gebhart/patrepeval huggingface dataset:
Cyclin D1 Over-Expressing Mantle Cell Lymphoma Cells Are Hypersensitive to Inhibition of Fatty Acid Synthase (FASN) (2011)

Abstract Abstract 1656 Mantle cell lymphoma (MCL) is an aggressive type of B-cell lymphoma characterized by a t(11;14)(q13;q32) chromosomal translocation resulting in a constitutive over-expression of cyclin D1. Cyclin D1 is a multifunctional protein not only regulating cell cycle progression but also affecting other cellular functions including glucose and lipid metabolism. In this study, we investigated the effects of the fatty acid synthase (FASN) inhibitors orlistat and C75 on viability of different MCL cell lines including JEKO-1, MINO, Granta-519, JVM-2, and Rec-1. In all cell lines inhibition of FASN alone induced apoptosis. In contrast, normal peripheral blood lymphocytes were resistant to these compounds. This proapoptotic effect was dependent on cyclin D1 as silencing of cyclin D1 partially rescued cells from induction of cell death following FASN inhibition. Inhibition of FASN led to a strong induction of the proapoptotic protein NOXA (PMAIP) in all MCL cell lines investigated independent of the p53 status. Pre-treatment of cells with NOXA siRNA significantly reduced induction of cell death demonstrating the predominant role of this proapoptotic protein for the observed effects. We then analyzed the combined effects of inhibition of FASN with a panel of compounds with potential clinical relevance. Combination of FASN inhibitors with the BH3 mimetic ABT737, the proteasome inhibitor Bortezomib, and the glycolysis inhibitor 2-deoxy-D-glucose (2-DG) led to an almost complete loss of viability. These combinatory effects were selective for MCL cells as the same treatments had almost no effects on cell viability of primary PBMCs or fibroblasts from healthy donors. Bortezomib, 2-DG, and ABT737 enhanced the proapoptotic effect of FASN inhibitors by further disturbing the balance of pro- and antiapoptotic Bcl-2 family proteins: FASN inhibitor mediated induction of NOXA was enhanced by Bortezomib whereas 2-DG significantly reduced the NOXA antagonist Mcl-1. In summary, our results suggest that FASN inhibitors exert significant antitumoral activity especially in combination with Bcl-2 family modulators in different MCL cell lines and may therefore represent an attractive model for the design of new therapeutic approaches for this entity. Disclosures: No relevant conflicts of interest to declare.
Protection traps and alternatives for memory management of an object-oriented language (1993)

Many operating systems allow user programs to specify the protection level (inaccessible, read-only, read-write) of pages in their virtual memory address space, and to handle any protection violations that may occur. Such page-protection techniques have been exploited by several user-level algorithms for applications including generational garbage collection and persistent stores. Unfortunately, modern hardware has made efficient handling of page protection faults more difficult. Moreover, page-sized granularity may not match the natural granularity of a given application. In light of these problems, we reevaluate the usefulness of page-protection primitives in such applications, by comparing the performance of implementations that make use of the primitives with others that do not. Our results show that for certain applications software solutions outperform solutions that rely on page-protection or other related virtual memory primitives.
Auger-electron therapeutic effectiveness in neuro-endocrine and non-tumors using indium-111 labelled pentetreotide (2000)

s: Abstracts of an International Conference on Peptide Radiopharmaceuticals in Diagnosis and Therapy Rome, Italy, 25-28 May 2000: Poster Presentations
Supplementary Table 2 from Gene Set Analysis of Survival Following Ovarian Cancer Implicates Macrolide Binding and Intracellular Signaling Genes (2023)

&lt;p&gt;PDF file - 130K&lt;/p&gt;
Synthesis of Lactose-Based S-Linked Sialylmimetics of α(2,3)-Sialosides (2003)

[reaction: see text] A new approach toward the synthesis of lactose-based S-linked sialylmimetics of alpha(2,3)-linked sialosides is described. These compounds, represented by the general structure 3, were prepared from methyl beta-d-lactoside in 11 steps. It was found that the choice of protecting group was crucial to allow the efficient introduction of sulfur at the 3-position of the galactose ring.
Simplified analytical model to describe wind loads and wind-induced tracking deviations of heliostats (2023)

