gebhart/patrepeval huggingface dataset:
Mucin glycan foraging in the human gut microbiome (2015)

The availability of host and dietary carbohydrates in the gastrointestinal (GI) tract plays a key role in shaping the structure-function of the microbiota. In particular, some gut bacteria have the ability to forage on glycans provided by the mucus layer covering the GI tract. The O-glycan structures present in mucin are diverse and complex, consisting predominantly of core 1-4 mucin-type O-glycans containing α- and β- linked N-acetyl-galactosamine, galactose and N-acetyl-glucosamine. These core structures are further elongated and frequently modified by fucose and sialic acid sugar residues via α1,2/3/4 and α2,3/6 linkages, respectively. The ability to metabolize these mucin O-linked oligosaccharides is likely to be a key factor in determining which bacterial species colonize the mucosal surface. Due to their proximity to the immune system, mucin-degrading bacteria are in a prime location to influence the host response. However, despite the growing number of bacterial genome sequences available from mucin degraders, our knowledge on the structural requirements for mucin degradation by gut bacteria remains fragmented. This is largely due to the limited number of functionally characterized enzymes and the lack of studies correlating the specificity of these enzymes with the ability of the strain to degrade and utilize mucin and mucin glycans. This review focuses on recent findings unraveling the molecular strategies used by mucin-degrading bacteria to utilize host glycans, adapt to the mucosal environment, and influence human health.
Multianalyte microspot immunoassay. The microanalytical 'compact disk' of the future. (1992)

Throughout the 1970s, controversy centered both on immunoassay 'sensitivity' per se and on the relative sensitivities of labelled antibody and labelled analyte methods. Our own theoretical studies in this period revealed that radioimmunoassay (RIA) sensitivities could be surpassed only by the use of very high specific activity non-isotopic labels in 'non-competitive' designs, preferably based on the use of monoclonal antibodies. The time-resolved fluorescence methodology known as Delfia - developed in collaboration with the instrument manufacturer LKB/Wallac - represented the first commercial 'ultra-sensitive' non-isotopic technique based on these theoretical insights, the same concepts being subsequently adopted in comparable methodologies relying on the use of chemiluminescent and enzyme labels. However, a second advantage of high specific activity labels is that they permit the development of 'multi-analyte' immunoassay systems combining ultra-sensitivity with the simultaneous measurement of tens, hundreds or thousands of analytes in a small biological sample. This possibility relies on simple, albeit hitherto unexploited, physicochemical concepts. The first is that all immunoassays rely on measurement of Ab occupancy by analyte. The second is that, provided the Ab concentration used is 'vanishingly small', fractional Ab occupancy is independent of both Ab concentration and sample volume. This leads to the notion of 'ratiometric' immunoassay, involving measurement of the ratio of signals (eg fluorescent signals) emitted by two labelled Ab's, the first ('sensor' Ab) deposited as a microspot on a solid support, the second a 'developing' Ab directed against either occupied or unoccupied sensor Ab binding sites.(ABSTRACT TRUNCATED AT 250 WORDS)
Pore Network Modeling: A New Technology for SCAL Predictions and Interpretations (2007)

Abstract There have been recently substantial advances in Pore Scale Physics Discipline. These advances can now be used for the benefit of special core analysis (SCAL) measurements and interpretations. This paper is devoted to explain these improvements from two perspectives: (i) Pore scale imaging and network extraction (ii) Fluid flow modeling applied on the extracted networks in order to predict some key petrophysical properties (capillary pressures, relative permeabilities). We use either thin sections or X-ray microtomograhy (micro-CT) to analyze rock cuttings of sandstones from Saudi Arabian oil and gas fields. These cuttings are a few mm across and are imaged with a resolution of 3 to 12 microns. Hence, the details of the three-dimensional pore space can be clearly seen. A maximal ball algorithm1,2 is used to extract a topologically equivalent pore-throat network: the largest inscribed spheres in the pore space representing the pores, with throats representing the connections between them. In parallel to this algorithm, thin section images are utilized to build 3D equivalent images, reproducing porosity by a similar spatial variation of the grain sizes obtained from the thin sections. This has been done through the so called process based technique3 which is based on honoring the geological depositional mode of the rock. The final aim is to input these network models into porescale fluid flow simulators to predict macroscopic properties such as relative permeability and capillary pressure. Blind tests are envisaged to compare the measured petrophysical properties and their corresponding numerical estimations. This acts as a valuable complement to special core analysis, enabling predictions of properties – such as three phase relative permeabilities and the impact of wettability trends − outside the range probed experimentally.
Lipopolyamine‐Mediated Transfection Allows Gene Expression Studies in Primary Neuronal Cells (1990)

