gebhart/patrepeval huggingface dataset:
OptimizingSalmonella entericaserovar Typhimurium for bacteria-mediated tumor therapy (2016)

Bacteria-mediated tumor therapy using Salmonella enterica serovar Typhimurium is a therapeutic option with great potential. Numerous studies explored the potential of Salmonella Typhimurium for therapeutic applications, however reconciling safety with vectorial efficacy remains a major issue. Recently we have described a conditionally attenuated Salmonella vector that is based on genetic lipopolysaccharide modification. This vector combines strong attenuation with appropriate anti-tumor properties by targeting various cancerous tissues in vivo. Therefore, it was promoted as an anti-tumor agent. In this addendum, we summarize these findings and demonstrate additional optimization steps that may further improve the therapeutic efficacy of our vector strain.
Fluorescence-Based Selection of Retrovirally Transduced Cells in the Absence of a Marker Gene: Direct Selection of Transduced Type B Niemann-Pick Disease Cells and Evidence for Bystander Correction (1995)

Types A and B Niemann-Pick disease (NPD) are lysosomal storage disorders resulting from the deficient activity of acid sphingomyelinase (ASM). Type A NPD is characterized by the absence of residual ASM activity, massive accumulation of sphingomyelin and cholesterol within lysosomes, and a rapid, neurodegenerative course that leads to death by 3 years of age. In contrast, type B NPD patients have low, but detectable, levels of residual ASM activity and little or no neurologic disease. Thus, individuals with type B NPD may survive into late adolescence or adulthood and are considered excellent candidates for somatic cell gene therapy. To facilitate the development of gene therapy for this disorder, a novel procedure was devised to isolate metabolically corrected type B NPD cells in the absence of marker gene expression. Type B NPD cells were transduced with retroviral vectors expressing ASM, labeled with lissamine rhodamine sphingomyelin (LR-SPM), and subjected to preparative fluorescence-activated cell sorting (FACS). Two non-overlapping cell populations were isolated, corresponding to enzymatically corrected (i.e., low fluorescence) and noncorrected (i.e., high fluorescence) cells. Quantitative PCR analysis demonstrated that the enzymatically corrected cells were enriched for vector sequences. Moreover, the corrected cells could be regrown and continued to express high levels of ASM activity after numerous passages, consistent with the fact that they were stably transduced. Notably, coculture of FACS-sorted, overexpressing cells with untreated type B NPD fibroblasts resulted in a homogeneous cell population with low fluorescence whose FACS distribution overlapped that of the corrected cells. Computerized fluorescence microscopy confirmed that nearly all of these cocultured cells expressed ASM activity and could hydrolyze LR-SPM.(ABSTRACT TRUNCATED AT 250 WORDS)
The centromere of budding yeast (1993)

Stable maintenance of genetic information during meiosis and mitosis is dependent on accurate chromosome transmission. The centromere is a key component of the segregational machinery that couples chromosomes with the spindle apparatus. Most of what is known about the structure and function of the centromeres has been derived from studies on yeast cells. In Saccharomyces cerevisiae, the centromere DNA requirements for mitotic centromere function have been defined and some of the proteins required for an active complex have been identified. Centromere DNA and the centromere proteins form a complex that has been studied extensively at the chromatin level. Finally, recent findings suggest that assembly and activation of the centromere are integrated in the cell cycle.
Improving the Data Transmission Throughput over the Home Electrical Wiring (2005)

Powerline communications (PLC) are receiving special attention since they use an already available and ubiquitous infrastructure. The main standard for PLC home networks is HomePlug. This work improves the throughput of HomePlug by modifying the medium access control sub-layer. The key idea is to define a fast collision avoidance mechanism where every station that wants to access the medium increments its contention window after sensing another ongoing transmission. The proposal reduces the number of collisions in the network improving the achievable throughput. We compared our mechanism to the original HomePlug standard through simulation and mathematical analysis. We verified that the improvement is independent from the packet size, the transmission rate and the number of nodes when the network is high loaded
Tau Oligomers as Potential Targets for Early Diagnosis of Tauopathy (2014)

