gebhart/patrepeval huggingface dataset:
Aspartate β-hydroxylase expression promotes a malignant pancreatic cellular phenotype (2014)

Pancreatic cancer (PC) is one of the leading causes of cancer related deaths due to aggressive progression and metastatic spread. Aspartate β-hydroxylase (ASPH), a cell surface protein that catalyzes the hydroxylation of epidermal growth factor (EGF)-like repeats in Notch receptors and ligands, is highly overexpressed in PC. ASPH upregulation confers a malignant phenotype characterized by enhanced cell proliferation, migration, invasion and colony formation in vitro as well as PC tumor growth in vivo. The transforming properties of ASPH depend on enzymatic activity. ASPH links PC growth factor signaling cascades to Notch activation. A small molecule inhibitor of β-hydroxylase activity was developed and found to reduce PC growth by downregulating the Notch signaling pathway. These findings demonstrate the critical involvement of ASPH in PC growth and progression, provide new insight into the molecular mechanisms leading to tumor development and growth and have important therapeutic implications.
The Relative Importance of Fuel Oxidation Chemistry and Physical Properties to Spray Ignition (2017)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;The ignition delay time for direct injection compression ignition engines is determined by complex physical and chemical phenomena that prepare the injected liquid fuel for gas phase ignition. In this work, Computational Fluid Dynamics (CFD) simulations of a reacting spray within a constant volume spray chamber are conducted to investigate the relative importance of liquid fuel physical properties and oxidation chemistry on the ignition delay time. The simulations use multi-component surrogates that emulate the physical and chemical properties of petroleum-derived (Jet-A) and natural-gas-derived (S-8) jet fuels. Results from numerical experiments isolating the fuel physical property and chemistry effects show that fuel chemistry is significantly more important to ignition delay than fuel physical properties under the conditions studied. In addition, as the air charge temperature increases, the effects of physical properties and oxidation chemistry decrease, indicating that the effect of variation in fuel properties on ignition timing may be mitigated through increased pre-ignition charge temperatures.&lt;/div&gt;&lt;/div&gt;
On-Chip electric power generation system from sound of portable music plyers and smartphones towerd portable uTAS (2012)

This paper demonstrates electric generation from sound to minimize and integrate microfluidic systems for point of care testing or in-situ analysis. In this work, 5.4 volts and 50 mW DC was generated from sound through an earphone cable, which is a versatile system and able to actuate small size and low power consumption devices like an electro osmotic pump.
Heat-Treated Campylobacter spp. and mRNA Stability as Determined by Reverse Transcriptase–Polymerase Chain Reaction (2005)

The detection method of reverse transcriptase-polymerase chain reaction (RT-PCR), which specifically targets mRNA, was developed and tested for detection of cultivable Campylobacter spp. The expression of four DNA targets- flaA, tkt, porA, and a putative haem-copper oxidase domain-were assayed in heat-inactivated Campylobacter spp. to determine an optimum target for RT-PCR amplification. A diversity of Campylobacter spp. was tested; however, the presented RT-PCR technique was specific for C. jejuni, C. coli, and C. lari. The durability of mRNA species detected by our RT-PCR technique was dependent upon the individual Campylobacter spp. examined, the condition of heat treatment and post-treatment holding time, as well as the transcript targeted. The putative oxidase was determined to be the most stable mRNA species for this assay. The mRNA of the putative oxidase gene was detectable even after Campylobacter spp. had been treated at temperatures of 95-99 degrees C. Using DNA-based PCR, the four DNA targets could be amplified after heat inactivation followed by a 48 h holding time, indicating that the chromosomal DNA was not substantially degraded by the heat treatment. PCR products from the putative oxidase gene were detected at 10(2) to 10(3) C. jejuni CFU per mL, exhibiting the highest level of sensitivity among the genes tested. The results in the present study indicate that mRNA from Campylobacter spp. may persist in a form that is detectable by RT-PCR amplification for an extended period after heat treatment, demonstrating a poor correlation between mRNA detection and cell cultivability. With these results in mind, further investigations are necessary to determine the correlation between RT-PCR amplification and viability.
Diagnosis by ELISA of bovine abortion due to Campylobacter fetus (1991)

