gebhart/patrepeval huggingface dataset:
Protection from Collagen-Induced Arthritis in Granulocyte-Macrophage Colony-Stimulating Factor-Deficient Mice (1998)

The involvement of granulocyte-macrophage CSF (GM-CSF) in collagen-induced arthritis (CIA) was examined using GM-CSF-deficient mice. Although CIA is generally considered to be restricted to mice of the H-2q or H-2r haplotypes, we examined the role of GM-CSF in the CIA model using GM-CSF-deficient (-/-) and wild-type (+/+) mice on a C57BL/6 (H-2b) background. Mice were immunized by intradermal injection at the base of the tail with chick type II collagen followed by a repeat injection 21 days later. We found, based on both clinical and histologic assessments, that wild-type mice on this background developed severe CIA, while the GM-CSF-deficient mice had virtually no disease. Mice that were heterozygous for the GM-CSF gene (+/-) collectively displayed an intermediate response between those of the GM-CSF(+/+) and GM-CSF(-/-) groups, suggesting a gene dosage effect. GM-CSF(+/+) and GM-CSF(+/-) mice exhibited CIA responses ranging from mild (single digits) to severe swelling of all four paws, while in the few GM-CSF(-/-) mice that developed CIA the disease was confined to single digits. Despite the putative role of GM-CSF in dendritic cell development, GM-CSF-deficient mice exhibited both humoral and cellular (delayed-type hypersensitivity) responses to type II collagen; however, the cellular response was significantly reduced in the GM-CSF-deficient mice compared with the wild-type controls. These findings suggest that GM-CSF is required for CIA development in mice and support the idea that GM-CSF is a key cytokine in inflammatory joint disease.
Ultrasound-Guided Robot for Flexible Needle Steering (2009)

The success rate of medical procedures involving needle insertion is often directly related to needle placement accuracy. Due to inherent limitations of commonly used freehand needle placement techniques, there is a need for a system providing for controlled needle steering for procedures that demand high positional accuracy. This paper describes a robotic system developed for flexible needle steering inside soft tissues under real-time ultrasound imaging. An inverse kinematics algorithm based on a virtual spring model is applied to calculate needle base manipulations required for the tip to follow a curved trajectory while avoiding physiological obstacles. The needle tip position is derived from ultrasound images and is used in calculations to minimize the tracking error, enabling a closed-loop needle insertion. In addition, as tissue stiffness is a necessary input to the control algorithm, a novel method to classify tissue stiffness from localized tissue displacements is proposed and shown to successfully distinguish between soft and stiff tissue. The system performance was experimentally verified by robotic manipulation of the needle base inside a phantom with layers of varying stiffnesses. The closed-loop experiment with updated tissue stiffness parameters demonstrated a needle-tip tracking error of approximately 1 mm and proved to be significantly more accurate than the freehand method.
Identification of Group B Streptococcal Sip Protein, Which Elicits Cross-Protective Immunity (2000)

A protein of group B streptococci (GBS), named Sip for surface immunogenic protein, which is distinct from previously described surface proteins, was identified after immunological screening of a genomic library. Immunoblots using a Sip-specific monoclonal antibody indicated that a protein band with an approximate molecular mass of 53 kDa which did not vary in size was present in every GBS strain tested. Representatives of all nine GBS serotypes were included in the panel of strains. Cloning and sequencing of the sip gene revealed an open reading frame of 1,305 nucleotides coding for a polypeptide of 434 amino acid residues, with a calculated pI of 6. 84 and molecular mass of 45.5 kDa. Comparison of the nucleotide sequences from six different strains confirmed with 98% identity that the sip gene is highly conserved among GBS isolates. N-terminal amino acid sequencing also indicated the presence of a 25-amino-acid signal peptide which is cleaved in the mature protein. More importantly, immunization with the recombinant Sip protein efficiently protected CD-1 mice against deadly challenges with six GBS strains of serotypes Ia/c, Ib, II/R, III, V, and VI. The data presented in this study suggest that this highly conserved protein induces cross-protective immunity against GBS infections and emphasize its potential as a universal vaccine candidate.
Ionization of Cyclic Aromatic Amines by Free Electron Transfer:  Products Are Governed by Molecule Flexibility (2005)

