gebhart/patrepeval huggingface dataset:
Regulation of Interferon-Stimulated Genes in Peripheral Blood Leukocytes in Pregnant and Bred, Nonpregnant Dairy Cows (2007)

In ruminants, pregnancy results in up-regulation of a large number of IFN-stimulated genes (ISG) in the uterus. Recently, one of these genes was also shown to increase in peripheral blood leukocytes (PBL) during early pregnancy in sheep. Our working hypothesis is that conceptus signaling activates maternal gene expression in PBL in dairy cattle. The objectives of this study were to characterize ISG expression in PBL from pregnant (n = 20) and bred, nonpregnant (n = 30) dairy cows. Steady-state levels of mRNA for Mx1, Mx2, beta2-microglobulin, ISG-15, IFN regulatory factor-1, and IFN regulatory factor-2 were quantified. Holstein cows were synchronized to estrus and artificially inseminated (d 0). Blood samples were collected (coccygeal venipuncture) on d 0 and 16, 18, and 20 d after insemination for progesterone analysis and PBL isolation. Pregnancy was confirmed by transrectal ultrasonography at approximately 40 d after breeding. A status x day interaction was detected for Mx1, Mx2, and ISG-15 gene expression. When analyzed within day, levels of mRNA for ISG-15 and Mx1 were greater in pregnant compared with bred, nonpregnant cows on d 18 and 20, respectively. Expression of the Mx2 gene increased in the pregnant group compared with bred, nonpregnant cows on d 16, 18, and 20 after insemination. beta2-Microglobulin, IFN regulatory factor-1, and IFN regulatory factor-2 were not different between groups. The results clearly indicated that components of the innate immune response are activated in PBL during the period of pregnancy recognition and early embryo signaling. The physiological implications of these changes on maternal immune function are as yet unknown; however, they do provide a unique opportunity to identify bred, nonpregnant, cows 18 d after insemination in dairy cattle.
Increased lipid peroxidation in sera of ALS patients (2004)

These data confirm the presence of increased oxidative stress and immune activation in ALS patients. HNE is also suggested as a possible biomarker of disease.
Bendable GaN high electron mobility transistors on plastic substrates (2006)

A procedure for fabricating flexible forms of high electron mobility transistors (HEMTs) supported on plastic substrates is described. The process uses a combination of conventional top-down, wafer scale fabrication protocols to define a printable form of ultrathin, device quality multilayer AlGaN∕GaN single crystalline microstructures—a so-called microstructured semiconductor ink—and soft-lithographic printing methods to effect their registered transfer to a plastic substrate. These procedures yield high performance, bendable HEMT arrays that are mechanically durable—ones with effective transconductances exceeding nearly all reported forms of printed thin-film transistors.
Development of a Xeno-Free Feeder-Layer System from Human Umbilical Cord Mesenchymal Stem Cells for Prolonged Expansion of Human Induced Pluripotent Stem Cells in Culture (2016)

Various feeder layers have been extensively applied to support the prolonged growth of human pluripotent stem cells (hPSCs) for in vitro cultures. Among them, mouse embryonic fibroblast (MEF) and mouse fibroblast cell line (SNL) are most commonly used feeder cells for hPSCs culture. However, these feeder layers from animal usually cause immunogenic contaminations, which compromises the potential of hPSCs in clinical applications. In the present study, we tested human umbilical cord mesenchymal stem cells (hUC-MSCs) as a potent xeno-free feeder system for maintaining human induced pluripotent stem cells (hiPSCs). The hUC-MSCs showed characteristics of MSCs in xeno-free culture condition. On the mitomycin-treated hUC-MSCs feeder, hiPSCs maintained the features of undifferentiated human embryonic stem cells (hESCs), such as low efficiency of spontaneous differentiation, stable expression of stemness markers, maintenance of normal karyotypes, in vitro pluripotency and in vivo ability to form teratomas, even after a prolonged culture of more than 30 passages. Our study indicates that the xeno-free culture system may be a good candidate for growth and expansion of hiPSCs as the stepping stone for stem cell research to further develop better and safer stem cells.
Adenoviral Transduction of Human Acid Sphingomyelinase into Neo-Angiogenic Endothelium Radiosensitizes Tumor Cure (2013)