An enzyme-linked immunosorbent assay (ELISA) was developed to detect antigen-specific secretory IgA antibody in bovine vaginal mucus after abortion due to Campylobacter fetus subsp venerealis. Abortions were diagnosed by isolating the organism from 8 foetuses and/or foetal membranes and by histopathology. Vaginal mucus was collected from 7 cows shortly after abortion. All showed a high level of IgA antibody in their vaginal mucus when they were compared with an uninfected control group. The new ELISA is simple and practical and provides a useful tool for diagnosis of bovine venereal campylobacteriosis.
Problems on the MR micropayment schemes (2006)

We discuss the security of the MR schemes and especially point out the vulnerability of the MR3 scheme. The probabilistic deposit mechanism utilized in the MR3 scheme contributes to the reduction of the bank's processing cost. However, as shown in our paper, it also decreases the security of the entire scheme.
Evaluating Metal–Ligand Interactions of Metal-Binding Isosteres Using Model Complexes (2021)

Bioisosteres are a useful approach to address pharmacokinetic liabilities and improve drug-like properties. Specific to developing metalloenzyme inhibitors, metal-binding pharmacophores (MBPs) have been combined with bioisosteres, to produce metal-binding isosteres (MBIs) as alternative scaffolds for use in fragment-based drug discovery (FBDD). Picolinic acid MBIs have been reported and evaluated for their metal-binding ability, pharmacokinetic properties, and enzyme inhibitory activity. However, their structural, electronic, and spectroscopic properties with metal ions other than Zn(II) have not been reported, which might reveal similarities and differences between MBIs and the parent MBPs. To this end, [M(TPA)(MBI)]<sup>+</sup> (M = Ni(II) and Co(II), TPA = tris(2-pyridylmethyl)amine) is presented as a bioinorganic model system for investigating picolinic acid, four heterocyclic MBIs, and 2,2'-bipyridine. These complexes were characterized by X-ray crystallography as well as NMR, IR, and UV-vis spectroscopies, and their magnetic moments were accessed. In addition, [(Tp<sup>Ph,Me</sup>)Co(MBI)] (Tp<sup>Ph,Me</sup> = hydrotris(3,5-phenylmethylpyrazolyl)borate) was used as a second model compound, and the limitations and attributes of the two model systems are discussed. These results demonstrate that bioinorganic model complexes are versatile tools for metalloenzyme inhibitor design and can provide insights into the broader use of MBIs.
Physical Entrainment versus Chemical Binding: Carbon Nanofoam, Metal Nanoparticles, and the Role of Thiophene Linkers (2016)

High-surface-area mesoporous carbon nanofoams with pore networks interconnected in 3D are particularly versatile electrodes because the surface of the networked carbon can be modified with energy-storing or catalytic materials. The resulting carbon nanostructured papers are device-ready electrodes decorated with well-dispersed, electron-wired, nanoscale functional materials directly sited in the flow field within the through-connected 3D pore network. We can also pre–modify the carbon paper–supported nanofoams with thiophene-like "hooks" to anchor pre–formed Au nanoparticles adsorbed from colloidal sols. We characterize these native or thiophenylated carbon architectures before and after adsorbing either 5-nm or 15-nm Au colloids by scanning electron microscopy, X-ray photoelectron spectroscopy, and in terms of their electrochemical activity for ethanol oxidation. With these four sets of structurally related electrodes, we can assess whether the metal nanoparticles chemically bind at heterocyclic sulfur in the carbon walls or if they are physically entrained within the nanometric nooks of the ultraporous carbon nanofoam paper.
ChemInform Abstract: An Improved Procedure for the Conversion of 3,3‐Disubstituted 1,4‐Cyclohexadienes to 2,5‐Cyclohexadien‐1‐ones. (1989)

Abstract The 1,4‐cyclohexadienes (I) are converted into the cyclohexadienones (II) by oxidation with tert‐butyl hydroperoxide and pyridinium dichromate.
2-O-α-D-Glucopyranosyl-L-ascorbic Acid Scavenges 1,1-Diphenyl-2-picrylhydrazyl Radicalsviaa Covalent Adduct Formation (2007)