Wind-induced tracking deviations of heliostats can be analyzed through numerical simulations or experimental studies on a full-scale heliostat. However, these methods are relatively costly and often, simpler estimations are necessary and sufficient. One simpler approach is to use an analytical model that describes the wind-induced tracking deviations and which requires only a few input parameters that can be determined through straightforward measurements at the full-scale heliostat. Therefore, this paper presents the derivation of an analytical model and describes the development process in a detailed way to clarify the necessary assumptions and simplifications. For verification purposes, the developed model is furthermore applied to measurement data of a field study. It is shown that the results of the model application agree well with the expectations and that the measured heliostat response matches the predicted response well, provided the underlying assumptions of the model fully apply to the investigated heliostat. Overall, no unexplainable inconsistencies are identified and the results support the model well. Thus, a method is provided which allows the estimation and prediction of wind-induced tracking deviations with comparatively little effort. In addition, the developed model helps to identify and analyze those parameters that have the greatest impact on the wind-induced tracking deviations of different types of heliostats.
Supplementary File 3 from Distinct TP63 Isoform-Driven Transcriptional Signatures Predict Tumor Progression and Clinical Outcomes (2023)

&lt;p&gt;Components of tumor development TAp63 (3.1) and Î"Np63 (3.2) signatures used in this study. Pathways enriched in TAp63 (3.3) and Î"Np63 (3.4) tumor development signatures.&lt;/p&gt;
Wnt Signaling Mediates LTP-Dependent Spine Plasticity and AMPAR Localization through Frizzled-7 Receptors (2018)

The structural and functional plasticity of synapses is critical for learning and memory. Long-term potentiation (LTP) induction promotes spine growth and AMPAR accumulation at excitatory synapses, leading to increased synaptic strength. Glutamate initiates these processes, but the contribution from extracellular modulators is not fully established. Wnts are required for spine formation; however, their impact on activity-mediated spine plasticity and AMPAR localization is unknown. We found that LTP induction rapidly increased synaptic Wnt7a/b protein levels. Acute blockade of endogenous Wnts or loss of postsynaptic Frizzled-7 (Fz7) receptors impaired LTP-mediated synaptic strength, spine growth, and AMPAR localization at synapses. Live imaging of SEP-GluA1 and single-particle tracking revealed that Wnt7a rapidly promoted synaptic AMPAR recruitment and trapping. Wnt7a, through Fz7, induced CaMKII-dependent loss of SynGAP from spines and increased extrasynaptic AMPARs by PKA phosphorylation. We identify a critical role for Wnt-Fz7 signaling in LTP-mediated synaptic accumulation of AMPARs and spine plasticity.
Regulation of extra-embryonic endoderm stem cell differentiation by Nodal and Cripto signaling (2011)

The signaling pathway for Nodal, a ligand of the TGFβ superfamily, plays a central role in regulating the differentiation and/or maintenance of stem cell types that can be derived from the peri-implantation mouse embryo. Extra-embryonic endoderm stem (XEN) cells resemble the primitive endoderm of the blastocyst, which normally gives rise to the parietal and the visceral endoderm in vivo, but XEN cells do not contribute efficiently to the visceral endoderm in chimeric embryos. We have found that XEN cells treated with Nodal or Cripto (Tdgf1), an EGF-CFC co-receptor for Nodal, display upregulation of markers for visceral endoderm as well as anterior visceral endoderm (AVE), and can contribute to visceral endoderm and AVE in chimeric embryos. In culture, XEN cells do not express Cripto, but do express the related EGF-CFC co-receptor Cryptic (Cfc1), and require Cryptic for Nodal signaling. Notably, the response to Nodal is inhibited by the Alk4/Alk5/Alk7 inhibitor SB431542, but the response to Cripto is unaffected, suggesting that the activity of Cripto is at least partially independent of type I receptor kinase activity. Gene set enrichment analysis of genome-wide expression signatures generated from XEN cells under these treatment conditions confirmed the differing responses of Nodal- and Cripto-treated XEN cells to SB431542. Our findings define distinct pathways for Nodal and Cripto in the differentiation of visceral endoderm and AVE from XEN cells and provide new insights into the specification of these cell types in vivo.
A new fiber length measuement method with high precision and large absolute length based on FDL (2010)