The bimolecular electron transfer from secondary aromatic amines to parent radical cations of nonpolar solvents such as alkanes and alkyl chlorides results in the synchronous formation of amine radical cations as well as aminyl radicals, in comparable amounts. If as for cyclic aromatic amines (c-Ar(2)NH) the intramolecular bending motion around the amine group is restricted in varying degrees (acridane, phenothiazine) or completely prevented (carbazole), then this picture is modified. In the free electron transfer, the completely rigid carbazole yields exclusively amine radical cations. Acridane exhibits preferred radical cations, but phenothiazine with the more flexible six-membered ring involving sulfur as a further heteroatom follows the common two-product rule; see above. The phenomenon is reasoned by a peculiarity in the bimolecular free electron transfer where after diffusional approach the actual electron jump proceeds in the ultrashort time range. Therefore, it reflects femtosecond molecular motions which, in the case of free mobility, continuously pass through different molecule conformers, combined with fluctuation of the electrons of the responsible molecular n-orbitals. The rigid systems, however, do not show this effect because of a nonexistent bending motion.
Collaborative, programmable intelligent agents (1998)

article Free Access Share on Collaborative, programmable intelligent agents Authors: Bonnie A. Nardi AT&T Labs Research, Menlo Park, Calif. AT&T Labs Research, Menlo Park, Calif.View Profile , James R. Miller Apple's Advanced Technology Apple's Advanced TechnologyView Profile , David J. Wright Apple's Operating Systems Technologies Apple's Operating Systems TechnologiesView Profile Authors Info & Claims Communications of the ACMVolume 41Issue 3March 1998 pp 96–104https://doi.org/10.1145/272287.272331Online:01 March 1998Publication History 86citation1,307DownloadsMetricsTotal Citations86Total Downloads1,307Last 12 Months28Last 6 weeks9 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
High background in ELISpot assays is associated with elevated levels of immune activation in HIV‐1‐seronegative individuals in Nairobi (2018)

These findings suggest that increased basal immune responses may be a biological mechanism contributing to higher background ELISpot SFU. Systematic exclusion of data from individuals with increased background in IFN-γ release assays may bias results in population-based studies.
The oestrous cycle in the mouse (1922)

Resunien por el ailtor, Edgar Allen E l ciclo Cstrico del ratbn.$2 autor coinpara 1:ts observaciones llevadas a cabo en aninisles vivos con 10s carnbios histolhgicos en el tracto genital y 10s ovarios.Estos cambios son de naturaleza ciclica y re-( uieren un periodo medio de cuatro a seis dias.Los estados r.i6n represent ados por quiescencia, crecimiento, el climax &trico y degeneracihn.Se manifiestan en la vagina por la forinacihn ciclica y la degeneracihn dt una capa chrnea.L o b caiiibos tlcgencrativos en el epitelio uterino no siguen a t-u extirpacibn : conio consecuencia de esto la hemorragia uterina es rara.La extrusihn de 10s nilcleos en el cpitelio ciliado del oviducto es paralela a las fascs degeneratiras dcl titpro y la \.:igina.E n le ovario existen grandes foliculos durante la fase anabhlica y son reemplazados por cuerpos aniarillos en la fase catabblica.I'or consiguicntc, la ovulacih separa a estas fases y tierie lugar clurante el cstro.I,a clasificncihn del rathn entre las cspecies de orulacihn espont6ne:t cs errOnea.Algunos ovulan con regularidad, otros tan solo c k un niodo espoddico, y otros tan d o ovulan con un estiiiiulo sexual adicional.Difcrentes modos en la lonpitud del ciclo son pcculiares tie diversas razas de rutones.Puesto clue cl ciclo cs corto y la ovulachn puetle per c-pont8nea o no serlo.10s ovarios pceden contencr tres o cuatro series de cuerpos amarillos \-oluniinokos o no contrner ninguno.Eli anibos caws se presentan ciclos nornialcs.ai conwccencia tle esto parece juhtificada la conclubiGn de que 10s cuerpos aniaril-105 dcl estro no poseen funcihi causatira en 10s procehos :inabhlicos o catabOlicos dcl cico estrico.Las pruebas acuniu-1atlas iridican
Crystal Structure of Nucleotide-Free Diphtheria Toxin, (1997)