A simple and efficient transfection technique based on lipopolyamine-coated DNA that can be used for gene transfer in cerebellar granular neurons is described. Gene transfer is achieved by exposure of cells to a DNA/lipid complex obtained by simple mixing of lipopolyamine and plasmid DNA. This procedure may represent a general tool of physiological investigations in primary cells. We show that the promoters of the introduced chimera genes are regulated by their respective trans-acting factors and may be modulated via membrane receptors and second messengers. This procedure has no noticeable toxic effects, nor does it seem to interfere with complex physiological behavior like neuronal differentiation.
Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions (2017)

Age-associated hypo- and hypermethylation events occur at distinct regulatory features of the genome. Distinct longevity-promoting interventions, specifically genetic, dietary and drug interventions, suppress some age-associated methylation changes, consistent with the idea that these interventions exert their beneficial effects, in part, by modulation of the epigenome. This study is a foundation to understand the epigenetic contribution to healthy aging and longevity and the molecular basis of the DNA methylation clock.
Effects of crosstalk in demultiplexers for photonic analog-to-digital converters (2001)

Time interleaving of samples digitized by a parallel array of analog-to-digital (A/D) converters provides a means of increasing the sampling rate beyond that possible with a single A/D converter. For time-interleaved photonic A/D converters, optical demultiplexers can be used to advantage. Both time-division and wavelength-division demultiplexers must yield low crosstalk between the parallel output channels in order to yield accurate A/D conversion. An analysis predicts the level and form of the resulting errors. The analytical results compare well with experiment.
Surgical management of spinal epidural hematoma: relationship between surgical timing and neurological outcome (1995)

Thirty patients were treated surgically for spinal epidural hematoma (SEH). Twelve of these cases resulted from spinal surgery, seven from epidural catheters, four from vascular lesions, three from anticoagulation medications, two from trauma, and two from spontaneous causes. Pain was the predominant initial symptom, and all patients developed neurological deficits. Eight patients had complete motor and sensory loss (Frankel Grade A); six had complete motor loss but some sensation preserved (Frankel Grade B); and 16 had incomplete loss of motor function (10 patients Frankel Grade C and six patients Frankel Grade D). The average interval from onset of initial symptom to maximum neurological deficit was 13 hours, and the average interval from onset of symptom to surgery was 23 hours. Surgical evacuation of the hematoma was performed in all patients; 26 of these improved; four remained unchanged, and no patients worsened (mean follow up 11 months). Complete recovery (Frankel Grade E) was observed in 43% of the patients and functional recovery (Frankel Grades D or E) was observed in 87%. One postoperative death occurred from a pulmonary embolus (surgical mortality 3%). Preoperative neurological status correlated with outcome; 83% of Frankel Grade D patients recovered completely compared to 25% of Frankel Grade A patients. The rapidity of surgical intervention also correlated with outcome; greater neurological recovery occurred as the interval from symptom onset to surgery decreased. Patients taken to surgery within 12 hours had better neurological outcomes than patients with identical preoperative Frankel grades whose surgery was delayed beyond 12 hours. This large series of SEH demonstrates that rapid diagnosis and emergency surgical treatment maximize neurological recovery. However, patients with complete neurological lesions or long-standing compression can improve substantially with surgery.
Sequential mutations associated with adaptation of human cytomegalovirus to growth in cell culture (2010)