These studies define a new mechanism-based approach to radiosensitize tumor cure by single dose radiotherapy (SDRT). Published evidence indicates that SDRT induces acute microvascular endothelial apoptosis initiated via acid sphingomyelinase (ASMase) translocation to the external plasma membrane. Ensuing microvascular damage regulates radiation lethality of tumor stem cell clonogens to effect tumor cure. Based on this biology, we engineered an ASMase-producing vector consisting of a modified pre-proendothelin-1 promoter, PPE1(3x), and a hypoxia-inducible dual-binding HIF-2α-Ets-1 enhancer element upstream of the asmase gene, inserted into a replication-deficient adenovirus yielding the vector Ad5H2E-PPE1(3x)-ASMase. This vector confers ASMase over-expression in cycling angiogenic endothelium in vitro and within tumors in vivo, with no detectable enhancement in endothelium of normal tissues that exhibit a minute fraction of cycling cells or in non-endothelial tumor or normal tissue cells. Intravenous pretreatment with Ad5H2E-PPE1(3x)-ASMase markedly increases SDRT cure of inherently radiosensitive MCA/129 fibrosarcomas, and converts radiation-incurable B16 melanomas into biopsy-proven tumor cures. In contrast, Ad5H2E-PPE1(3x)-ASMase treatment did not impact radiation damage to small intestinal crypts as non-dividing small intestinal microvessels did not overexpress ASMase and were not radiosensitized. We posit that combination of genetic up-regulation of tumor microvascular ASMase and SDRT provides therapeutic options for currently radiation-incurable human tumors.
CRISPR/Cas9‐mediated MSTN disruption and heritable mutagenesis in goats causes increased body mass (2018)

Genetic engineering in livestock has been greatly enhanced through the use of artificial programmed nucleases such as the recently emerged clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system. We recently reported our successful application of the CRISPR/Cas9 system to engineer the goat genome through micro-injection of Cas9 mRNA and sgRNAs targeting MSTN and FGF5 in goat embryos. The phenotypes induced by edited loss-of-function mutations of MSTN remain to be evaluated extensively. We demonstrate the utility of this approach by disrupting MSTN, resulting in enhanced body weight and larger muscle fiber size in Cas9-mediated gene-modified goats. The effects of genome modifications were further characterized by H&E staining, quantitative PCR, Western blotting and immunofluorescence staining. Morphological and genetic analyses indicated the occurrence of phenotypic and genotypic modifications. We further provide sufficient evidence, including breeding data, to demonstrate the transmission of the knockout alleles through the germline. By phenotypic and genotypic characterization, we demonstrated the merit of using the CRISPR/Cas9 approach for establishing genetically modified livestock with an enhanced production trait.
A new multichamber counterflow centrifugation rotor with high-separation capacity and versatile potentials. (1988)

A new closed system for counterflow centrifugation (elutriation) is described. The system was developed to increase the capacity of counterflow centrifugation in order to be able to separate bone marrow intended for allogeneic bone marrow transplantation within 3 h. The rotor has the capacity for up to four separation chambers, offering the possibility of separating either a single-cell suspension under equal or differing conditions, or four different suspensions simultaneously. Profiles of low-density nucleated cells from normal blood were shown to be identical after elutriation in four different chambers. Leucocytes could be depleted from platelet concentrates without significant loss. Most (98%) of the lymphocytes were removed from donor marrow intended for transplantation within 3 h and the recovery of myeloid and erythroid clonogenic cells in the graft was similar to that obtained from the standard single chamber centrifuge.
Evolution of structural proteins of feline immunodeficiency virus: molecular epidemiology and evidence of selection for change (1993)

The DNA sequences of structural genes of several U.K. and European isolates of feline immunodeficiency virus (FIV) were determined and compared with those of other worldwide isolates. Phylogenetic analyses of both gag and env sequences demonstrate that a Japanese isolate represents a distinct sequence subgroup, with corrected amino acid distances to the other isolates averaging 23% in env and 8% in gag. Analysis also reveals that an evolutionary radiation of FIV occurred with many isolates diverging at approximately the same time, and that although isolates from similar geographical sources often cluster together, there is evidence of more than one origin for FIV in the U.K., The Netherlands and Italy. Estimation of the numbers of silent and replacement nucleotide substitutions indicates the presence of constraints against amino acid changes in gag and conserved regions of env but suggests that positive selection for protein sequence changes operates in variable regions of env. The possible immunological forces underlying these changes are discussed.
Antiproliferative Effects of IFN- α Correlate with the Downregulation of Nuclear Factor- κ B in Human Burkitt Lymphoma Daudi Cells (2001)