The crystal structure of diphtheria toxin (DT) in the absence of nucleotide (nucleotide-free DT) has been determined at 2.3 A resolution to a crystallographic R factor and free R factor of 18.2 and 28.2%, respectively. A comparison of this structure to the previously determined structures of DT in complex with adenyly(3'-5')uridine monophosphate (ApUp) and DT in complex with nicotinamide adenine dinucleotide (NAD) reveals that there are no significant movements of the two subdomains of the catalytic (C) domain associated with dinucleotide binding. The side chains of six residues within the active-site cleft, including Tyr65, Pro38, Tyr27, Thr23, Glu148, and Tyr54, show movements of up to 3 A upon dinucleotide binding. In the structure of nucleotide-free DT, the active-site loop residues 39-47 of the C domain are well ordered and extend over the active-site cleft in approximately the same position as in the structure of DT in complex with ApUp. This is in contrast to the structure of the DT-NAD complex, in which the active-site loop is disordered. On the basis of a comparison of the nucleotide-free and NAD-bound DT structures, we suggest that the interaction of NAD with Pro38 and also possibly Tyr54 and Trp153 could disrupt the network of hydrogen bonds that stabilizes the position of the active-site loop over the active-site cleft, allowing this loop to become disordered. This may be an important step in binding of the C domain of DT to its substrate, elongation factor-2.
Human induced pluripotent stem cells are capable of B-cell lymphopoiesis (2011)

Induced pluripotent stem (iPS) cells offer a unique potential for understanding the molecular basis of disease and development. Here we have generated several human iPS cell lines, and we describe their pluripotent phenotype and ability to differentiate into erythroid cells, monocytes, and endothelial cells. More significantly, however, when these iPS cells were differentiated under conditions that promote lympho-hematopoiesis from human embryonic stem cells, we observed the formation of pre-B cells. These cells were CD45(+)CD19(+)CD10(+) and were positive for transcripts Pax5, IL7αR, λ-like, and VpreB receptor. Although they were negative for surface IgM and CD5 expression, iPS-derived CD45(+)CD19(+) cells also exhibited multiple genomic D-J(H) rearrangements, which supports a pre-B-cell identity. We therefore have been able to demonstrate, for the first time, that human iPS cells are able to undergo hematopoiesis that contributes to the B-cell lymphoid lineage.
Zwitterionic Polysaccharides Stimulate T Cells with No Preferential Vβ Usage and Promote Anergy, Resulting in Protection against Experimental Abscess Formation (2004)

Abstract Zwitterionic polysaccharides (Zps) from pathogenic bacteria, such as Bacteroides fragilis, are virulence factors responsible for abscess formation associated with intra-abdominal sepsis. The underlying cellular mechanism for abscess formation requires T cell activation. Conversely, abscess formation can be prevented by prophylactic s.c. injection of purified Zps alone, a process also dependent on T cells. Hence, the modulatory role of T cells in abscess formation was investigated. We show that Zps interact directly with T cells with fast association/dissociation kinetics. Vβ repertoire analysis using RT-PCR demonstrates that Zps have broad Vβ usage. Zps-specific hybridomas responded to a variety of other Zps, but not to a nonzwitterionic polysaccharide, indicating cross-reactivity between different Zps. Furthermore, Zps-reactive T cell hybridomas could effectively transfer protection against abscess formation. Analysis of the proliferative capacity of T cells recovered from Zps-treated animals revealed that these T cells are anergic to subsequent stimulation by the different Zps or to alloantigens in an MLR. This anergic response was relieved by addition of IL-2. Taken together, the data show that this class of polysaccharides interacts directly with T cells in a nonbiased manner to elicit an IL-2-dependent anergic response that confers protection against abscess formation.
Outbreak of Vancomycin-Resistant Enterococci in a Burn Unit (2000)

