gebhart/patrepeval huggingface dataset:
Cyclophosphamide for the treatment of systemic lupus erythematosus (2001)

Aggressive immunosuppressive therapy with cyclophosphamide has improved the outcome of major organ disease in lupus patients. Controlled trials have shown that pulse cyclophosphamide is the treatment of choice for patients with moderate to severe proliferative nephritis. Long-term follow-up of patients participating in these controlled trials suggests that combining pulse cyclophoshamide with pulse methylprednisolone increases efficacy but not toxicity. Retrospective case series have also shown that pulse cyclophosphamide therapy may be effective for the management of severe or refractory to standard therapy neuropsychiatric, pulmonary, cardiovascular and hematologic disease. Pulse cyclophosphamide is associated with an increased risk for herpes zoster infections in the short term and with sustained amenorrhea in the long-term. Recent studies have also drawn attention to the lack of response (or incomplete response) and flare of lupus after an initial response. In an effort to circumvent these limitations, current investigations explore the therapeutic potential of high-dose, immunoablative cyclophosphamide therapy or low-dose cyclophosphamide in combination with nucleoside analogs or biologic response modifiers.
Molecular, Clinical Studies in Spinocerebebellar Ataxia Type 2 (2001)

The spinocerebellar atrophy type 2 (SCA2) is caused by a CAG trinucleotide repeat expansion within ataxin-2 gene that has been mapped to chromosome 12q23-q24.1. Herein we present a 40-year-old native Taiwanese male and his family members. The patient presented with progressive ataxia and severe postural and action tremor. Three affected subjects also had prominent auditory myoclonus, DNA analysis of the SCA2 gene in this patient revealed one normal allele containing 22 CAG repeats and one expanded allele containing 39 CAG repeats. Such a finding is comparable to that observed in Caucasians, for which normal allele in the SCA2 gene contained 22-23 CAG repeats and the mutant allele contained more than 34 repeats. This is the first family study of SCA2 with the clinical manifestation involving auditory myoclonus and ataxia gait.
A toolbox and procedural notes for characterizing novel zinc finger nucleases for genome editing in plant cells (2008)

The induction of double-strand breaks (DSBs) in plant genomes can lead to increased homologous recombination or site-specific mutagenesis at the repair site. This phenomenon has the potential for use in gene targeting applications in plant cells upon the induction of site-specific genomic DSBs using zinc finger nucleases (ZFNs). Zinc finger nucleases are artificial restriction enzymes, custom-designed to cleave a specific DNA sequence. The tools and methods for ZFN assembly and validation could potentially boost their application for plant gene targeting. Here we report on the design of biochemical and in planta methods for the analysis of newly designed ZFNs. Cloning begins with de novo assembly of the DNA-binding regions of new ZFNs from overlapping oligonucleotides containing modified helices responsible for DNA-triplet recognition, and the fusion of the DNA-binding domain with a FokI endonuclease domain in a dedicated plant expression cassette. Following the transfer of fully assembled ZFNs into Escherichia coli expression vectors, bacterial lysates were found to be most suitable for in vitro digestion analysis of palindromic target sequences. A set of three in planta activity assays was also developed to confirm the nucleic acid digestion activity of ZFNs in plant cells. The assays are based on the reconstruction of GUS expression following transient or stable delivery of a mutated uidA and ZFN-expressing cassettes into target plants cells. Our tools and assays offer cloning flexibility and simple assembly of tested ZFNs and their corresponding target sites into Agrobacterium tumefaciens binary plasmids, allowing efficient implementation of ZFN-validation assays in planta.
Gliomas are driven by glycolysis: putative roles of hexokinase, oxidative phosphorylation and mitochondrial ultrastructure. (1997)

