gebhart/patrepeval huggingface dataset:
Monitoring Eukaryotic Gene Expression Using Oligonucleotide Microarrays (2004)

An increasing number of biological and medical research questions depend on obtaining global views of gene expression. In this chapter, we will describe how oligonucleotide microarrays have been used to accomplish this goal. In particular, we will focus on the use of GeneChip arrays, which provide high levels of reproducibility, sensitivity, and specificity. Target preparation, hybridization, washing, signal detection, and data analysis will be described in detail. Additionally, we will discuss options for facilitating data sharing, including the creation of databases, and the use of internet tools that help users place their results in the context of data from public and proprietary databases. There is so much interest and innovation in the field of genomics that protocols are constantly evolving. This chapter should be used as a genomic profiling guide only. We urge readers to consult www.affymetrix.com for the most current products and protocols.
Cell lineages in liver carcinogenesis: possible clues from studies of the distribution of alpha-fetoprotein RNA sequences in cell populations isolated from normal, regenerating, and preneoplastic rat livers. (1985)

We analyzed in isolated rat liver cell populations and in fetal and neoplastic livers the distribution of RNA sequences which hybridize with alpha-fetoprotein (AFP) complementary DNA clones. Parenchymal and nonparenchymal cell populations were isolated from normal, regenerating, preneoplastic, and bile duct-ligated rat livers. We found that oval cells, fetal liver, and a primary hepatocellular carcinoma contain the full length 2.3-kilobase AFP messenger RNA (mRNA); in normal adult rat liver, 2.3-kilobase AFP mRNA is found at low levels in an unidentified subpopulation of nonparenchymal cells but is not detected in hepatocytes; both parenchymal and nonparenchymal cells from normal or preneoplastic livers contain in variable proportion a smaller AFP RNA which hybridizes only with complementary DNA clones containing sequences located near the 5' end of the rat AFP gene; during liver regeneration induced by CCl4, elevation of the full length AFP mRNA occurs in nonparenchymal cells but seemingly not in hepatocytes. The results suggest that some cells in the nonparenchymal cell fraction of normal adult rat liver might retain the capacity to produce the 2.3-kilobase AFP mRNA found in large amounts in fetal livers, oval cells, and hepatic tumors. Although the nature of these cells remains to be determined, we suggest that such cells might be the source of the small amounts of AFP synthesized in normal rat liver and may constitute the proposed but as yet uncharacterized "facultative stem cell" compartment in rat liver.
Dynamic observation of X-ray Laue diffraction on single-crystal tungsten during pulsed heat load (2019)

The dynamics of the diffraction peak shape during pulsed heat load on mosaic single-crystal tungsten were measured at the `Plasma' scattering station on the eighth beamline of the VEPP-4 synchrotron radiation source at the Budker Institute of Nuclear Physics. The observed evolution of the diffraction peak shape agrees with theoretical predictions based on calculations of deformation caused by pulsed heating. Three clearly distinguishable stages of the diffraction-peak evolution were found, correlating with the evolution of temperature and deformation distributions. The residual plastic deformation increased with subsequent heating pulses.
Detection of cancer cells using immune reaction with a terahertz chemical microscope (2021)

Recently, analyzing cancer genome is attracted to personalize cancer treatment. The ratio of cancer cells in a specimen is essential for precise analysis of the genome. In our group, a terahertz chemical microscope (TCM) has been proposed and developed to measure the number of cancer cells in solution. In this study, a biotin-tagged AE1/AE3 was immobilized on a sensing plate using avidin-biotin reaction, and we succeed in detecting lung cancer cells in solutions.
Efficacy and Synergy of Small Molecule Inhibitors Targeting FLT3-ITD+ Acute Myeloid Leukemia (2021)