A VRE outbreak in a BICU over 13 months was caused by a single clone. After apparent eradication of VRE from a BICU, recrudescence of the outbreak occurred, evidently from a small inapparent source of environmental contamination. Changes in gastrointestinal (GI) tract function (motility) and administration of medications, other than antibiotics, that have an effect on the GI tract may increase the risk of GI tract colonization by VRE in burn patients. Application of barrier isolation and an aggressive environmental decontamination program can eradicate VRE from a burn population.
Position Control of Motion Compensation Cardiac Catheters (2011)

Robotic catheters have the potential to revolutionize cardiac surgery by enabling minimally invasive structural repairs within the beating heart. This paper presents an actuated catheter system that compensates for the fast motion of cardiac tissue using 3D ultrasound image guidance. We describe the design and operation of the mechanical drive system and catheter module and analyze the catheter performance limitations of friction and backlash in detail. To mitigate these limitations, we propose and evaluate mechanical and control system compensation methods, including inverse and model-based backlash compensation, to improve the system performance. Finally, in vivo results are presented that demonstrate that the catheter can track the cardiac tissue motion with less than 1 mm RMS error. The ultimate goal of this research is to create a fast and dexterous robotic catheter system that can perform surgery on the delicate structures inside of the beating heart.
Limit cycle control and its application to the animation of balancing and walking (1996)

Article Free Access Share on Limit cycle control and its application to the animation of balancing and walking Authors: Joseph Laszlo Department of Electrical and Computer Engineering, University of Toronto Department of Electrical and Computer Engineering, University of TorontoView Profile , Michiel van de Panne Department of Computer Science, University of Toronto Department of Computer Science, University of TorontoView Profile , Eugene Fiume Department of Computer Science, University of Toronto Department of Computer Science, University of TorontoView Profile Authors Info & Claims SIGGRAPH '96: Proceedings of the 23rd annual conference on Computer graphics and interactive techniquesAugust 1996Pages 155–162https://doi.org/10.1145/237170.237231Published:01 August 1996Publication History 133citation2,030DownloadsMetricsTotal Citations133Total Downloads2,030Last 12 Months130Last 6 weeks14 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Publisher SiteeReaderPDF
The Golgi-associated long coiled-coil protein NECC1 participates in the control of the regulated secretory pathway in PC12 cells (2012)

Golgi-associated long coiled-coil proteins, often referred to as golgins, are involved in the maintenance of the structural organization of the Golgi apparatus and the regulation of membrane traffic events occurring in this organelle. Little information is available on the contribution of golgins to Golgi function in cells specialized in secretion such as endocrine cells or neurons. In the present study, we characterize the intracellular distribution as well as the biochemical and functional properties of a novel long coiled-coil protein present in neuroendocrine tissues, NECC1 (neuroendocrine long coiled-coil protein 1). The present study shows that NECC1 is a peripheral membrane protein displaying high stability to detergent extraction, which distributes across the Golgi apparatus in neuroendocrine cells. In addition, NECC1 partially localizes to post-Golgi carriers containing secretory cargo in PC12 cells. Overexpression of NECC1 resulted in the formation of juxtanuclear aggregates together with a slight fragmentation of the Golgi and a decrease in K+-stimulated hormone release. In contrast, NECC1 silencing did not alter Golgi architecture, but enhanced K+-stimulated hormone secretion in PC12 cells. In all, the results of the present study identify NECC1 as a novel component of the Golgi matrix and support a role for this protein as a negative modulator of the regulated trafficking of secretory cargo in neuroendocrine cells.
A longitudinal study of T1 hypointense lesions in relapsing MS (2000)

The development of T1 hypointense lesions is strongly influenced by prior inflammatory disease activity, as indicated by enhancing lesions. These results suggest that treatment with once weekly IM IFNbeta-1a (30 mcg) slows the 2-year accumulation of these lesions in the brain.
Polarization effects in fiber Raman and Brillouin lasers (1979)

Raman and Brillouin gains in fibers are a factor of 2 higher if linear polarization is maintained. Birefringent single-mode fibers are used to demonstrate this gain difference. Threshold powers of 200 mW have been achieved in Raman oscillators.
Antibodies against Hemolysin and Cytotoxic Necrotizing Factor Type 1 (CNF1) Reduce Bladder Inflammation in a Mouse Model of Urinary Tract Infection with Toxigenic Uropathogenic Escherichia coli (2015)

