gebhart/patrepeval huggingface dataset:
Insulin and TNFα Induce Expression of the Forkhead Transcription Factor GeneFoxc2in 3T3-L1 Adipocytes via PI3K and ERK 1/2-Dependent Pathways (2002)

We have recently identified the winged helix/forkhead gene Foxc2 as a key regulator of adipocyte metabolism that counteracts obesity and diet-induced insulin resistance. This study was performed to elucidate the hormonal regulation of Foxc2 in adipocytes. We find that TNF alpha and insulin induce Foxc2 mRNA in differentiated 3T3-L1 cells with the kinetics of an immediate early response (1-2 h with 100 ng/ml insulin or 5 ng/ml TNF alpha). This induction is, in both cases, attenuated by the PI3K inhibitor wortmannin as well as the MAPK kinase inhibitor PD98059. Furthermore, we show that stimulation of 3T3-L1 adipocytes with phorbol-12-myristate-13-acetate or 8-(4-chlorophenyl)thio-cAMP induces the expression of Foxc2. Interestingly, we find that the basal level of Foxc2 mRNA is down-regulated whereas hormonal responsiveness increases during differentiation of 3T3-L1 from preadipocytes to adipocytes. At the protein level, immunoblots with Foxc2 antibody demonstrated an induction of Foxc2 by insulin and TNF alpha in nuclear extracts of 3T3-L1 adipocytes. EMSA of nuclear proteins from phorbol-12-myristate-13-acetate- and TNF alpha-treated 3T3-L1 adipocytes using a forkhead consensus oligonucleotide revealed specific binding of a Foxc2/DNA complex. In conclusion, our data suggest that insulin and TNF alpha regulate the expression of Foxc2 via a PI3K- and ERK 1/2-dependent pathway in 3T3-L1 adipocytes. Also, signaling pathways downstream of PKA and PKC induce the expression of Foxc2 mRNA.
Salmonella SdiA Recognizes N-acyl Homoserine Lactone Signals from Pectobacterium carotovorum in Vitro, but Not in a Bacterial Soft Rot (2010)

Genomes of Salmonella enterica isolates, including those linked to outbreaks of produce-associated gastroenteritis, contain sdiA, which encodes a receptor of N-acyl homoserine lactones (AHL). AHL are the quorum-sensing signals used by bacteria to coordinately regulate gene expression within -their populations. Because S. enterica does not produce its own AHL, SdiA is hypothesized to function in the interspecies cross-talk with AHL-producing bacteria. Under laboratory conditions, S. enterica responded to AHL from phytobacteria by upregulating expression of srgE. AHL-dependent expression of srgE required a functional sdiA. Essentially, no sdiA-dependent resolution of the srgE recombinase-based (RIVET) reporter was observed inside a soft rot formed on a tomato by an AHL-producing strain of Pectobacterium carotovorum. The results of the control experiments suggest that sdiA is not expressed inside tomato, pepper, green onion, or carrot affected by the soft rot, and the lack of sdiA expression in planta prevents Salmonella spp. from responding to AHL. Despite its inability to detect and respond to AHL during colonization of soft rots, S. enterica reached higher final cell numbers inside a tomato soft rot compared with its growth in intact tomato fruit. The synergistic effect was the strongest under the conditions that are typical for the Florida fall/winter production season.
General and Prospective Views on Oxidation Reactions in Heterogeneous Catalysis (2018)

In this short review paper we have assembled the main characteristics of partial oxidation reactions (oxidative dehydrogenation and selective oxidation to olefins or oxygenates, as aldehydes and carboxylic acids and nitriles), as well as total oxidation, particularly for depollution, environmental issues and wastewater treatments. Both gas-solid and liquid-solid media have been considered with recent and representative examples within these fields. We have also discussed about their potential and prospective industrial applications. Particular attention has been brought to new raw materials stemming from biomass and to liquid-solid catalysts cases. This review paper also summarizes the progresses made in the use of unconventional activation methods for performing oxidation reactions, highlighting the synergy of these technologies with heterogeneous catalysis. Focus has been centered on usual catalysts activation methods but also on less usual ones, such as the use of ultrasounds, microwaves, grinding (mechanochemistry) and photo-activated processes, as well as their combined use.
Novel Sites of Adrenomedullin Gene Expression in Mouse and Rat Tissues1 (1998)