Constitutive activation of FLT3 by ITD mutations is one of the most common genetic aberrations in AML, present in ~1/3 of cases. Patients harboring <i>FLT3</i>-ITD display worse clinical outcomes. The integration and advancement of FLT3 TKI in AML treatment provided significant therapeutic improvement. However, due to the emergence of resistance mechanisms, <i>FLT3</i>-ITD<sup>+</sup> AML remains a clinical challenge. We performed an unbiased drug screen to identify 18 compounds as particularly efficacious against <i>FLT3</i>-ITD<sup>+</sup> AML. Among these, we characterized two investigational compounds, WS6 and ispinesib, and two approved drugs, ponatinib and cabozantinib, in depth. We found that WS6, although not yet investigated in oncology, shows a similar mechanism and potency as ponatinib and cabozantinib. Interestingly, ispinesib and cabozantinib prevent activation of AXL, a key driver and mechanism of drug resistance in <i>FLT3</i>-ITD<sup>+</sup> AML patients. We further investigated synergies between the selected compounds and found that combination treatment with ispinesib and cabozantinib or ponatinib shows high synergy in <i>FLT3</i>-ITD<sup>+</sup> AML cell lines and patient samples. Together, we suggest WS6, ispinesib, ponatinib and cabozantinib as novel options for targeting <i>FLT3</i>-ITD<sup>+</sup> AML. Whether combinatorial tyrosine kinase and kinesin spindle blockade is effective in eradicating neoplastic (stem) cells in <i>FLT3</i>-ITD<sup>+</sup> AML remains to be determined in clinical trials.
POSTNATAL DEVELOPMENT OF UREA CONCENTRATION IN THE NEWBORN RABBIT'S KIDNEY (1971)

It has been demonstrated that the osmotic gradient from the renal cortex to the papillary tip of the medullary tissue plays an important role in the mechanisms to concentrate or dilute the urine. The major solutes maintaining the osmolality are Na and urea. However, the mechanism to maintain high osmolality in the medullary tissue is not yet completely explained, particularly the mechanism of accumulation of the urea in such high concentration. Therefore, the experiments to be reported here are undertaken to elucidate the mechanism above mentioned. The experiments are designed to investigate the transport mechanism of Na and urea separately.
“Self” versus “Non-Self” Connectivity Dictates Properties of Synaptic Transmission and Plasticity (2013)

Autapses are connections between a neuron and itself. These connections are morphologically similar to "normal" synapses between two different neurons, and thus were long thought to have similar properties of synaptic transmission. However, this has not been directly tested. Here, using a micro-island culture assay in which we can define the number of interconnected cells, we directly compared synaptic transmission in excitatory autapses and in two-neuron micronetworks consisting of two excitatory neurons, in which a neuron is connected to one other neuron and to itself. We discovered that autaptic synapses are optimized for maximal transmission, and exhibited enhanced EPSC amplitude, charge, and RRP size compared to interneuronal synapses. However, autapses are deficient in several aspects of synaptic plasticity. Short-term potentiation only became apparent when a neuron was connected to another neuron. This acquisition of plasticity only required reciprocal innervation with one other neuron; micronetworks consisting of just two interconnected neurons exhibited enhanced short-term plasticity in terms of paired pulse ratio (PPR) and release probability (Pr), compared to autapses. Interestingly, when a neuron was connected to another neuron, not only interneuronal synapses, but also the autaptic synapses on itself exhibited a trend toward enhanced short-term plasticity in terms of PPR and Pr. Thus neurons can distinguish whether they are connected via "self" or "non-self" synapses and have the ability to adjust their plasticity parameters when connected to other neurons.
Hierarchical watermarking for protection of DSP filter cores (2003)

A hierarchical watermarking approach is developed that incorporates an ownership identification directly into the design development process. This approach offers a high degree of tamper resistance and provides easy, noninvasive copy detection. We present two FIR digital filter cores, one watermarked at the algorithm level and the second at the algorithm and architecture levels. A unique ownership signature (watermark) is placed at each level. At the algorithm level, the watermark is embedded in the filter coefficients during the development of the transfer function. At the architecture level, we use circuit transformations to watermark the design. Experimental results show approximately 7% area overhead of the algorithm-level watermarked design over a non-watermarked design. The cost of area for the design watermarked at both the algorithm and architecture levels is less than 40%.
Model-based Diagnosis of an Automotive Electric Power Generation and Storage System (2013)