Mutations that occurred during adaptation of human cytomegalovirus to cell culture were monitored by isolating four strains from clinical samples, passaging them in various cell types and sequencing ten complete virus genomes from the final passages. Mutational dynamics were assessed by targeted sequencing of intermediate passages and the original clinical samples. Gene RL13 and the UL128 locus (UL128L, consisting of genes UL128, UL130 and UL131A) mutated in all strains. Mutations in RL13 occurred in fibroblast, epithelial and endothelial cells, whereas those in UL128L were limited to fibroblasts and detected later than those in RL13. In addition, a region containing genes UL145, UL144, UL142, UL141 and UL140 mutated in three strains. All strains exhibited numerous mutations in other regions of the genome, with a preponderance in parts of the inverted repeats. An investigation was carried out on the kinetic growth yields of viruses derived from selected passages that were predominantly non-mutated in RL13 and UL128L (RL13+UL128L+), or that were largely mutated in RL13 (RL13-UL128L+) or both RL13 and UL128L (RL13-UL128L-). RL13-UL128L- viruses produced greater yields of infectious progeny than RL13-UL128L+ viruses, and RL13-UL128L+ viruses produced greater yields than RL13+UL128L+ viruses. These results suggest strongly that RL13 and UL128L exert at least partially independent suppressive effects on growth in fibroblasts. As all isolates proved genetically unstable in all cell types tested, caution is advised in choosing and monitoring strains for experimental studies of vulnerable functions, particularly those involved in cell tropism, immune evasion or growth temperance.
Years of Life Lost Due to Obesity (2003)

Obesity appears to lessen life expectancy markedly, especially among younger adults.
Prickle 1 regulates cell movements during gastrulation and neuronal migration in zebrafish (2003)

During vertebrate gastrulation, mesodermal and ectodermal cells undergo convergent extension, a process characterised by prominent cellular rearrangements in which polarised cells intercalate along the medio-lateral axis leading to elongation of the antero-posterior axis. Recently, it has become evident that a noncanonical Wnt/Frizzled (Fz)/Dishevelled (Dsh) signalling pathway, which is related to the planar-cell-polarity (PCP) pathway in flies, regulates convergent extension during vertebrate gastrulation. Here we isolate and functionally characterise a zebrafish homologue of Drosophila prickle (pk), a gene that is implicated in the regulation of PCP. Zebrafish pk1 is expressed maternally and in moving mesodermal precursors. Abrogation of Pk1 function by morpholino oligonucleotides leads to defective convergent extension movements, enhances the silberblick (slb)/wnt11 and pipetail (Ppt)/wnt5 phenotypes and suppresses the ability of Wnt11 to rescue the slb phenotype. Gain-of-function of Pk1 also inhibits convergent extension movements and enhances the slb phenotype, most likely caused by the ability of Pk1 to block the Fz7-dependent membrane localisation of Dsh by downregulating levels of Dsh protein. Furthermore, we show that pk1 interacts genetically with trilobite (tri)/strabismus to mediate the caudally directed migration of cranial motor neurons and convergent extension. These results indicate that, during zebrafish gastrulation Pk1 acts, in part, through interaction with the noncanonical Wnt11/Wnt5 pathway to regulate convergent extension cell movements, but is unlikely to simply be a linear component of this pathway. In addition, Pk1 interacts with Tri to mediate posterior migration of branchiomotor neurons, probably independent of the noncanonical Wnt pathway.
Distinct RIG-I and MDA5 Signaling by RNA Viruses in Innate Immunity (2007)