Adrenomedullin (AM) was originally identified in pheochromocytoma tissue and was characterized as a hypotensive peptide. The tissue distribution and cellular localization of AM messenger RNA (mRNA) were determined in mouse and rat tissues by in situ hybridization. Three probes were used: two nonoverlapping probes to the pro-AM N-terminal 20 peptide (PAMP) and AM peptide regions of mouse pro-AM, and a larger complementary DNA (cDNA) probe spanning both the PAMP- and AM peptide-coding regions. The most intense expression of AM mRNA was in endometrium and epithelial cells lining the uterus and mouse adrenal medulla. Moderate levels of expression were detected in kidney glomerulus and cortical distal tubules, ovarian corpus luteum and follicles, epithelial cells lining the bronchioles, cardiac atrium and ventricle, posterior pituitary (particularly in female rats), stomach, small intestine (microvilli, mucosa and submucosa), spleen, and pancreas. Lower levels were observed in pulmonary alveoli, anterior pituitary, and submandibular gland. No expression was detected in the testis, thymus, skeletal muscle, or liver. The localization of AM mRNA in epithelial cells lining the uterus, bronchioles, and gastrointestinal tract indicates novel roles for AM, possibly as an antimicrobial agent. The strong expression of AM in uterus, ovary, and posterior pituitary suggests that AM plays a role in female reproduction.
Flow-mediated dilation reference values for evaluation of endothelial function and cardiovascular health (2022)

We provide an age-adapted frame of FMD reference intervals in apparently healthy individuals for use as a biomarker of cardiovascular health. As the degree of vascular endothelial function integrates environmental and genetic factors with classical CV risk factors, FMD may more comprehensively classify individuals with and without standard modifiable cardiovascular risk factors and serve as a target for cardiovascular prevention.
Fluctuations in local shear-fault energy produce unique and dominating strengthening in metastable complex concentrated alloys (2023)

Local chemical short-range ordering (SRO) and spatial fluctuations of planar fault energy are important features of multi-element and metastable complex concentrated alloys (CCAs). Arising from them, dislocations in such alloys are distinctively wavy in both static and migrating conditions; yet, such effects on strength have remained unknown. In this work, molecular dynamics simulations are used to show that the wavy configurations of dislocations and their jumpy motion in a prototypic CCA of NiCoCr are due to the local fluctuations of the energy of SRO shear-faulting that accompanies dislocation motion, with the dislocation getting pinned at sites of hard atomic motifs (HAMs) associated with high local shear-fault energies. Unlike the global averaged shear-fault energy which in general will subdue on successive dislocation passes, the local fluctuations in the fault energy always remain in a CCA, thus offering a strength contribution that is unique in such alloys. Analysis of the magnitude of this form of dislocation resistance shows that this is dominating over contributions due to elastic misfit of alloying elements and is in good agreement with strengths predicted from molecular dynamics simulations and experiments. This work has unfolded the physical basis of strength in CCAs, which is important for the development of these alloys into useful structural materials.
Supplementary Data from Results and Molecular Correlates from a Pilot Study of Neoadjuvant Induction FOLFIRINOX Followed by Chemoradiation and Surgery for Gastroesophageal Adenocarcinomas (2023)

&lt;p&gt;Supplemental Appendix 8: TCGA gastric tumor analysis&lt;/p&gt;
Sequential Observation of Gastric Ulcer Healing by Endoscopic Ultrasonography (1994)

Sequential observation by EUS showed that the healing of the ulcer surface strongly reflected the healing within the ulcers.
Dual Coordination of Ti and Pb Using Bilinkable Ligands Improves Perovskite Solar Cell Performance and Stability (2020)