To elucidate the reasons for glycolytic deviation commonly found in brain tumors, hexokinase (HK) activity, mitochondria-HK binding, oxidative phosphorylation and mitochondrial ultrastructure were studied in 4 human xenografted gliomas. Lactate/pyruvate ratios were increased 3-4 fold and HK activity was of 2-4 fold lower than that of normal rat brain tissue, used as the control. The mitochondria-bound HK (mHK) fraction varied considerably and represented 9 to 69% of the total HK of that normal rat brain. The respiratory activity of glioma mitochondria, assessed by polarography and spectrophotometry, was within the normal range. However, the mitochondrial content of gliomas was lower than in the rat brain tissue, as revealed by the markedly decreased, activities of two unrelated mitochondrial enzymes, cytochrome c oxidase and citrate synthase in glioma homogenates. Electron microscopical studies confirmed the reduced number of mitochondria in 3 out of the 4 gliomas. Profound alterations of mitochondrial ultrastructure, namely of cristae and matrix densities, were observed in the 4 gliomas. The intercrista space was wider in all gliomas and the crista area was larger in 3 out of the 4 gliomas than in normal rat brain. Finally, the outer membrane of glioma mitochondria interacted intimately and extensively with the rough endoplasmic reticulum (RER) and/or nuclear membrane. These results suggest that, because of the very low content of normally functioning mitochondria, gliomas shift their energy metabolism towards a high-level glycolysis to generate their cellular ATP supply, probably through RER-mitochondria interactions and transformation-dependent redistribution of particulate HK from non-mitochondrial to mitochondrial receptors.
Tissue injury caused by deposition of immune complexes is L-arginine dependent. (1991)

Nitric oxide (NO.), a free radical that is generated from L-arginine by stimulated endothelial cells, neutrophils, activated macrophages, and other cell types, reacts with superoxide anion (O2.-) to form peroxynitrite, which itself may be tissue toxic or can then react further to form the highly reactive and toxic hydroxyl radical (HO.). Because vascular injury produced by tissue deposition of immune complexes is linked to formation of toxic products derived from activated neutrophils, we have assessed whether immune complex-induced injury of rat lung and dermal vasculature is arginine dependent. The arginine analogue, NG-monomethyl-L-arginine (N-MeArg), which blocks NO. formation, protects against immune complex-induced vascular injury in rats. The protective effects of N-MeArg are reversed by the presence of L-arginine but not D-arginine. Additionally, in the absence of N-MeArg, injury is enhanced by the presence of L-arginine but not by D-arginine. Protection by N-MeArg is not associated with diminished recruitment of polymorphonuclear leukocytes. Bronchoalveolar lavage fluids from animals undergoing immune complex deposition in lung contain the decomposition products of NO.--namely, nitrite and nitrate. In the presence of N-MeArg these products are greatly diminished. These data suggest that immune complex-induced injury of rat lung and skin is L-arginine dependent. These data also suggest that in vivo metabolic products of L-arginine, such as NO(.), are directly or indirectly linked to immune complex-induced tissue injury.
MIL-96, a Porous Aluminum Trimesate 3D Structure Constructed from a Hexagonal Network of 18-Membered Rings and μ3-Oxo-Centered Trinuclear Units (2006)

A new aluminum trimesate Al12O(OH)18(H2O)3(Al2(OH)4)[btc]6.24H2O, denominated MIL-96, was synthesized under mild hydrothermal conditions (210 degrees C, 24 h) in the presence of 1,3,5-benzenetricarboxylic acid (trimesic acid or H3btc) in water. Hexagonal crystals, allowing a single-crystal XRD analysis, are grown from a mixture of trimethyl 1,3,5-benzenetricarboxylate (Me3btc), HF, and TEOS. The MIL-96 structure exhibits a three-dimensional (3D) framework containing isolated trinuclear mu3-oxo-bridged aluminum clusters and infinite chains of AlO4(OH)2 and AlO2(OH)4 octahedra forming a honeycomb lattice based on 18-membered rings. The two types of aluminum groups are connected to each other through the trimesate species, which induce corrugated chains of aluminum octahedra, linked via mu2-hydroxo bonds with the specific -cis-cis-trans- sequence. The 3D framework of MIL-96 reveals three types of cages. Two of them, centered at the special positions 0 0 0 and 2/3 1/3 1/4, have estimated pore volumes of 417 and 635 A3, respectively, and encapsulate free water molecules. The third one has a smaller pore volume and contains disordered aluminum octahedral species (Al(OH)6). The solid-state NMR characterization is consistent with crystal structure and elemental and thermal analyses. The four aluminum crystallographic sites are resolved by means of 27Al 3QMAS technique. This product is able to sorb both carbon dioxide and methane at room temperature (4.4 mmol.g(-1) for CO2 and 1.95 mmol.g(-1) for CH4 at 10 bar) and hydrogen at 77 K (1.91 wt % under 3 bar).
HEAT Repeats Associated with Condensins, Cohesins, and Other Complexes Involved in Chromosome-Related Functions (2000)