Alpha/beta interferon immune defenses are essential for resistance to viruses and can be triggered through the actions of the cytoplasmic helicases retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5). Signaling by each is initiated by the recognition of viral products such as RNA and occurs through downstream interaction with the IPS-1 adaptor protein. We directly compared the innate immune signaling requirements of representative viruses of the Flaviviridae, Orthomyxoviridae, Paramyxoviridae, and Reoviridae for RIG-I, MDA5, and interferon promoter-stimulating factor 1 (IPS-1). In cultured fibroblasts, IPS-1 was essential for innate immune signaling of downstream interferon regulatory factor 3 activation and interferon-stimulated gene expression, but the requirements for RIG-I and MDA5 were variable. Each was individually dispensable for signaling triggered by reovirus and dengue virus, whereas RIG-I was essential for signaling by influenza A virus, influenza B virus, and human respiratory syncytial virus. Functional genomics analyses identified cellular genes triggered during influenza A virus infection whose expression was strictly dependent on RIG-I and which are involved in processes of innate or adaptive immunity, apoptosis, cytokine signaling, and inflammation associated with the host response to contemporary and pandemic strains of influenza virus. These results define IPS-1-dependent signaling as an essential feature of host immunity to RNA virus infection. Our observations further demonstrate differential and redundant roles for RIG-I and MDA5 in pathogen recognition and innate immune signaling that may reflect unique and shared biologic properties of RNA viruses whose differential triggering and control of gene expression may impact pathogenesis and infection.
Weed Control and Seedling Performance Using Oust, Velpar, and Velpar+Oust Impregnated Diammonium Phosphate (2002)

Technology that combines herbicide and fertilizer into one treatment thereby reducing application costs while enhancing growth is needed. Four clean and well-prepared sites in TX, MS, and AL were tested. Study objectives were to evaluate the effectiveness of diammonium phosphate (DAP) impregnated with Oust, Velpar, or Velpar+Oust for herbaceous weed control and newly planted loblolly pine (Pinus taeda L.) seedling growth. In 1999, treatments were applied early post weed-emergence to 60percent bare ground in East TX. Impregnated DAP provided about 38percent less competitor control than separate liquid and fertilizer applications at similar rates. Best seedling survival and growth resulted from liquid sprays of Oust and Velpar+Oust. Treatments in 2000 were applied to bare ground in TX, MS, and AL. Weed control for Oust-impregnated DAP, Velpar+Oust-impregnated DAP, Velpar impregnated on 250 pounds of DAP and liquid herbicide treatments was similar 120 days after treatment. Seedling survival and growth for impregnated DAP treatments was similar to that for conventional herbicide and DAP treatments. Growth trends are preliminary and will be followed. Drought probably influenced study results.
Electrical engineering between energy and information (2002)

The present discussion in industrial countries about the future of electrical engineering revolves almost exclusively around communication and information, as a consequence of the advances of microelectronics into molecular dimensions. In contrast, the field of energy is said to be matured, offering little future prospects. This is a one-sided opinion, considering the shortage of energy in many regions of the world and the unsolved problems of providing an equitable supply to growing populations. The issue is examined with the aim of achieving a more balanced discussion by looking at the available resources and the future role of the electrical energy grid as a clearing facility, as well as the potential of power electronics for efficient and flexible generation.
Phonon-pumped SiGe-Si interminiband terahertz laser (2001)

The first phonon-pumped semiconductor laser has been proposed and theoretically investigated. The active region is an unbiased boron-doped Si/sub 0.94/Ge/sub 0.06/-Si superlattice with Si/sub 0.97/Ge/sub 0.03/ buffer layers embedded in a surface-plasmon strip waveguide. Warm and cool heat sinks create a temperature gradient across the waveguide. A heat buffer layer adjacent to the cool sink reflects optical phonons and transmits acoustic phonons, Within the resonator, the difference in effective temperatures of optical and acoustic phonons provides hole pumping for the lasing transition between the heavy-hole 2 (HH2) and heavy-hole 1 (HH1) minibands. A gain of 280/cm at the 5 THz emission frequency is predicted for 6/spl times/10/sup 17//cm/sup 3/ doping at temperatures of 300 K and 77 K for optical and acoustic phonons, respectively. A range of operating conditions in phonon-pumped IV-IV, III-V, and II-VI materials appears feasible.
Southern blot patterns, frequencies, and junctional diversity of T-cell receptor-delta gene rearrangements in acute lymphoblastic leukemia (1993)