The discovery of tau mutations in frontotemporal dementia has been a key event in neurodegenerative disease research. The rTg4510 mouse line expressing human tau with P301L FTDP-17-tau mutation has been established to understand the role of tau in neurodegeneration. Our histological analyses with tau antibodies and fluorescent tau ligands on rTg4510 mice revealed that tau oligomer formation was distinct from tangle formation. While in vivo imaging of mature tangles is now available, imaging biomarkers for tau oligomers would be useful for clarifying their roles in neurotoxicity and for diagnosing early-stage tau pathology.
Crash, Boom, Bang - Reload: Metamorphosen eines Softwareprojekts in Zeiten des New Economy-Hypes (2003)

In diesem Essay werden die Metamorphosen eines Software-Projekts nachgezeich-net, das von der choice mobilitätsproviding GmbH initiiert wurde. Das Ziel des Vor-habens war, die informationstechnische Unterstützung für eine Dienstleistung des Integrierten Verkehrs bereit zu stellen. Das Papier verfolgt die drastischen Volten im Projekt, welche in Folge des Anpassungsdrucks an sich permanent ändernde Umweltbedingungen vorgenommen wurden. Das Projekt kann als Fallstudie des Auf-stiegs und Niedergangs der New Economy angesehen werden: Zunächst war da eine gute Idee von enthusiastischen Gründern. Dann brach der Internet-Boom aus und es konnte eine beträchtliche Summe Geld für die Realisierung der neuen Software akquiriert werden. Wenig später tauchten die Glücksritter der New Economy auf und transformierten die anwenderspezifische Mittelstands-Software in eine Big-Busi-ness-Application. Dafür benötigten sie immer mehr Geld. Schließlich kam der große Knall. Die New Economy-Blase platzte, und nachdem die ausführende Software-Firma beinahe bankrott gegangen wäre, stellte sie alle Arbeiten daran ein. Das Millionen-projekt endete als Datentorso. Trotzdem gab es für das Projekt ein Leben nach dem Tod.
Calcium Phosphate Cement (CPC): A Critical Development Path (2007)

The first generation of synthetic bone substitute materials (BSM) was initially investigated in the mid 1970s using hydroxyapatite (HA) as a biomaterial for remodeling of bone defects. The concepts established by CPC pioneers in the early 1980s were used as a platform to initiate a second generation of BSM for commercialization. Since then, advances have been made in composition, performance and manufacturing. A self-setting and injectable calcium phosphate cement (CPC) based on amorphous calcium phosphate (ACP) with calcium to phosphate (Ca/P) atomic ratio less than 1.5, combined with dicalcium phosphate dihydrate (DCPD or brushite, seeded with apatite), is proposed. Amorphization of raw material was observed following high energy mechano-chemical processing. Upon hydration, the cement hardened in less than 3 minutes at 37°C and reached a maximum compressive strength of about 50 MPa. The final product was a low crystalline calcium deficient carbonated apatite similar to the composition and structure of bone mineral. In vivo performance of this cement in mediating bone healing was compared to α-BSM® in a rabbit femoral defect model. Performance characteristics of some commercially available CPC products are compared. The concerns of CPC designers and the needs of product users (surgeons) are discussed.
A 5000-gate CMOS EPLD with multiple logic and interconnect arrays (1989)

A description is given of a CMOS electrically programmable logic device (EPLD) with over 220000 programmable elements organized into multiple logic array blocks (LABs) that communicate through a separate programmable interconnect array. Redundancy, for the first time ever in programmable logic devices, is implemented in both arrays to improve yield. Devices of different sizes can be easily constructed by varying the number of LABs and/or macrocells within one LAB. A 2× improvement in yield has been observed
Short-Term Augmentation of Fluoxetine With Clonazepam in the Treatment of Depression: A Double-Blind Study (1998)