Interferon-alpha (IFN-alpha) is known to exhibit antiviral, antiproliferative, and immunomodulatory properties through mechanisms still not fully understood. Nuclear transcription factor-kappaB (NF-kappaB) plays a major role in viral replication, cell proliferation, and immune response. Whether antiproliferative effects of IFN are mediated through suppression of NF-kappaB is not known. We, therefore, examined the relationship between the antiproliferative effects of IFN-alpha and NF-kappaB activity in a human Burkitt lymphoma Daudi cell line. These cells were found to constitutively express high levels of active NF-kappaB that cannot be further activated by tumor necrosis factor (TNF). Treatment of cells with IFN-alpha suppressed the activated NF-kappaB in a dose-dependent manner, with an optimum effect at 10 U/ml in 72 h. Suppression of NF-kappaB correlated with a concomitant decrease in the cytoplasmic levels of IkappaBalpha, the inhibitory protein of NF-kappaB, known to be regulated by NF-kappaB. Downregulation of constitutive NF-kappaB activity correlated with a decrease in cell proliferation by IFN-alpha. Overall, our results suggest that IFN-alpha is a potent suppressor of constitutive NF-kappaB, which may contribute to the inhibition of cell proliferation.
Successful Bone-Marrow Transplantation for Infantile Malignant Osteopetrosis (1980)

A five-month-old girl with autosomal-recessive osteopetrosis received a bone-marrow transplant from her five-year-old HLA-MLC-identical brother after preparation with cyclophosphamide and modified total-body irradiation. Engraftment was documented by chromosomal analysis. Anemia, thrombocytopenia, and leukoerythroblastosis corrected within 12 weeks of transplantation. Low serum calcium and elevated serum alkaline and acid phosphatase levels became normal. Serial x-ray studies revealed bony remodeling and new nonsclerotic bone formation. A pretransplantation bone biopsy revealed small marrow spaces, rare marrow elements, increased osteoclasts, and no bony resorption. After transplantation, osteoclasts were actively resorbing bone, and medullary cavities contained normal bone marrow. Fluorescent Y-body analysis after transplantation revealed donor (male) osteoclasts and recipient (female) osteoblasts. Monocyte bactericidal activity, markedly decreased before transplantation, became normal. Vision, hearing, growth, and development were progressively improving 16 months after transplantation. Allogeneic bone-marrow transplantation appears to be the treatment of choice in this fatal disorder.
A discrete dynamic contour model (1995)

A discrete dynamic model for defining contours in 2-D images is developed. The structure of this model is a set of connected vertices. With a minimum of interaction, an initial contour model can be defined, which is then automatically modified by an energy minimizing process. The internal energy of the model depends on local contour curvature, while the external energy is derived from image features. Solutions are presented to avoid undesirable deformation effects, like shrinking and vertex clustering, which are common in existing active contour models. The deformation process stops when a local minimum of the energy function is reached. The final shape of the model is a reproducible approximation of the desired contour. Results of applying the method to computer-generated images, as well as clinical images, are presented.
HITS‐CLIP: panoramic views of protein–RNA regulation in living cells (2010)

The study of gene regulation in cells has recently begun to shift from a period dominated by the study of transcription factor-DNA interactions to a new focus on RNA regulation. This was sparked by the still-emerging recognition of the central role for RNA in cellular complexity emanating from the RNA World hypothesis, and has been facilitated by technologic advances, in particular high throughput RNA sequencing and crosslinking methods (RNA-Seq, CLIP, and HITS-CLIP). This study will place these advances in context, and, focusing on CLIP, will explain the method, what it can be used for, and how to approach using it. Examples of the successes, limitations, and future of the technique will be discussed.
Effects of Crystallinity on Dilute Acid Hydrolysis of Cellulose by Cellulose Ball-Milling Study (2005)