Abstract Charge recombination due to interfacial defects is an important source of loss in perovskite solar cells. Here, a two‐sided passivation strategy is implemented by incorporating a bilinker molecule, thiophene‐based carboxylic acid (TCA), which passivates defects on both the perovskite side and the TiO 2 side of the electron‐extracting heterojunction in perovskite solar cells. Density functional theory and ultrafast charge dynamics reveal a 50% reduction in charge recombination at this interface. Perovskite solar cells made using TCA‐passivated heterojunctions achieve a power conversion efficiency of 21.2% compared to 19.8% for control cells. The TCA‐containing cells retain 96% of initial efficiency following 50 h of UV‐filtered MPP testing.
Comparison of Four Dual-Energy CT Scanner Technologies for Determining Renal Stone Composition: A Phantom Approach (2022)

Background Studies have investigated the value of various dual-energy CT (DECT) technologies for determining renal stone composition. However, sparse multivendor comparison data exist. Purpose To compare the performance of four DECT technologies in determining renal stone composition at standard- and low-dose acquisitions. Materials and Methods This was an in vitro phantom study. Seventy-one urinary stones (size: 2.7-14.1 mm) of known chemical composition (51 calcium, four struvite, four cystine, and 12 urate) were placed in a custom-made cylindrical phantom. Consecutive scans with manufacturer-recommended protocols and dose-optimized institutional protocols (up to 80% reduction in volumetric CT dose index) were obtained with rapid kilovolt peak switching DECT (rsDECT) (<i>n</i> = 2), dual-source DECT (<i>n</i> = 2), twin-beam DECT (tbDECT) (<i>n</i> = 1), and dual-layer detector-based CT (dlDECT) (<i>n</i> = 1) scanners. The image data sets were analyzed using effective atomic number and dual-energy ratio indexes of maximally available and comparable spectra. The performance of each combination of scanner technology, method, and acquisition was assessed. Logistic regression models were used to calculate the area under the receiver operating characteristic curve (AUC). Results After image analysis, all scanners except tbDECT had an AUC greater than 0.95 in at least one acquisition in distinguishing urate from other stones. All DECT techniques were able to help differentiate calcium oxalate monohydrate stones with moderate accuracy (AUC: 0.70-0.83), and brushite was differentiated from urate with AUC greater than 0.99. There was no correlation between performance and acquisition with dose-optimized and/or vendor-recommended settings. Conclusion All four dual-energy CT (DECT) technologies enabled accurate determination of stone composition at standard- and low-dose acquisitions; however, performance varied based on the scanner parameters, DECT technique, and stone type. © RSNA, 2022 <i>Online supplemental material is available for this article.</i> See also the editorial by Ringl and Apfaltrer in this issue.
Testing machine learning models for heuristic building damage assessment applied to the Italian Database of Observed Damage (DaDO) (2023)

Abstract. Assessing or forecasting seismic damage to buildings is an essential issue for earthquake disaster management. In this study, we explore the efficacy of several machine learning models for damage characterization, trained and tested on the database of damage observed after Italian earthquakes (DaDO). Six regression- and classification-based machine learning models were considered: random forest, gradient boosting and extreme gradient boosting. The structural features considered were divided into two groups: all structural features provided by DaDO or only those considered to be the most reliable and easiest to collect (age, number of storeys, floor area, building height). Macroseismic intensity was also included as an input feature. The seismic damage per building was determined according to the EMS-98 scale observed after seven significant earthquakes occurring in several Italian regions. The results showed that extreme gradient boosting classification is statistically the most efficient method, particularly when considering the basic structural features and grouping the damage according to the traffic-light based system used, for example, during the post-disaster period (green, yellow and red). The results obtained by the machine learning-based heuristic model for damage assessment are of the same order of accuracy as those obtained by the traditional Risk-UE method. Finally, the machine learning analysis found that the importance of structural features with respect to damage was conditioned by the level of damage considered.
Timing Characterization for RSFQ Cell Library (2019)

As superconducting circuits grow in complexity, full transient simulation and verification at the Josephson junction level using analog circuit simulators become increasingly computationally expensive. To enable faster functional and timing verification using timing back annotation and static timing analysis, logic models of rapid single flux quantum library cells are developed using hardware description languages like Verilog together with the required timing characteristics. These include propagation delays and minimum pin-to-pin pulse arrival time separation at various process and operating corners. These timing parameters must satisfy required margins and yield using Monte Carlo simulations with statistical variations. For each library cell, these timing parameters depend not only on the adjacent cells but also on their internal states. These delay variations are driven by bias current redistribution, load inductance, and load junction critical currents. We present our methodology for extracting these timing parameters to enable timing back annotation and static timing analysis. We demonstrate our methodology with a parallel counter as a reference circuit and show that timing back annotated simulation can closely match results from full circuit simulation.
Piezoresistive micromechanical transducer operation in a pulsed neutron and gamma ray environment (2003)