Clonazepam augmentation of fluoxetine was superior to fluoxetine alone in the first 3 weeks of treatment. This strategy may reduce suffering during early SSRI treatment, may partially suppress SSRI side effects, may increase compliance, and could possibly reduce the risk of suicide.
A Facile One Stage Synthesis of Oxazolines Under Microwave Irradiation (1996)

Abstract A rapid, high yielding procedure for the synthesis of 2-substituted oxazolines has been achieved under microwave irradiation from alkyl and aryl nitriles and β-amino alcohols using a mild Lewis acid catalyst.
Immunochemical Applications of Avidin–Biotin Technology (2003)

The major advantage in the use of avidin-biotin technology for isolation purposes is that an improved capacity for purification of an antigen often results (1,2). The antibody, bound to the column via an avidin-biotin bridge, is less affected by the chemistry of immobilization or by physical interactions (hydrophobic, electrostatic, salting-out effects, precipitation, and so on) with the solid support. Such potential deleterious effects are borne by avidin, which is a highly stable protein, and thus serves as a physicochemical buffer for the antibody.
A guaranteed approach for kinematic analysis of continuum robot based catheter (2009)

Controlling a continuum robot in a constrained environment constitutes a real challenge due to the nature of this robot and its bending properties. The navigation in un-structured environments, such as surgical operations, presents a potential application of the use of such robots. In this paper, a new formulation of a continuum robot forward kinematics is presented firstly. In a second step, an analytical inverse kinematics of the continuum robot is developed. It computes the continuum robot bellows length as a function of the robot end-tool position and orientation in the task space. Then a resolution of the inverse kinematics is shown based on the use of interval analysis. This technique has the advantage of dealing with uncertainties that may occur in the system modeling, parameter identification and could be used as well for robot control. System redundancies when computing the inverse kinematics are solved by a branch and bound based algorithm that minimizes a given quadratic criterion.
Chromosomal mutations induced by triplex-forming oligonucleotides in mammalian cells (1999)

Specific recognition of a region of duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Based on this, we have investigated the ability of the triplex-directed approach to induce mutations at a chromosomal locus in living cells. A mouse fibroblast cell line was constructed containing multiple chromosomal copies of the lambdasupFG1 vector carrying the supFG1 mutation-reporter gene. Cells were treated with specific (psoAG30) or control (psoSCR30) psoralen-conjugated TFOs in the presence and absence of UVA irradiation. The results demonstrated a 6- to 10-fold induction of supFG1 mutations in the psoAG30-treated cells as compared with psoSCR30-treated or untreated control cells. Interestingly, UVA irradiation had no effect onthe mutation frequencies induced by the psoralen-conjugated TFOs, suggesting a triplex-mediated but photoproduct-independent process of mutagenesis. Sequencing data were consistent with this finding since the expected T.A-->A.T transversions at the predicted psoralen crosslinking site were not detected. However, insertions and deletions were detected within the triplex binding site, indicating a TFO-specific induction of mutagenesis. This result demonstrates the ability of triplex-forming oligonucleotides to influence mutation frequencies at a specific site in a mammalian chromosome.
Hypertension Produced by Reduced Uterine Perfusion in Pregnant Rats Is Associated With Increased Soluble Fms-Like Tyrosine Kinase-1 Expression (2007)