The dilute acid (0.05 M H2SO4) hydrolysis at 175 °C of samples comprised of varying fractions of crystalline (α-form) and amorphous cellulose was studied. The amorphous content, based on XRD and CP/MAS NMR, and the product (glucose) yield, based on HPLC, increased by as much as a factor of 3 upon ball milling. These results are interpreted in terms of a model involving mechanical disruption of crystallinity by breaking hydrogen bonds in α-cellulose, opening up the structure, and making more β-1,4 glycosidic bonds readily accessible to the dilute acid. However, in parallel with hydrolysis to form liquid-phase products, there are reactions of amorphous cellulose that form solid degradation products.
Fcγ receptor gene polymorphisms in Japanese patients with systemic lupus erythematosus: Contribution of FCGR2B to genetic susceptibility (2002)

These results demonstrate the association of a new polymorphism of FCGR2B (I232T) with susceptibility to SLE in the Japanese.
Estudio del antagonismo de algunas especies de Trichoderma sobre Fusarium Oxysporum y Rhizoctonia Solani (1989)

En este trabajo se estudió el antagonismo de algunos aislamientos del hongo Trichoderma obtenidos de suelos colornbianos en el control de Fusarium oxysporum y Rhizoctonia solani. En los ensayos "in vitre" se observó un marcado antagonismo entre las colonias de los aislamientos de Trichoderma sobre R. sotsni, con una reducción apreciabledel tamaño de la colonia y un antaqonismo menor sobre F. oxysporum. En los ensayos de parasitismo a nivel microscópico, se observó una gran interacción entre alqunosde los aislamientos de T. harzianum y T. hamatum y el patógéno R. solani rnanifestado por el enrollamiento, penetración, fragmentación y lisis de las hifas del patoqeno.Los aislamientos de Trichoderma causaron un retraso en la aparición de los síntomas, una reducción en la severidad de laenfermedad. y un menor número de plantas enfermas ocasionadas por F. oxysporum f. sp, cucumerinum en pepino cohombro, y su efecto fue superior en todos los casos a laaplicación del fungicida benomil. Los aislamientos del antagonista aumentaron la qerminación de las semillas, la emergencia y el tamaño de las plántulas y redujeron la severidad de la enfermedad ocasionada por R. solani en fríjol.
Human microcephaly protein RTTN interacts with STIL and is required to build full-length centrioles (2017)

Mutations in many centriolar protein-encoding genes cause primary microcephaly. Using super-resolution and electron microscopy, we find that the human microcephaly protein, RTTN, is recruited to the proximal end of the procentriole at early S phase, and is located at the inner luminal walls of centrioles. Further studies demonstrate that RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly. CRISPR/Cas9-mediated RTTN gene knockout in p53-deficient cells induce amplification of primitive procentriole bodies that lack the distal-half centriolar proteins, POC5 and POC1B. Additional analyses show that RTTN serves as an upstream effector of CEP295, which mediates the loading of POC1B and POC5 to the distal-half centrioles. Interestingly, the naturally occurring microcephaly-associated mutant, RTTN (A578P), shows a low affinity for STIL binding and blocks centriole assembly. These findings reveal that RTTN contributes to building full-length centrioles and illuminate the molecular mechanism through which the RTTN (A578P) mutation causes primary microcephaly.Mutations in many centriolar protein-encoding genes cause primary microcephaly. Here the authors show that human microcephaly protein RTTN directly interacts with STIL and acts downstream of STIL-mediated centriole assembly, contributing to building full-length centrioles.
Immunohistological Assessment of Intestinal Eosinophil Activation in Patients With Eosinophilic Gastroenteritis and Inflammatory Bowel Disease (1999)

Our data strongly suggest that the EG1 to EG2 ratio may be a marker of tissue eosinophil activation. Low ratios (<1) indicate eosinophil activation, whereas ratios > or =1 are found in healthy controls. Furthermore, we show that EOG is characterized by a pronounced intestinal eosinophil accumulation and activation, whereas in CD and UC, eosinophils seem to be activated but their number is not or only slightly elevated compared to controls.
Polymer light-emitting electrochemical cells with frozen junctions (1999)