We completed the third in a series of experiments using commercially available, piezoresistive microelectromechanical system (MEMS) transducers to instrument articles exposed to the intense, pulsed neutron and gamma ray radiation environment of Sandia National Laboratories' Annular Core Research Reactor.Based on analyzing the survival of pressure transducers and accelerometers in the first two experiments, we identified candidate piezoresistive, MEMS transducers and then tested them by exposure to pulses, each with 10 15 neutrons/cm 2 and 10 4 Gy (1 Mrad) of gamma radiation.Simultaneous measurement of temperature indicates that the pressure transducers retain their calibrations and may provide a means of quickly identifying temperature-induced offset shifts of accelerometer calibrations.Comparison to other sensors that do not survive in this environment and implications for using these transducers to instrument test articles are also presented.
Rhodium bis-phosphine catalysts on mesoporous silica supports: new highly efficient catalysts for the hydrogenation of alkenes (2001)

A bidentate rhodium phosphine complex anchored onto a mesoporous molecular sieve was shown to be an active catalyst for the hydrogenation of alkenes, with the activity dependent on the method of grafting, and in general, exceeding that of related homogeneous catalysts.
Tools for practical Quantum cryptography (2001)

Quantum cryptography is moving from laboratory demonstrations towards technical devices. We present a miniature realization of a BB84-based system, and discuss a true solid-state single photon source based on fluorescence from NV-centers in diamond.
Genetic profiling of colorectal cancer liver metastases by combined comparative genomic hybridization and G‐banding analysis (2002)

The majority of genetic studies of colorectal carcinogenesis have focused on changes found in primary tumors. Despite the fact that liver metastases are a leading cause of colorectal cancer deaths, the molecular genetic basis of the advanced disease stages remains poorly understood. We performed comparative genomic hybridization (CGH) on 17 liver metastases from colorectal carcinomas and compared the quantitative profile with the qualitative profile previously obtained with chromosome banding. An average of 12.6 aberrations per tumor was found by CGH. Chromosome 18 and chromosome arms 4q, 8p, and 17p were most frequently lost, whereas chromosomes 7 and 20 and chromosome arms 6p, 8q, and 13q were most frequently gained. We compared the chromosome banding and CGH data after converting the karyotypes into net copy number gains and losses. Ten tumors showed agreement between the findings of the two techniques, whereas five tumors did not (in two cases, no mitotic cells were obtained for banding analysis). All five discordant cases had a "simple" abnormal or normal karyotype, but revealed multiple changes by CGH. A likely explanation for this discrepancy is that in vitro growth before G-banding selected against the cancer cells. Interestingly, by comparing the CGH profiles of the "complex" vs. the "simple"/normal karyotype groups, deletion of 8p and gain of 16q were seen more frequently in the former group. The liver metastases had the same aberrations as seen in primary colorectal carcinomas, summarized in a literature survey. However, these aberrations were seen more frequently in liver metastases, which may be attributable to increased genetic instability.
Adhesion, Spreading, and Aggregation of Platelets in Flowing Blood and the Reliability of the Retention Test Homburg (2005)

Adhesion and aggregation are important parameters characterizing the function of intact platelets in flowing blood and in contact with a more or less thrombogenic surface. In the retention test Homburg (RTH), platelets are exposed to a standardized textured surface (Sysmex retention tubes) under defined conditions of flow. Platelet counts are performed before and after the Sysmex retention tube passage. The difference between these values indicates the percentage of retained platelets (retention index). Decreased retention in the RTH indicates a loss of function or defective platelet function; increase is associated with an increased activation of platelets, for example, in patients with vascular diseases. For further evaluation of the retention phenomenon the filters were fixed after cell passage and examined by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). SEM and TEM micrographs show activated platelets adhering and spreading on the filter surface, comparable with platelets on a disturbed endothelium. Also, we examined the influence of different G forces and centrifugation times on the retention behavior of the platelets in citrated platelet-rich plasma (PRP) and whole blood (WB). G forces influenced the retention index in PRP and WB significantly and in a different way. Finally, we used a platelet standard, as customary in the quality check, to determine the serial as well as the day-to-day precision.
[Antibiotic treatment of acute otitis media]. (1991)