We propose and demonstrate a new fiber length measurement method, which supports large absolute length and high accuracy measurement of fiber. This method is based on multi-stage optical fiber delay lines structure and self-calibration method with Precision Reflectometer. The precision maintains 20 μm and the enlarged measurement range reaches to 6395.43mm.
ChemInform Abstract: Novel Phosphido‐Bridged Cations (M2(CO)8(μ‐PPh2))BF4 (M: Fe, Ru): Synthesis, Reactivity, and X‐Ray Structure of an Isoelectronic and Structural Analogue of Ru2(CO)9. (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
The interaction between the cytokine LIF and the neurotrophins on spiral ganglion cells [Abstract] (1997)

The survival of auditory neurones depends on the continuous supply of trophic factors. Hair cells within the cochlea are known to produce supply growth factors responsible for the survival and growth of The survival of auditory neurones depends on the continuous supply of trophic factors. Hair cells within the cochlea are known to produce supply growth factors responsible for the survival and growth of [ ] neurones. As a result of trauma, disease or ageing cochlear hair cells are lost, and consequently, the supply of growth factors is reduced, leading to secondary wave of auditory nerve degeneration.
Molecular Genetics of Signal Transduction in Dictyostelium (1996)

In conditions of starvation, the free living amoebae of Dictyostelium enter a developmental program: The cells aggregate by chemotaxis to form a multicellular structure that undergoes morphogenesis and cell-type differentiation. These processes are mediated by a family of cell surface CAMP receptors (CARS) that act on a specific heterotrimeric G protein to stimulate actin polymerization, activation of adenylyl and guanylyl cyclases, and a host of other responses. Most of the components in these pathways have mammalian counterparts. The accessible genetics of this unicellular organism facilitate structure-function analysis and enable the discovery of novel genes involved in the regulation of these important pathways.
In silico prediction and control of ADME properties. (2003)

During the last decade, drug discovery process has been dramatically changed by new technologies such as combinatorial chemistry and high throughput screening. A tremendous number of compounds can be synthesized and screened routinely. However, most of drug candidates found by these technologies possess inappropriate pharmacokinetic properties and therefore fail during pre-clinical and clinical studies. To solve this problem, ADME screening has to be performed in the earlier stage of drug discovery. While Caco-2 cells and recombinant P 450 enzymes are being used as in vitro models for high throughput ADME screening, computational screening of virtual combinatorial libraries is increasingly an attractive approach in terms of speed and cost. In this article, we review the methods of analyzing structure/property relationship and the models of pharmacokinetic properties such as solubility, permeability, and metabolism.
CIAPIN1 nuclear accumulation predicts poor clinical outcome in epithelial ovarian cancer (2012)

CIAPIN1 might play a crucial role in the differentiation of EOC cells. Elevated expression of nuclear CIAPIN1 negatively correlated with the survival of EOC patients, suggesting that nuclear CIAPIN1 might serve as a prognostic biomarker for EOC patients.
Enhanced immunofluorescence measurement resolution of surface antigens on highly autofluorescent, glutaraldehyde-fixed cells analyzed by phase-sensitive flow cytometry (1999)

Phase-sensitive detection improves the immunofluorescence measurement resolution of surface antigens on highly autofluorescent, glutaraldehyde-fixed cells. Cytometry 37: 275-283, 1999. Published 1999 Wiley-Liss, Inc.
Faculty Opinions recommendation of Terminal complement inhibitor eculizumab in atypical hemolytic-uremic syndrome. (2013)