We report on polymer light-emitting electrochemical cells (LECs) with frozen p-i-n junctions. The dynamic p-i-n junction in polymer LECs is stabilized by lowering the temperature below the glass transition temperature of the ion-transport polymer. Detailed studies have shown that the frozen p-i-n junction in LECs based on the luminescent polymer poly[5-(2′ethylhexyloxy)-2-methoxy-1,4-phenylene vinylene] and polyethylene oxide containing lithium triflate (PEO:LiCF3SO3) is stable at temperatures up to 200 K. Frozen-junction LECs offer a number of advantages; they exhibit unipolar light emission, balanced injection, fast response, high brightness, low operating voltage, and insensitivity to electrode materials and film thickness.
Challenges in DNA motion control and sequence readout using nanopore devices (2015)

Nanopores are being hailed as a potential next-generation DNA sequencer that could provide cheap, high-throughput DNA analysis. In this review we present a detailed summary of the various sensing techniques being investigated for use in DNA sequencing and mapping applications. A crucial impasse to the success of nanopores as a reliable DNA analysis tool is the fast and stochastic nature of DNA translocation. We discuss the incorporation of biological motors to step DNA through a pore base-by-base, as well as the many experimental modifications attempted for the purpose of slowing and controlling DNA transport.
All-optical polarisation switch with long low-birefringence fibre (1991)

Nonlinear polarisation switching of picosecond pulses from the linear polarisation eigenstates of a 200 m-long low-birefringence spun fibre is reported. The relatively low switching peak power of 20 W is promising for applications to all-optical processing and intensity discrimination of ultra-short pulses.
Quantitative biochemical rationale for differences in transmissibility of 1918 pandemic influenza A viruses (2008)

The human adaptation of influenza A viruses is critically governed by the binding specificity of the viral surface hemagglutinin (HA) to long (chain length) alpha2-6 sialylated glycan (alpha2-6) receptors on the human upper respiratory tissues. A recent study demonstrated that whereas the 1918 H1N1 pandemic virus, A/South Carolina/1/1918 (SC18), with alpha2-6 binding preference transmitted efficiently, a single amino acid mutation on HA resulted in a mixed alpha2-3 sialylated glycan (alpha2-3)/alpha2-6 binding virus (NY18) that transmitted inefficiently. To define the biochemical basis for the observed differences in virus transmission, in this study, we have developed an approach to quantify the multivalent HA-glycan interactions. Analysis of the molecular HA-glycan contacts showed subtle changes resulting from the single amino acid variations between SC18 and NY18. The effect of these changes on glycan binding is amplified by multivalency, resulting in quantitative differences in their long alpha2-6 glycan binding affinities. Furthermore, these differences are also reflected in the markedly distinct binding pattern of SC18 and NY18 HA to the physiological glycans present in human upper respiratory tissues. Thus, the dramatic lower binding affinity of NY18 to long alpha2-6 glycans, as against a mixed alpha2-3/6 binding, correlates with its inefficient transmission. In summary, this study establishes a quantitative biochemical correlate for influenza A virus transmission.
Screening for mammalian neural genes via fluorescence-activated cell sorter purification of neural precursors from Sox1 - gfp knock-in mice (2003)

The transcription factor Sox1 is the earliest and most specific known marker for mammalian neural progenitors. During fetal development, Sox1 is expressed by proliferating progenitor cells throughout the central nervous system and in no tissue but the lens. We generated a reporter mouse line in which egfp is inserted into the Sox1 locus. Sox1GFP animals faithfully recapitulate the expression of the endogenous gene. We have used the GFP reporter to purify neuroepithelial cells by fluorescence-activated cell sorting from embryonic day 10.5 embryos. RNAs prepared from Sox1GFP+ and Sox1GFP- embryo cells were then used to perform a pilot screen of subtracted cDNAs prepared from differentiating embryonic stem cells and arrayed on a glass chip. Fifteen unique differentially expressed genes were identified, all previously associated with fetal or adult neural tissue. Whole mount in situ hybridization against two genes of previously unknown embryonic expression, Lrrn1 and Musashi2, confirmed the selectivity of this screen for early neuroectodermal markers.