent in an indirect immunofluorescent assay of specific cell-surface antigen expression. The results are documented with fluorescence microscopy and flow cytometry.
A White Scholar and the Black Community, 1945-1965: Essays and Reflections. (1993)

To teachers of African-American history, August Meier is well respected as a first-rank scholar and editor. But few people are aware of his formative experiences in the two decades following World War II, as a white professor teaching at black colleges and as an activist in the civil rights movement. This volume brings together sixteen of his essays written between 1945 and 1965. Meier has added a substantial introduction, reflecting on those years and setting the context in which the essays were written. John H. Bracey, Jr., contributes an afterword which speaks to the uniqueness of Meier's experience among historians of African-American studies. The essays range from an analysis of the work of black sociologists in the twentieth century to an examination of race relations at predominantly black colleges in the 1950s, to case studies of nonviolent direct action in which Meier participated during the early 1960s. Of particular interest is an account of his debate with Malcolm X at Morgan State College in 1962, in which Malcolm X made the case for black nationalism and Meier defended the integrationist position. Collected for the first time, these essays provide a novel perspective on the early years of the civil rights movement and on the experience of historically black colleges such as Tougaloo, Fisk, and Morgan State.
POS Polyline Smoothing: Reduction of Polyline Vertices (2004)

The POS polyline smoothing algorithm was developed to reduce the needed storage and rendering complexity of polylines by the removal of vertices with two goals in mind. First was to define a single algorithm that would produce a "good enough" result with varying characteristics, which are user defined. The concept of "good enough" is built on the trade of time vs. precision, where the best result takes the longest time and the quickest maybe less than desirable form. The second goal was to incorporate surrounding data into the set of control factors. To accomplish this, the concept of Points of Significance (POS) was developed. POS can be a group of individual points, or the point that represents more complex shapes or regions. The complete Set of POS is divided into subsets by the polyline, and by maintaining these subsets the algorithm insures that the polyline maintains a proper relationship with the surrounding data. It is the use of POS that makes this algorithm so powerful. The smoothing is complete after a maximum number of successive passes are made through the polyline, or no additional removals can be made without violating the control factors. -
On <i>de novo</i> interpretation of tandem mass spectra for peptide identification (2003)

The correct interpretation of tandem mass spectra is a difficult problem, even when it is limited to scoring peptides against a database. De novo sequencing is considerably harder, but critical when sequence databases are incomplete or not available. In this paper we build upon earlier work due to Dancik et al., and Chen et al. to provide a dynamic programming algorithm for interpreting de novo spectra. Our method can handle most of the commonly occurring ions, including a; b; y, and their neutral losses. Additionally, we shift the emphasis away from sequencing to assigning ion types to peaks. In particular, we introduce the notion of core interpretations, which allow us to give confidence values to individual peak assignments, even in the absence of a strong interpretation. Finally, we introduce a systematic approach to evaluating de novo algorithms as a function of spectral quality. We show that our algorithm, in particular the core-interpretation, is robust in the presence of measurement error, and low fragmentation probability.
HybridSpace: Integrating 3D freehand input and stereo viewing into traditional desktop applications (2014)

Technologies for 3D input and output are rapidly advancing, and are becoming more common in home and workplace environments. However, viewing a stereoscopic display can cause eye strain and fully relying on 3D spatial interactions can be fatiguing and may be less efficient for common 2D tasks. In this paper we explore the design possibilities of transitioning between 2D and 3D modalities to best support the user's current task. In a formal study, we demonstrate that a Hybrid interaction technique, that transitions between 2D display and input, to 3D, mid-task, outperforms 2D only and 3D only techniques. Guided by this result, we present HybridSpace, a proof-of-concept modeling environment that combines the benefits of 2D and 3D input and output modalities within a single coherent interface.
Optimal Design of Clock Trees for Multigigahertz Applications (2004)

With the onset of gigahertz frequencies on clocked digital systems, inductance effects become significant. We investigate appropriate regimes where signal propagation on an IC can be characterized as resulting from transmission line (TL) behavior. The signals propagate at a speed in the proximity of the speed of light in the medium. Our starting points are exact solutions in the time domain to the TL equations. A methodology to evaluate the feasible domains of physical and electrical variables that permit TL propagation is given. We develop fast and accurate computational methods for inductance and capacitance calculations. A general expression of the time delay in the presence of finite rise time and finite load capacitance for TL propagation is derived. We analyze a clock-synthesis method based on sandwiched balanced H-trees consistent with TL propagation. We find the feasible physical domains by solving iteratively two nonlinear equations in a space spanned by two continuous variables, with four parameters. To further assert its applicability we remove common assumptions such as the constancy of the electromagnetic parameters, zero rise time, and load capacitance. The spectrum of configurations is satisfactory at 130 nm and scales well into the 45-nm generation.
Distribution of phosphodiesterase I in normal human tissues. (1987)

Phosphodiesterase I (PDE I) is an exonuclease capable of hydrolyzing a variety of phosphate ester and pyrophosphate bonds. Cell fractionation and histochemical studies in animal tissues have localized PDE I in the plasma membrane of various epithelia. This suggests a role for the enzyme in active transport. Distribution of PDE I in human tissues has not previously been studied. We have produced a polyclonal antiserum to bovine intestinal PDE I and have demonstrated crossreactivity with the human intestinal enzyme. This polyclonal antiserum was used in PAP immunocytochemistry to localize immunoreactive PDE I in a variety of human tissues. Localization was prominent in the gastrointestinal tract, including the cytoplasm of gastric mucosa parietal cells, cytoplasm of surface epithelium and isolated crypt cells in small intestine, and the colonic epithelial cytoplasm and brush border. Parotid gland acinar cells and scattered ductal cells showed positive cytoplasmic staining. Acinar and scattered pancreatic islet cells contained immunoreactive PDE I, as did Kupffer cells of the liver sinusoids. Immunoreactive PDE I was found in all vascular endothelia. The epithelium of the urinary tract showed extensive immunoreactivity. This included the distal convoluted and collecting tubules of the kidney, and ureteral and bladder urothelium. In previous histochemical studies of animal tissues, no evidence of PDE I activity was noted in male or female reproductive tract. In this study, immunoreactive PDE I was localized to human Sertoli cells and to basal epithelium of the epididymis and prostate acini. Fallopian tube epithelium of female reproductive tract also demonstrated immunoreactive PDI I, as did several cell types in term placenta. Our immunocytochemical results with human tissues differ significantly from previous histochemical studies in animal tissues, principally in the genitourinary system. This may be due in part to the different detection systems employed as well as the higher sensitivity of the immunoperoxidase technique. This underscores the importance of adjunct techniques in tissue surveys. The widespread epithelial distribution of immunoreactive PDE I detected by this polyclonal antibody implies an integral role in cell function, probably in active transport.