HEAT repeats correspond to tandemly arranged curlicue-like structures that appear to serve as flexible scaffolding on which other components can assemble. Using sensitive sequence analysis techniques we detected HEAT repeats in various chromosome-associated proteins, including four families of proteins associated with condensins and cohesins, which are nuclear complexes that contain structural maintenance of chromosome (SMC) proteins. Among the proteins detected were the XCAP-D2 and XCAP-G subunits of the Xenopus laevis 13S condensin complex, the Aspergillus BimD and Sordaria macrospora Spo76p proteins, the budding yeast Scc2p protein, and the related Drosophila transcriptional activator Nipped-B. Clathrin adaptor and COP-I coatomer subunits, which function in vesicle coat assembly and were previously noted to share weak sequence similarity to condensin subunits, also contain HEAT repeats. HEAT repeats were also found in the TBP-associated TIP120 protein, a global enhancer of transcription, and in the budding yeast Mot1p protein, which is a member of the SWI2/SNF2 family. SWI2/SNF2 proteins, some of which are helicases, perform diverse roles in transcription control, DNA repair, and chromosome segregation and form chromatin-remodeling complexes. HEAT repeats also were found in dis1-TOG family and cofactor D family microtubule-associated proteins, which, owing to their roles in microtubule dynamics, perform functions related to mitotic progression and chromosome segregation. Hence, our analysis predicts structural features of these proteins and suggests that HEAT repeats may play important roles in chromosome dynamics.
Optical cross-connect system based on the White cell and three-state microelectromechanical system: experimental demonstration of the quartic cell (2006)

We present a proof of concept (design, simulations, and experimental results) for an optical cross-connection device based on the optical White cell and a three-state microelectromechanical system tilting mirror array. We describe in detail the implementation of an underpopulated quartic White cell configuration. We discuss the aberrations associated with the output of the system.
Early Biomarker Activity in Severe Sepsis and Septic Shock and a Contemporary Review of Immunotherapy Trials (2013)

Improving time to diagnosis and intervention has positively impacted outcomes in acute myocardial infarction, stroke, and trauma through elucidating the early pathogenesis of those diseases. This insight may partly explain the futility of time-insensitive immunotherapy trials for severe sepsis and septic shock. The aim of this study was to examine the early natural history of circulatory biomarker activity in sepsis, relative to previous animal and human outcome trials. We conducted a literature search using PubMed, MEDLINE, and Google Scholar to identify outcome trials targeting biomarkers with emphasis on the timing of therapy. These findings were compared with the biomarker activity observed over the first 72 h of hospital presentation in a cohort of severe sepsis and septic shock patients. Biomarker levels in animal and human research models are elevated within 30 min after exposure to an inflammatory septic stimulus. Consistent with these findings, the biomarker cascade is activated at the most proximal point of hospital presentation in our patient cohort. These circulatory biomarkers overlap; some have bimodal patterns and generally peak between 3 and 36 h while diminishing over the subsequent 72 h of observation. When this is taken into account, prior outcome immunotherapy trials have generally enrolled patients after peak circulatory biomarker concentrations. In previous immunotherapy sepsis trials, intervention was delayed after the optimal window of peak biomarker activity. As a result, future studies need to recalibrate the timing of enrollment and administration of immunotherapy agents that still may hold great promise for this deadly disease.
Sleep Apnea: (2004)

In the general adult population, prevalence of sleep apnea syndrome reaches 4% in men and 2% in women. Continuous positive airway pressure is the most efficient treatment. At the present time, although severe atrial bradycardias could occur during sleep apnea episodes, cardiac pacing has not been demonstrated as an efficient treatment for those bradycardias. Treating sleep apnea generally reduces the number of bradyarrhythmias. However, recent studies reported a beneficial effect of atrial pacing on the sleep apnea burden. The mechanisms rely on two phenomena: first to counteract nocturnal hypervagotonia, and second to treat heart failure. By increasing the heart rate, cardiac output improves, which mitigates pulmonary subedema. Consequently, stimulation of the pulmonary afferent vagal fibers is diminished, which reduces central sleep apnea incidence. During nocturnal hypervagotonia, snoring and obstructive apnea episodes are increased, mainly due to an excessive muscular relaxation of the upper airway area inducing cyclical substantial decreases in the airway caliper. In patients with a low heart rate, atrial pacing can counteract hypervagotonia by enhancing the sympathetic tone and modifying the degree of vigilance. Accordingly, in the near future, sleep apnea treatment might potentially rely on atrial pacing in bradycardic patients with hypervagotonia (with or without heart failure). The role of the physician would then be not only to diagnose sleep apnea, but also to identify potential responders to cardiac pacing.
Interleukin‐10 reduces scar formation in both animal and human cutaneous wounds: Results of two preclinical and phase II randomized control studies (2013)