This paper presents mathematical models, design and experimental validation, and calibration of a model-based diagnostic algorithm for an electric-power generation and storage automotive system, including a battery and an alternator with a rectifier and a voltage regulator. Mathematical models of these subsystems are derived, based on the physics of processes involved as characterized by time-varying nonlinear ordinary differential equations. The diagnostic problem focuses on detection and isolation of a specific set of alternator faults, including belt slipping, rectifier fault, and voltage regulator fault. The proposed diagnostic approach is based on the generation of residuals obtained using system models and comparing predicted and measured value of selected variables, including alternator output current, field voltage, and battery voltage. An equivalent input-output alternator model, which is used in the diagnostic scheme, is also formulated and parameterized. The test bench used for calibration of thresholds of the diagnostic algorithm and overall validation process are discussed. The effectiveness of the fault diagnosis algorithm and threshold selection is experimentally demonstrated.
Enantioselective hydrogenation of olefins with phosphinooxazoline-iridium catalysts (2000)

Cationic iridium complexes with chiral phosphinooxazoline ligands are efficient catalysts for the enantioselective hydrogenation of olefins. The complexes are readily prepared, air-stable, and easy to handle. In contrast to chiral rhodium- and ruthenium-phosphine catalysts, they do not require the presence of a polar coordinating group near the C=C bond. In the hydrogenation of unfunctionalized trisubstituted 1,2-diaryl-olefins, high enantioselectivities of >95% ee with full conversion and turnover frequencies of >7,000 h-1 can be achieved, using 0.1 mol% of catalyst with tetrakis[3, 5-bis(trifluoromethyl)phenyl]borate (TFPB or BARF) as the counterion. The corresponding hexafluorophosphate or tetrafluoroborate salts give low conversion due to deactivation of the catalyst during the reaction. Substrates with polar substituents such as allylic alcohols, on the other hand, afford better results with the hexafluorophosphate salts.
Three-dimensional assessment of the dimensions of the osteoarthritic glenoid (2013)

Osteoarthritis results in changes in the dimensions of the glenoid. This study aimed to assess the size and radius of curvature of arthritic glenoids. A total of 145 CT scans were analysed, performed as part of routine pre-operative assessment before total shoulder replacement in 91 women and 54 men. Only patients with primary osteoarthritis and a concentric glenoid were included in the study. The CT scans underwent three-dimensional (3D) reconstruction and were analysed using dedicated computer software. The measurements consisted of maximum superoinferior height, anteroposterior width and a best-fit sphere radius of curvature of the glenoid. The mean height was 40.2 mm (SD 4.9), the mean width was 29 mm (SD 4.3) and the mean radius of curvature was 35.4 mm (SD 7.8). The measurements were statistically different in men and women and had a Gaussian distribution with marked variation. All measurements were greater than the known values in normal subjects. With current shoulder replacement systems using a unique backside radius of curvature for the glenoid component, there is a risk of undertaking excessive reaming to adapt the bone to the component resulting in sacrifice of subchondral bone or under-reaming and instability of the component due to a 'rocking horse' phenomenon.
Follicular dendritic cells and the maintenance of IgE responses (1995)

Antigen (Ag) is retained for long periods of time in secondary lymphoid tissues in the form of immune complexes on follicular dendritic cells (FDC). Ag retained on FDC is thought to play a role in maintaining antibody (Ab) responses in vivo. A model for study of Ab production induced by retained Ag in vitro is the spontaneous Ab response. In this response, specific Ab production is induced spontaneously (no exogenous Ag needed) in cultures derived from secondary lymphoid tissues containing persisting Ag. Specific IgG is spontaneously induced and we reasoned that FDC may also play a role in the maintenance of specific IgE responses. To test this hypothesis, we monitored spontaneous anti-ovalbmin (OVA) IgE production in cultures of lymph node (LN) fragments from OVA-immunized mice. In addition, highly enriched preparations of OVA bearing FDC were added to OVA-specific memory cells in an attempt to stimulate OVA-specific IgE production. Months after secondary immunization, anti-OVA IgE responses were spontaneously induced when fragments from draining LN were placed into culture. Furthermore, FDC bearing OVA from draining LN induced anti-OVA IgE production when incubated with spleen cells from OVA-immune mice whereas identical cultures with FDC bearing environmental Ag from non-draining LN of the OVA immune animals did not. The anti-OVA IgE responses were elicited only in cultures containing OVA-immune memory cells indicating that specific memory cells were critical for these anti-OVA IgE responses. Removal of FDC from cultures with an FDC-specific mAb dramatically decreased anti-OVA IgE production. These studies demonstrate that FDC can induce specific memory T and B cells to produce IgE and help support the concept that FDC-associated antigen may be involved in the long-term maintenance of specific IgE responses.
ChemInform Abstract: Synthesis of 1,2,3,4,5,7‐Hexahydro‐6H‐azocino[4,3‐b]indol‐6‐ones as Intermediates for the Synthesis of Apparicine. (2011)