The balance between proangiogenic and antiangiogenic factors, such as vascular endothelial growth factor, placental growth factor, and soluble fms-like tyrosine kinase-1 (sFlt-1), is altered in preeclampsia, and this dysregulation of angiogenic factors may be important in the pathogenesis of preeclampsia. Although sFlt-1 is elevated in preeclampsia, the mechanisms responsible for increasing this antiangiogenic factor remain unclear. We hypothesized that the hypertension produced by reduced uterine perfusion pressure (RUPP) is associated with increased sFlt-1 expression and decreased plasma vascular endothelial growth factor and placental growth factor concentrations in the pregnant rat. Arterial pressure was increased (130+/-3 versus 100+/-2 mm Hg; P<0.01) in the RUPP rats compared with the normal pregnant control rats. Plasma sFlt-1 concentration (660+/-270 versus 82+/-26 pg/mL; P<0.05) was increased, whereas plasma free placental growth factor (0.28+/-0.05 versus 1.7+/-0.5 pg/mL; P<0.01) and vascular endothelial growth factor (594+/-34 versus 830+/-33 pg/mL; P<0.01) concentrations were decreased in the RUPP rats compared with normal pregnant rats. Plasma sFlt-1:placental growth factor (37.2+/-7.8 versus 8.9+/-1.6; P<0.02) and sFlt-1:vascular endothelial growth factor (0.86+/-0.22 versus 0.28+/-0.06; P<0.05) ratios were increased in the RUPP rats compared with normal pregnant rats. Immunoreactive placental sFlt-1 was increased (1.1+/-0.1 versus 0.3+/-0.1; P<0.01) in RUPP rats contrasted with the normal pregnant rats. These findings support our hypothesis that RUPP increases the expression of sFlt-1 and alters the balance of angiogenic factors in the maternal circulation. These data also indicate that the RUPP model of pregnancy-induced hypertension may provide an invaluable model for mechanistic studies into the role of sFlt-1 in the pathogenesis preeclampsia.
Demonstration of chalcogenide glass racetrack microresonators (2008)

We have demonstrated what we believe to be the first chalcogenide glass racetrack microresonator using a complementary metal-oxide semiconductor-compatible lift-off technique with thermally evaporated As(2)S(3) films. The device simultaneously features a small footprint of 0.012 mm x 0.012 mm, a cavity Q (quality factor) of 10,000, and an extinction ratio of 32 dB. These resonators exhibit a very high sensitivity to refractive index changes with a demonstrated detection capability of Dn(As(2)S(3)=(4.5 x 10(-6)+/-10%) refractive index unit. The resonators were applied to derive a photorefractive response of As(2)S(3) to lambda=550 nm light. The resonator devices are a versatile platform for both sensing and glass material property investigation.
Yersinia enterocolitica activates a T helper type 1-like T cell subset in reactive arthritis (1992)

The profile of lymphokines secreted by 14 T cell clones and 24 T cell lines reactive with Yersinia Ag isolated from the synovial fluid cells of two HLA-B27+ patients with Yersinia-triggered reactive arthritis was characterized. In response to Ag-specific or -nonspecific stimulation, all of the Yersinia-reactive T cell clones and lines had a pattern of lymphokine secretion resembling that of murine (Th1) cells. A total of 50% of T cell lines and clones randomly isolated from a reactive arthritis patient, without prior in vitro stimulation with Yersinia Ag, also exhibited a Th1-like profile of cytokine secretion upon nonspecific activation. This indicates that the selective expansion of this subset of T cells had already occurred in vivo. The possibility that the predominance of Th1-like T cells was an artefact generated by the T cell cloning procedure was excluded; 50% of the randomly isolated T cell clones and lines produced IL-4, IL-5, or both cytokines upon nonspecific activation. These results indicate that Yersinia Ag selectively activate a Th1-like subset of T cells in patients with Yersinia-triggered reactive arthritis. Accumulation of such cells in the synovial tissue of patients with reactive arthritis may play a key role in the pathogenesis of this disease.
X-ray Diffraction Analysis of Cytochrome P450 2B4 Reconstituted into Liposomes (1996)