Uropathogenic Escherichia coli (UPEC) is the leading cause of cystitis. Cytotoxic necrotizing factor 1 (CNF1) and hemolysin (Hly) are toxins made by approximately 50% of UPEC isolates. CNF1 and Hly contribute to the robust inflammatory response in the bladders of mice challenged with UPEC strain CP9. We hypothesized that antibodies against CNF1 and/or Hly would reduce cystitis caused by CP9. To test this theory, we immunized female C3H/HeOuJ mice subcutaneously with a genetically derived Hly toxoid or genetically derived CNF1 toxoid plus sublethal doses of CNF1. We collected serum and observed increasing titers of specific and neutralizing antibodies against Hly or CNF1 over time. We challenged the mice intraurethrally with CP9 and euthanized them 24 h later. We observed 10-fold lower bacterial titers in the urine of Hly-immunized mice than in that of sham-immunized mice but no difference in kidney bacterial titers. Immunized mice also exhibited significantly less cystitis than sham-immunized mice. In CNF1-vaccinated mice, we detected neither a difference in urine or kidney bacterial titers nor a reduction in the severity of cystitis versus that of sham-immunized mice. We then passively administered an anti-CNF1 monoclonal antibody intraperitoneally to female C3H/HeOuJ mice prior to intraurethral challenge with CP9. Upon challenge, we noted no difference in colonization of the urine or kidney; however, cystitis was reduced significantly in mice treated with the anti-CNF1 antibody versus that in the bladders of mice given an isotype control antibody. Taken together, our data demonstrate that antibodies against CNF1 or Hly reduce the bladder pathology caused by UPEC.
Fine Structure Genetic Analysis of a β-Globin Promoter (1986)

A novel procedure for saturation mutagenesis of cloned DNA was used to obtain more than 100 single base substitutions within the promoter of the mouse beta-major globin gene. The effects of these promoter substitutions on transcription were determined by transfecting the cloned mutant genes into HeLa cells on plasmids containing an SV40 transcription enhancer, and measuring the levels of correctly initiated beta-globin transcripts after 2 days. Mutations in three regions of the promoter resulted in a significant decrease in the level of transcription: (i) the CACCC box, located between -87 and -95, (ii) the CCAAT box, located between -72 and -77, and (iii) the TATA box, located between -26 and -30 relative to the start site of transcription. In contrast, two different mutations in nucleotides immediately upstream from the CCAAT box resulted in a 3- to 3.5-fold increase in transcription. With two minor exceptions, single base substitutions in all other regions of the promoter had no effect on transcription. These results precisely delineate the cis-acting sequences required for accurate and efficient initiation of beta-globin transcription, and they establish a general approach for the fine structure genetic analysis of eukaryotic regulatory sequences.
Gene-Engineered Varicella-Zoster Virus–Reactive CD4+ Cytotoxic T Cells Exert Tumor-Specific Effector Function (2007)

T cells with grafted specificities for surface antigens provide an avenue for rapidly producing immune effector cells with tumor specificity. However, the function of chimeric receptor (chRec) gene-modified T cells is limited by lack of T-cell expansion and persistence. We propose to use varicella zoster virus (VZV)-reactive T cells as host for the chRec because these cells can be expanded both in vitro and in vivo by stimulation of their native receptor during endogenous reexposure to the virus or by administration of VZV vaccine. We obtained human T cells reactive with VZV from the peripheral blood of seropositive donors by stimulation with VZV lysate and evaluated their characteristics after genetic modification with two tumor-specific model chRecs. Cultures dominated by cytolytic CD4(+) T cells (VZV-CTL) could be expanded and maintained in vitro. Gene-modified VZV-CTL recognized and lysed tumor targets in a MHC-independent manner while maintaining functional, MHC-restricted interaction with VZV antigen through their native receptor. Thus, chRec-transduced VZV-CTL may provide a source of potent tumor-reactive cells for adoptive immunotherapy of cancer. The availability of a safe and effective VZV vaccine provides the option of repeated in vivo stimulation to maintain high T-cell numbers until the tumor is eliminated.