Cutaneous scarring affects up to 100 million people per annum. There is no effective scar reducing/preventing therapeutic developed to date. Interleukin (IL)-10 is an anti-inflammatory and antifibrotic cytokine. In the embryo it is important for scarless wound repair. We investigated the effect on wound healing and scarring of a double deletion of the IL-10 and IL-4 genes in a knockout (KO) mouse model, and also the effect of exogenous addition of recombinant human (rh) IL-10 into rat and human cutaneous incisions. Mouse study: Two incisions were made on the dorsal skin of 20 double IL-4/IL-10 KO mice and 20 wild-type (WT) controls. Rat study: Three concentrations of rhIL-10 were investigated. Four incisions were made on the dorsal skin of 30 rats. Each rat received two concentrations. Each incision receiving a concentration of rhIL-10 was matched with a control incision, which received either placebo or standard care. Human study: Eight concentrations of rhIL-10 were investigated. Four incisions were made on each arm of 175 healthy volunteers. Four incisions received four different concentrations, which were matched with four control incisions that received either standard care or placebo. KO mice healed with poor scar histology and increased inflammation. rhIL-10-treated rat incisions healed with decreased inflammation, better scar histology, and better macroscopic scar appearance. rhIL-10-treated human incisions at low concentrations healed with better macroscopic scar appearance and less red scars. IL-10 is an important cytokine in wound healing and its suppression of inflammation and scarring is demonstrated in mice and rats with a translational effect in humans.
A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1 (1998)

The 3.0-A structure of a 190-residue fragment of intercellular adhesion molecule-1 (ICAM-1, CD54) reveals two tandem Ig-superfamily (IgSF) domains. Each of two independent molecules dimerizes identically with a symmetry-related molecule over a hydrophobic interface on the BED sheet of domain 1, in agreement with dimerization of ICAM-1 on the cell surface. The residues that bind to the integrin LFA-1 are well oriented for bivalent binding in the dimer, with the critical Glu-34 residues pointing away from each other on the periphery. Residues that bind to rhinovirus are in the flexible BC and FG loops at the tip of domain 1, and these and the upper half of domain 1 are well exposed in the dimer for docking to virus. By contrast, a residue important for binding to Plasmodium falciparum-infected erythrocytes is in the dimer interface. The presence of A' strands in both domains 1 and 2, conserved hydrogen bonds at domain junctions, and elaborate hydrogen bond networks around the key integrin binding residues in domain 1 make these domains suited to resist tensile forces during adhesive interactions. A subdivision of the intermediate (I) set of IgSF domains is proposed in which domain 1 of ICAM-1 and previously described I set domains belong to the I1 set and domain 2 of ICAM-1, ICAM-2, and vascular cell adhesion molecule-1 belong to the I2 set.
Hemato-lymphoidin vivoreconstitution potential of subpopulations derived fromin vitrodifferentiated embryonic stem cells (1997)

During differentiation in vitro, embryonic stem (ES) cells generate progenitors for most hemato-lymphoid lineages. We studied the developmental potential of two ES cell subpopulations that share the fetal stem cell antigen AA4.1 but differ in expression of the lymphoid marker B220 (CD45R). Upon transfer into lymphoid deficient mice, the B220+ population generated a single transient wave of IgM+ IgD+ B cells but failed to generate T cells. In contrast, transfer of the B220- fraction achieved long-term repopulation of both T and B lymphoid compartments and restored humoral and cell-mediated immune reactions in the recipients. To assess the hemato-lymphopoietic potential of ES cell subsets in comparison to their physiological counterparts, cotransplantation experiments with phenotypically homologous subsets of fetal liver cells were performed, revealing a more potent developmental capacity of the latter. The results suggest that multipotential and lineage-committed lymphoid precursors are generated during in vitro differentiation of ES cells and that both subsets can undergo complete final maturation in vivo.
Tyrosine Phosphorylation of Caveolin-2 at Residue 27:  Differences in the Spatial and Temporal Behavior of Phospho-Cav-2 (pY19 and pY27) (2004)