Two general models of the membrane topology of microsomal cytochrome P450 have been proposed: (1) deep immersion in the membrane, and (2) a P450cam-like heme domain anchored to the membrane with one or two membrane-spanning helices. Lamellar X-ray diffraction of oriented membrane multilayers was employed to distinguish these alternatives. Cytochrome P450 2B4 was reconstituted into unilamellar phospholipid proteoliposomes (molar protein to lipid ratio 1:90). Sedimentation of the proteoliposomes produced an ordered stack of bilayers with a one-dimensional repeat distance (d) perpendicular to the plane of the bilayer. The stacked multilayers were exposed to an X-ray beam (lambda = 1.54 A) at near grazing incidence, and lamellar diffraction patterns were recorded. With proteoliposome multilayers, up to six diffraction orders could be observed. Their spacing corresponded to a d of 63.6 A, calculated according to Bragg's Law, comprising the lipid bilayer, the projection of the incorporated protein beyond the bilayer, and the intermembrane water layer. With liposome multilayers containing no P450, the observed d was 59.6 A. These data suggest that the increase of distance between successive bilayers in the stack due to the presence of P450 2B4 was only about 4 A. This distance is much less than would be expected with the "N-terminal membrane-anchor" model of the membrane topology, in which the P450 molecules largely extend beyond the surface of the membrane (> or = 35 A). Furthermore, the mass distribution deduced from Fourier synthesis confirms that the protein is deeply immersed in the membrane.
Landscape of Somatic Retrotransposition in Human Cancers (2012)

Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.
Sirolimus-Eluting Stents versus Standard Stents in Patients with Stenosis in a Native Coronary Artery (2003)

In this randomized clinical trial involving patients with complex coronary lesions, the use of a sirolimus-eluting stent had a consistent treatment effect, reducing the rates of restenosis and associated clinical events in all subgroups analyzed.
Spike Timing and the Coding of Naturalistic Sounds in a Central Auditory Area of Song Birds (2002)

In nature, animals encounter high dimensional sensory stimuli that have complex statistical and dynamical structure.Attempts to study the neural coding of these natural signals face challenges both in the selection of the signal ensemble and in the analysis of the resulting neural responses.For zebra finches, naturalistic stimuli can be defined as sounds that they encounter in a colony of conspecific birds.We assembled an ensemble of these sounds by recording groups of 10-40 zebra finches, and then analyzed the response of single neurons in the songbird central auditory area (field L) to continuous playback of long segments from this ensemble.Following methods developed in the fly visual system, we measured the information that spike trains provide about the acoustic stimulus without any assumptions about which features of the stimulus are relevant.Preliminary results indicate that large amounts of information are carried by spike timing, with roughly half of the information accessible only at time resolutions better than 10 ms; additional information is still being revealed as time resolution is improved to 2 ms.Information can be decomposed into that carried by the locking of individual spikes to the stimulus (or modulations of spike rate) vs. that carried by timing in spike patterns.Initial results show that in field L, temporal patterns give at least ∼ 20% extra information.Thus, single central auditory neurons can provide an informative representation of naturalistic sounds, in which spike timing may play a significant role.
Interaction of sphingosine 1-phosphate with plasma components, including lipoproteins, regulates the lipid receptor-mediated actions (2000)

The concentration of sphingosine 1-phosphate (S1P) in plasma or serum is much higher than the half-maximal concentration of the sphingolipid needed to stimulate its receptors. Nevertheless, the inositol phosphate response to plasma or serum mediated by Edg-3, one of the S1P receptors, which was overexpressed in Chinese hamster ovary cells, was much smaller than the response expected from the total amount of S1P in these samples. The inositol phosphate response to exogenous S1P was markedly attenuated in the presence of charcoal-treated low-S1P serum. The inhibitory effect was lost by boiling but not by dialysis of the serum. The inhibitory action of the serum was specific to S1P and was associated with the trapping of exogenous S1P; the inositol phosphate response to P(2)-purinergic agonists was somewhat enhanced by the charcoal-treated serum. Among the components of plasma or serum, lipoproteins such as low-density and high-density lipoproteins showed a stronger activity for trapping S1P than lipoprotein-deficient serum. Consistent with this observation, we detected a 15-100-fold higher amount of S1P per unit amount of protein in lipoproteins than in the lipoprotein-deficient serum. Thus even though the protein content of the lipoprotein fraction contributes to only 4% of the total protein content of plasma or serum, more than 60% of S1P is distributed in this fraction. These results suggest that the tight binding of S1P to the components of serum or plasma, including lipoproteins, may interfere with the S1P binding to its receptors and thereby attenuate the lipid-receptor-mediated actions in the cells.