Abstract Pyrrolidone (I) undergoes a selective ring opening reaction upon reaction with lithiated phenylsulfonylindole (II) generating key ketone (III), whose acidic N‐hydrogen can be utilized for further N‐alkylations.
Etude des effets de contraintes sur des catalyseurs bimétalliques PdNi supportés (2006)

To study strain effects on catalytic properties for supported particles, core-shell Ni-Pd bimetallic nanoparticles have been prepared by chemical synthesis, characterized by multiple techniques (EDS, TEM, EXAFS, etc. ) and studied in buta-1,3-diene hydrogenation. The core-shell structure of Ni-Pd particles and the compressive stress induced on Pd surface atoms, due to its larger atomic radius compared to Ni, have been evidenced by EXAFS. On PdNi model catalysts, Pd activity is amplified. In our case, no amplification of the Pd activity is observed for a monolayer of strained Pd on Ni particles. As a consequence, compressive strain on Pd surface atoms of nanoparticles seems not to play a major role in the amplification of the activity for the buta-1,3-diene hydrogenation; surface reconstruction appearing on extended surfaces to relax the surface stress seems to be the key point
Sustainability of Adalimumab in Fistula Healing and Response: 2-Year Data from CHARM and 12-Month Open-Label Extension Follow-Up Study (2007)

Purpose: Adalimumab (ADA), a fully human monoclonal antibody that targets tumor necrosis factor, has been shown to be efficacious in the induction and maintenance of remission in patients (pts) with Crohn's disease (CD). Fistulizing disease complicates the course of CD in 20–30% of pts, in many cases leading to surgical resection. The CHARM study has previously shown efficacy of ADA in fistula closure and response. We assessed long-term efficacy of ADA in fistula healing and response in CD pts from the CHARM trial in an open-label extension (OLE) follow-up study. Methods: Pts in CHARM were randomized to placebo (PBO), 40 mg every other week (EOW) or 40 mg weekly (EW). Pts with flare or non-response could receive OL ADA at/after Week 12. At the end of CHARM (56 weeks), pts were allowed to enroll into an open-label extension (OLE). In the OLE, pts received EOW OL or remained on EW OL, and could change from EOW to OL EW for flares or non-response. In this analysis, pts with fistulas at baseline (BL) of CHARM were studied, pooling the 2 doses, using an ITT, non-responder imputation analysis. Pts were analyzed for the percentage (%) of healed fistulas and% with ≥50% fistula response at 6 and 12 months in the blinded study and at 6 and 12 months of the OLE follow-up study (for a total of 24 months of therapy). Results: Results are in the table below.Table: Long-Term Efficacy of Fistula Healing and Response with ADA Through 2 YearsConclusion: Sustainable efficacy of ADA in fistula healing and response is evident after 2 years. ADA has shown sustained response in almost two-thirds of the patients in the OLE who had fistulas at baseline of CHARM and sustained closure in more than half of the ADA-treated patients.
Research on a New Cooling System of Airborne Electronic Equipment (2011)

In order to solve centralized installation and cooling problems of airborne electronic equipment with big power and high heat flow density in aircraft, the paper put forward an innovative closed-loop forced ventilation cooling system, expatiated system compositions and operation principles, and also took a cabinet system for example to introduce new cooling system design method and simulation results.
Bimetallic Sites for Catalysis: From Binuclear Metal Sites to Bimetallic Nanoclusters and Nanoparticles (2023)