Southern blot analysis of T-cell receptor (TCR)-delta gene rearrangements is useful for diagnostic studies on the clonality of lymphoproliferative diseases. We have developed 18 new TCR-delta gene probes by use of the polymerase chain reaction (PCR) techniques. Application of these probes for detailed analysis of the TCR-delta genes in normal control samples, 138 T-cell acute lymphoblastic leukemias (T-ALL), and 91 precursor B-ALL allowed us to determine the TCR-delta gene restriction map for five restriction enzymes, as well as the Southern blot restriction enzyme patterns of all theoretically possible TCR-delta gene rearrangements. Based on this information, it appeared that 97% of all 213 detected TCR-delta gene rearrangements in our series of ALL could be detected by use of the TCRDJ1 probe and that the majority (76%) of the 213 rearrangements could be identified precisely. In T-ALL, we found a strong preference for the complete rearrangements V delta 1-J delta 1 (33%), V delta 2-J delta 1 (10%), and V delta 3-J delta 1 (7%) and the incomplete rearrangement D delta 2-J delta 1 (11%). In precursor B-ALL, the majority of rearrangements consisted of V delta 2-D delta 3 (72%) and D delta 2-D delta 3 (10%). The junctional diversity of these 6 preferential TCR-delta rearrangements was analyzed and showed an extensive junctional insertion (approximately 30 nucleotides) for complete V delta-J delta rearrangements, whereas incomplete rearrangements had correspondingly smaller junctional regions. The detailed TCR-delta gene restriction map and probes presented here, in combination with the Southern blot patterns of TCR-delta gene rearrangements, are important for TCR-delta gene studies in ALL; all TCR-delta gene rearrangements can be detected and the majority can be identified precisely. Identification of rearrangements is a prerequisite for subsequent PCR analysis of TCR-delta gene junctional regions, eg, for detection of minimal residual disease during follow-up of ALL patients.
Selective cell elimination in vitro and in vivo from tissues and tumors using antibodies conjugated with a near infrared phthalocyanine (2015)

Cell cultures and tissues often contain cellular subpopulations that potentially interfere with or contaminate other cells of interest. However, it is difficult to eliminate unwanted cells without damaging the very cell population one is seeking to protect, especially established tissue. Here, we report a method of eliminating a specific subpopulation of cells from a mixed 2D or 3D cell culture <i>in vitro</i> and a mixed-population <i>in vivo</i> tumor model by using antibody-photosensitizer conjugates (APC) with a near infrared (NIR) phthalocyanine-derivative (IRdye700DX, IR700) combined with NIR light exposure with minimal damage to non-targeted cells. Thus, APC combined with NIR light exposure holds promise as a method of removing specific cells from mixed cell cultures and tumors.
Asymmetric Synthesis of 4‘-Ethoxy-2‘,3‘-didehydro-2‘,3‘-dideoxynucleosides by Palladium-Catalyzed Kinetic Discrimination between the Corresponding Diastereoisomeric Lactol Acetates (2002)

4'-Substituted nucleoside analogues have been synthesized using palladium-catalyzed asymmetric allylic amination conditions. A kinetic discrimination between the diastereomeric lactol acetates (3) produced the desired aminated products (6a-d) and recovered acetate (alpha-3) in high yields and <97:3 diastereoselectivity. Epimerization of the recovered lactol acetate (alpha-3) produced a 60:40 alpha/beta mixture of (3), which could be resubjected, in principle, to the palladium-catalyzed asymmetric allylic amination conditions.
N-Terminal E-Cadherin Peptides Act as Decoy Receptors for Listeria monocytogenes (2003)

The observation that E-cadherin is the principal epithelial receptor for the bacterial pathogen Listeria monocytogenes led us to investigate whether N-terminal fragments of E-cadherin containing the L. monocytogenes binding domain could inhibit entry of the bacteria into cultured epithelial cells. Here we demonstrate that a conditioned medium from a gastric cancer cell line (Kato III) that carries a truncating CDH-1 mutation 3' of the L. monocytogenes binding domain can inhibit the uptake of the bacteria into Caco-2 cells. The inhibitory activity of the Kato III conditioned medium could be mimicked by incubation of the bacteria with a recombinant 26-kDa N-terminal E-cadherin peptide prior to infection. Furthermore, these data suggest that cleavage of the 80-kDa extracellular domain of E-cadherin from the cell surface may provide an innate form of pathogen defense by acting as a decoy receptor for L. monocytogenes.