BACKGROUND: Atypical hemolytic-uremic syndrome is a genetic, life-threatening, chronic disease of complement-mediated thrombotic microangiopathy. Plasma exchange or infusion may transiently maintain normal levels of hematologic measures but does not treat the underlying systemic disease.METHODS: We conducted two prospective phase 2 trials in which patients with atypical hemolytic-uremic syndrome who were 12 years of age or older received eculizumab for 26 weeks and during long-term extension phases. Patients with low platelet counts and renal damage (in trial 1) and those with renal damage but no decrease in the platelet count of more than 25% for at least 8 weeks during plasma exchange or infusion (in trial 2) were recruited. The primary end points included a change in the platelet count (in trial 1) and thrombotic microangiopathy event-free status (no decrease in the platelet count of >25%, no plasma exchange or infusion, and no initiation of dialysis) (in trial 2).RESULTS: A total of 37 patients (17 in trial 1 and 20 in trial 2) received eculizumab for a median of 64 and 62 weeks, respectively. Eculizumab resulted in increases in the platelet count; in trial 1, the mean increase in the count from baseline to week 26 was 73×10(9) per liter (P< 0.001). In trial 2, 80% of the patients had thrombotic microangiopathy event-free status. Eculizumab was associated with significant improvement in all secondary end points, with continuous, time-dependent increases in the estimated glomerular filtration rate (GFR). In trial 1, dialysis was discontinued in 4 of 5 patients. Earlier intervention with eculizumab was associated with significantly greater improvement in the estimated GFR. Eculizumab was also associated with improvement in health-related quality of life. No cumulative toxicity of therapy or serious infection-related adverse events, including meningococcal infections, were observed through the extension period.CONCLUSIONS: Eculizumab inhibited complement-mediated thrombotic microangiopathy and was associated with significant time-dependent improvement in renal function in patients with atypical hemolytic-uremic syndrome. (Funded by Alexion Pharmaceuticals; C08-002 ClinicalTrials.gov numbers, NCT00844545 [adults] and NCT00844844 [adolescents]; C08-003 ClinicalTrials.gov numbers, NCT00838513 [adults] and NCT00844428 [adolescents]). PMID: 23738544
Shared Control Schemes for Middle Ear Surgery (2022)

This paper deals with the control of a redundant cobot arm to accomplish peg-in-hole insertion tasks in the context of middle ear surgery. It mainly focuses on the development of two shared control laws that combine local measurements provided by position or force sensors with the globally observed visual information. We first investigate the two classical and well-established control modes, i.e., a position-based end-frame tele-operation controller and a comanipulation controller. Based on these two control architectures, we then propose a combination of visual feedback and position/force-based inputs in the same control scheme. In contrast to the conventional control designs where all degrees of freedom (DoF) are equally controlled, the proposed shared controllers allow teleoperation of linear/translational DoFs while the rotational ones are simultaneously handled by a vision-based controller. Such controllers reduce the task complexity, e.g., a complex peg-in-hole task is simplified for the operator to basic translations in the space where tool orientations are automatically controlled. Various experiments are conducted, using a 7-DoF robot arm equipped with a force/torque sensor and a camera, validating the proposed controllers in the context of simulating a minimally invasive surgical procedure. The obtained results in terms of accuracy, ergonomics and rapidity are discussed in this paper.
Optically pumped blue-green vertical-cavity surface-emitting laser (1995)

While brisk progress is being made with the II-VI edge-emitting blue-green diode lasers, other device configurations, such as a vertical-cavity surface-emitting laser (VCSEL), offer important complementary opportunities. A number of fabrication and design questions can be addressed by the demonstration of an optically pumped laser as a first step. Here we demonstrate such VCSEL operation in the 480–490 nm range, at present up to T = 200 K, in ZnCdSe/ZnSSSe/ZnMgSSe pseudomorphic separate-confinement heterostructures (SCH) containing three active QW layers and equipped with dielectric high-reflectivity mirrors.
Vibration Behaviour of a Disc Assembly with a Cracked Lacing Wire (2005)

In this paper, mathematical descriptions of the static and dynamic behaviour of the bladed disc with the undamaged and damaged lacing wire are briefly explained. For a steam turbine disc with 70 axial blades coupled by the lacing wire, the centrifugal static analysis is performed. Then, the free and forced vibrations are computed to find differences in vibrations of the bladed disc with and without a failure in the lacing wire. The tip timing measurement is considered as an experimental tool for identifications of possible failures. According to the obtained FE results, a failure of the lacing wire in the rotating disc assembly can be identified by monitoring the centrifugal deformations of the blade tips, resonance frequencies and response amplitudes of the whole bladed disc. The dynamic behaviours of the failure-free disc and with cracked wire connection are compared to each other to outline differences in the known nodal diameter and dispersion curve definition.
Phased Array Feed Calibration, Beamforming and Imaging (2016)