Heterogeneous bimetallic catalysts have broad applications in industrial processes, but achieving a fundamental understanding on the nature of the active sites in bimetallic catalysts at the atomic and molecular level is very challenging due to the structural complexity of the bimetallic catalysts. Comparing the structural features and the catalytic performances of different bimetallic entities will favor the formation of a unified understanding of the structure-reactivity relationships in heterogeneous bimetallic catalysts and thereby facilitate the upgrading of the current bimetallic catalysts. In this review, we will discuss the geometric and electronic structures of three representative types of bimetallic catalysts (bimetallic binuclear sites, bimetallic nanoclusters, and nanoparticles) and then summarize the synthesis methodologies and characterization techniques for different bimetallic entities, with emphasis on the recent progress made in the past decade. The catalytic applications of supported bimetallic binuclear sites, bimetallic nanoclusters, and nanoparticles for a series of important reactions are discussed. Finally, we will discuss the future research directions of catalysis based on supported bimetallic catalysts and, more generally, the prospective developments of heterogeneous catalysis in both fundamental research and practical applications.
Apoptotic and non-apoptotic programmed cardiomyocyte death in ventricular remodelling (2008)

A defining cellular event in the transition from compensated hypertrophy to dilated cardiomyopathy is cardiomyocyte drop-out due to apoptosis, programmed necrosis, and autophagy. The importance of apoptosis in heart failure has been recognized for over a decade, while other forms of programmed cell death have more recently been appreciated, and their pathophysiological roles continue to be defined in experimental and clinical heart failure. The major focus of this review is on apoptosis in heart failure, with a discussion of molecular cross-talk between apoptosis, autophagy, and programmed necrosis.
Premature transcription termination at the expanded GAA repeats and aberrant alternative polyadenylation contributes to theFrataxintranscriptional deficit in Friedreich’s ataxia (2022)

Frataxin deficiency in Friedreich's ataxia results from transcriptional downregulation of the FXN gene caused by expansion of the intronic trinucleotide guanine-adenine-adenine (GAA) repeats. We used multiple transcriptomic approaches to determine the molecular mechanism of transcription inhibition caused by long GAAs. We uncovered that transcription of FXN in patient cells is prematurely terminated upstream of the expanded repeats leading to the formation of a novel, truncated and stable RNA. This FXN early terminated transcript (FXN-ett) undergoes alternative, non-productive splicing and does not contribute to the synthesis of functional frataxin. The level the FXN-ett RNA directly correlates with the length of the longer of the two expanded GAA tracts. Targeting GAAs with antisense oligonucleotides or excision of the repeats eliminates the transcription impediment, diminishes expression of the aberrant FXN-ett, while increasing levels of FXN mRNA and frataxin. Non-productive transcription may represent a common phenomenon and attractive therapeutic target in diseases caused by repeat-mediated transcription aberrations.
Tunable VUV Frequency Comb for $^{\mathrm{229m}}$Th Nuclear Spectroscopy (2022)

Laser spectroscopy of the $^{\mathrm{229m}}$Th nuclear clock transition is necessary for the future construction of a nuclear-based optical clock. Precision laser sources with broad spectral coverage in the vacuum ultraviolet are needed for this task. Here, we present a tunable vacuum-ultraviolet frequency comb based on cavity-enhanced seventh-harmonic generation. Its tunable spectrum covers the current uncertainty range of the $^{\mathrm{229m}}$Th nuclear clock transition.
The role of cyclosporin eye drops in ocular inflammatory diseases (1993)

Fifty-nine patients were treated with cyclosporin A (CsA) eye drops for various diseases. Most patients with severe vernal keratoconjunctivitis responded well to the treatment. Treatment had little or no effect on anterior uveitis (acute and chronic) or on the fate of high-risk corneal grafts. The response of patients suffering from peripheral corneal melting, ocular pemphigoid or Stevens-Johnson syndrome was variable. Among these, some patients responded well to the treatment with CsA drops while others had no detectable clinical benefit. The large differences in the observed treatment responses may be interpreted to indicate that a different pathological mechanism may take place within a group of patients with similar diagnoses and clinical manifestations.