Caveolin-2 is an accessory molecule and the binding partner of caveolin-1. Previously, we showed that c-Src expression leads to the tyrosine phosphorylation of Cav-2 at position 19. To further investigate the tyrosine phosphorylation of Cav-2, we have now generated a novel phospho-specific antibody directed against phospho-Cav-2 (pY27). Here, we show that Cav-2 is phosphorylated at both tyrosines 19 and 27. We reconstituted this phosphorylation event by recombinantly coexpressing c-Src and Cav-2. We generated a series of Cav-2 constructs harboring the mutation of each tyrosine to alanine, singly or in combination, i.e., Cav-2 Y19A, Y27A, and Y19A/Y27A. Recombinant expression of these mutants in Cos-7 cells demonstrated that neither tyrosine is the unique phosphorylation site, and that double mutation of tyrosines 19 and 27 to alanine abrogates Cav-2 tyrosine phosphorylation. Immunofluorescence analysis of NIH 3T3 cells revealed that the two tyrosine-phosphorylated forms of Cav-2 exhibited some distinct properties. Phospho-Cav-2 (pY19) is concentrated at cell edges and at cell-cell contacts, whereas phospho-Cav-2 (pY27) is distributed in a dotlike pattern throughout the cell surface and cytoplasm. Further functional analysis revealed that tyrosine phosphorylation of Cav-2 has no effect on its targeting to lipid rafts, but clearly disrupts the hetero-oligomerization of Cav-2 with Cav-1. In an attempt to identify upstream mediators, we investigated Cav-2 tyrosine phosphorylation in an endogenous setting. We found that in A431 cells, EGF stimulation is sufficient to induce Cav-2 phosphorylation at tyrosines 19 and 27. However, the behavior of the two phosphorylated forms of Cav-2 diverges upon EGF stimulation. First, phospho-Cav-2 (pY19) and phospho-Cav-2 (pY27) display different localization patterns. In addition, the temporal response to EGF stimulation appears to be different. Cav-2 is phosphorylated at tyrosine 19 in a rapid and transient fashion, whereas phosphorylation at tyrosine 27 is sustained over time. Three SH2 domain-containing proteins, c-Src, Nck, and Ras-GAP, were found to associate with Cav-2 in a phosphorylation-dependent manner. However, phosphorylation at tyrosine 27 appears to be more critical than phosphorylation at tyrosine 19 for this binding to occur. Taken together, these results suggest that, in addition to the common characteristics that these two sites appear to share, phospho-Cav-2 (pY19) and phospho-Cav-2 (pY27) may each possess a set of unique functional roles.
Cell alignment is induced by cyclic changes in cell length: studies of cells grown in cyclically stretched substrates (2001)

Many types of cells, when grown on the surface of a cyclically stretched substrate, align away from the stretch direction. Although cell alignment has been described as an avoidance response to stretch, the specific deformation signal that causes a cell population to become aligned has not been identified. Planar surface deformation is characterized by three strains: two normal strains describe the length changes of two initially perpendicular lines and one shear strain describes the change in the angle between the two lines. The present study was designed to determine which, if any, of the three strains was the signal for cell alignment. Human fibroblasts and osteoblasts were grown in deformable, rectangular, silicone culture dishes coated with ProNectin, a biosynthetic polymer containing the RGD ligand of fibronectin. 24 h after plating the cells, the dishes were cyclically stretched at 1 Hz to peak dish stretches of 0% (control), 4%, 8%, and 12%. After 24 h of stretching, the cells were fixed, stained, and their orientations measured. The cell orientation distribution was determined by calculating the percent of cells whose orientation was within each of eighteen 5 degrees angular intervals. We found that the alignment response was primarily driven by the substrate strain which tended to lengthen the cell (axial strain). We also found that for each cell type there was an axial strain limit above which few cells were found. The axial strain limit for fibroblasts, 4.2 +/- 0.4%, (mean +/- 95% confidence), was lower than for osteoblasts, 6.4 +/- 0.6%. We suggest that the fibroblasts are more responsive to stretch because of their more highly developed actin cytoskeleton.
Filtering duplicate reads from 454 pyrosequencing data (2013)

Supplementary data are available at Bioinformatics online.