The strategy of antimicrobial therapy in acute otitis media rests on bacteriologic and pharmacokinetic data. Pneumococci and Haemophilus are still the two most prevalent pathogens in acute otitis media and raise problems regarding susceptibility: 25% of Haemophilus beta-strains produce beta-lactamases and 6 to 12% of pneumococci are intermediate or resistant to penicillin. Pharmacologic features required of antimicrobials used in acute otitis media include good penetration in the ear and sustained supra-MIC levels in middle ear fluid. Kinetics of drugs in the ear are still often incompletely understood. The last selection criterion is analysis of comparative trials. Available data do not point to superiority of any drug over the others. Amoxicillin should no longer be given as first-line therapy. Amoxicillin combined with clavulanic acid (Augmentin) is effective on the entire spectrum of causative organisms. Higher levels of amoxicillin may be needed (concomitant use of amoxicillin and (Augmentin). First-generation cephalosporins are effective but may prove unsuccessful in patients with large inocula. Pediazole is clinically effective although penetration of erythromycin in the ear is delayed. The new oral third generation cephalosporins are effective in infections due to beta-lactamase-producing Haemophilus strains. A bacteriologic study should be performed routinely whenever otitis media occurs in an infant under three months of age.
Anomalous high carrier mobility in smectic E phase of a 2-phenylnaphthalene derivative (1998)

Ambipolar carrier transport properties in different phases of a liquid-crystalline photoconductor, 2-(4-octylphenyl)–6-n-butoxynaphthalene, were investigated by a time-of-flight technique. Carrier mobilities were increased stepwise when phase transition took place as the temperature decreased. The smectic E phase in the range of 55–125 °C exhibited nondispersive ambipolar carrier transport with an anomalous high carrier mobility of 1.0×10−2 cm2/V s, while the smectic A phase between 125 and 129 °C had similar carrier transport with a smaller mobility of 4×10−4 cm2/V s. In contrast to the crystalline phase, structural defects in the smectic E phase, which were obvious under microscopic observation with polarized illumination, did not deteriorate the carrier transport properties.
Models of Organization (2010)

The essence of XP, but in general of AMs, is making the customer a part of the team who works very closely with the developers, ideally communicating on a daily basis. However, this is not always feasible: this is due to a number of different reasons, some connected with difficulties of the customer, but others may exist, for instance, situations where the development team is offshore. In this document, we will illustrate the organizational models of XP, also throughout a number of techniques used to obtain at least a part of the benefits of close interactions in case where they are impossible. In fact, the momentum to the development of a project deriving from an ongoing communication flow is the key point of AMs and XP, in order to have a prompt integration of the deliverables into the customer’s production environment.
Non-rigid registration to determine strain fields during mouse brain fixation and embedding (2021)

Biological matter may change shape via water absorption or loss. For example, brain tissue shows non-uniform shrinkage during formalin fixation and paraffin embedding, which is the most common tissue preparation for conventional histological analysis. Local deformations can be analyzed with non-rigid registration of non-destructive three-dimensional imaging datasets. We utilized synchrotron radiation microtomography at the ANATOMIX beamline of Synchrotron SOLEIL to image a mouse brain with 3 micron voxel length after formalin fixation, immersion in ascending alcohol series and xylene, and after paraffin embedding. We created a pipeline for non- rigid registration to align the volumes and extract volumetric strain fields. In this way, we could visualize the swelling/shrinkage of anatomical features. This method avoids time-consuming segmentation of brain regions, however it is sensitive to the registration parameters. In this proceedings paper, we discuss the selection of registration parameters in order to generate plausible volumetric strain fields. This protocol can be deployed to any type of shape change of biological matter and allows for the quantification of the related processes.