Phased array feeds (PAFs) for reflector antennas offer the potential for increased reflector field of view and faster survey speeds. To address some of the development challenges that remain for scientifically useful PAFs, including calibration and beamforming algorithms, sensitivity optimization, and demonstration of wide field of view imaging, we report experimental results from a 19 element room temperature L-band PAF mounted on the Green Bank 20 Meter Telescope. Formed beams achieved an aperture efficiency of 69% and a system noise temperature of 66 K. Radio camera images of several sky regions are presented. We investigate the noise performance and sensitivity of the system as a function of elevation angle with statistically optimal beamforming and demonstrate cancelation of radio frequency interference sources with adaptive spatial filtering.
RECOLED: A group-aware collaborative text editor for capturing document history (2005)

This paper presents a usability analysis of RECOLED, a shared document editor which supports recording of audio communication in remote collaborative writing sessions, and transparent monitoring of interactions, such as editing, gesturing and scrolling. The editor has been designed so that the collaboration results in the production of a multimedia document history which enriches the final product of the writing activity and can serve as a basis for post-meeting information retrieval. A discussion is presented on how post-meeting processing can highlight the usefulness of such histories in terms of tracking information that would be normally lost in usual collaborative editing settings.
Pleomorphobacterium xiamenense Yin et al. 2013 is a later heterotypic synonym of Oceanicella actignis Albuquerque et al. 2012 (2017)

Pleomorphobacterium xiamenense CLWT was compared with Oceanicella actignis PRQ-67T to examine the taxonomic relationship between the two organisms. The 16S rRNA gene sequence comparison showed that the two strains had 99.9 % sequence similarity. Phylogenetic analysis showed the two strains formed an independent tight cluster, distinctly branching from the closely related species in the family Rhodobacteraceae. Whole genomic comparison between the two strains revealed a digital DNA-DNA hybridization estimate of 88.4 % and average nucleotide identity of 98.8 %, strongly supporting that the two strains represented a single species. In addition, neither strain displayed any striking difference in biochemical characteristics, fatty acid composition, and polar lipid profile. According to priority, Pleomorphobacterium xiamenense is reclassified as a later heterotypic synonym of Oceanicella actignis based on the phylogenetic relationship, whole genomic comparison, fatty acid composition and polar lipid profile, and other phenotypic and biochemical properties.
Synaptic Scaling Requires the GluR2 Subunit of the AMPA Receptor (2009)

Two functionally distinct forms of synaptic plasticity, Hebbian long-term potentiation (LTP) and homeostatic synaptic scaling, are thought to cooperate to promote information storage and circuit refinement. Both arise through changes in the synaptic accumulation of AMPA receptors (AMPARs), but whether they use similar or distinct receptor-trafficking pathways is unknown. Here, we show that TTX-induced synaptic scaling in cultured visual cortical neurons leads to the insertion of GluR2-containing AMPARs at synapses. Similarly, visual deprivation with monocular TTX injections results in synaptic accumulation of GluR2-containing AMPARs. Unlike chemical LTP, synaptic scaling is blocked by a GluR2 C-tail peptide but not by a GluR1 C-tail peptide. Knockdown of endogenous GluR2 with an short hairpin RNA (shRNA) also blocks synaptic scaling but not chemical LTP. Scaling can be rescued with expression of exogenous GluR2 resistant to the shRNA, but a chimeric GluR2 subunit with the C-terminal domain swapped with the GluR1 C-terminal domain (GluR2/CT1) does not rescue synaptic scaling, indicating that regulatory sequences on the GluR2 C-tail are required for the accumulation of synaptic AMPARs during scaling. Together, our results suggest that synaptic scaling and LTP use different trafficking pathways, making these two forms of plasticity both functionally and molecularly distinct.
The parsimony principle for a class of model structures (1985)

A new form of the parsimony principle is presented for a class of model structures containing a common subset of parameters. The principle is applied to the problem of estimating the autoregressive (AR) parameters of an AR process corrupted by white measurement noise.
Zymomonas with improved xylose utilization in stress conditions (2023)

Strains of xylose utilizing Zymomonas with improved xylose utilization and ethanol production during fermentation in stress conditions were obtained using an adaptation method. The adaptation involved continuously growing xylose utilizing Zymomonas in media containing high sugars, acetic acid, ammonia, and ethanol.