The 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging mechanism of 2-O-alpha-D-glucopyranosyl-L-ascorbic acid (AA-2G) was studied. We found two undefined products, named X and Y, in the reaction mixture of AA-2G and the DPPH radical under acidic conditions by HPLC analysis. The reaction mixture was further subjected to LC-MS analysis. X was found to be a covalent adduct of AA-2G and the DPPH radical. On the other hand, Y could not be identified, probably because it was a mixture. A time-course study of the radical-scavenging reaction revealed that one molecule of AA-2G scavenged one molecule of DPPH radical to generate an AA-2G radical, which readily reacted with another molecule of the DPPH radical to form a covalent adduct (X). Subsequently, this adduct slowly quenched a third molecule of the DPPH radical, resulting in reaction products (Y). Therefore, one molecule of AA-2G has only one oxidizable -OH group, but can scavenge three molecules of the DPPH radical. The radical-scavenging mechanism of AA-2G elucidated in this study should be useful in understanding the biological roles of AA-2G per se in the food and cosmetic fields.
Expression and functional involvement of N-cadherin in embryonic limb chondrogenesis (1994)

ABSTRACT Cell adhesion molecules have been shown to be important mediators of morphogenesis and pattern formation. In this study, we have shown that N-cadherin is expressed in a specific spatiotemporal manner in the developing limb bud during chondrogenesis in vivo and in cultured limb mesenchyme in vitro. The time period of maximal expression of N-cadherin corresponds to the period of active cellular condensation, an event believed to be a necessary prerequisite for chondrogenic differentiation. To directly assess the functional involvement of N-cadherin in cellular condensation, we have examined the effects of perturbing N-cadherin activity on both cell aggregation and chondrogenesis using NCD-2, a rat monoclonal antibody directed against the binding region of N-cadherin. Non-immune rat IgG was used as a control. Our results show that functional N-cadherin is necessary for chondrogenesis to proceed both in vivo and in vitro. Limb mesenchymal cells exhibited characteristic Ca2+-dependent cell aggregation in suspension, which was inhibited in the presence of exogenous NCD-2. In micromass cultures of limb mesenchymal cells, NCD-2 inhibited overt chondrogenesis in a dose-dependent manner. Furthermore, NCD-2 inhibition of chondrogenesis in micromass cultures was time-dependent, suggesting that N-cadherin is crucially involved during the latter half of the first 24 hours of culture, a time period most likely corresponding to active cellular condensation. NCD-2 also significantly influenced limb development when injected into embryonic limb buds in vivo. In addition to significant inhibition of chondrogenesis and developmental delays, gross developmental deformities and perturbation of overall pattern formation were also observed. Taken together, these results demonstrate that N-cadherin is functionally required in mediating the cell-cell interactions among mesenchymal cells important for chondrogenesis in micromass culture in vitro and in the intact limb bud in vivo.
Morphological MR imaging of the articular cartilage of the knee at 3T: value of ultrashort echo time (UTE) sequence? (2015)

Poster: ECR 2015 / C-0442 / Morphological MR imaging of the articular cartilage of the knee at 3T: value of ultrashort echo time (UTE) sequence? by: Van Dyck1, F. Vanhevel1, D. Grodzki2, F. M. H. M. Vanhoenacker1, J. Gielen1, P. M. Parizel1; 1Edegem/BE, 2Erlangen/DE
Optimization of Grignard Addition to Esters: Kinetic and Mechanistic Study of Model Phthalide Using Flow Chemistry (2018)

The kinetics of sequential addition of a distinct Grignard species onto a lactone is studied by flow chemistry. The experimental data are shown to be consistent with a kinetic model based on four reaction steps, reaction of ester to magnesium hemiacetal, rearrangement to ketone (forward and backward), and reaction of ketone to tertiary alcohol upon quenching. The experimental derived reaction mechanism is supported by ab initio molecular computations, and the predicted activation energy is in good agreement with the experimental observations. The Grignard reaction follows a substrate-independent, reductive [2 + 2] cycloaddition of the Meisenheimer/Casper type. Moreover, the rearrangement equilibrium between magnesium hemiacetal and ketone is characterized and found to be feasible. Monoaddition of the ester carbonyl group is demonstrated for fluorophenylmagnesium bromide but at reaction conditions at −40 °C with several hours of residence time. Working under cryogenic temperature conditions is essential to realizing monoaddition of the ester carbonyl group with Grignard reagents.
High anti-lymphoma activity of bendamustine/mitoxantrone/rituximab in rituximab pretreated relapsed or refractory indolent lymphomas and mantle cell lymphomas. A multicenter phase II study of the German Low Grade Lymphoma Study Group (GLSG) (2007)

On the basis of a preceding phase I study, the current trial explored bendamustine in combination with mitoxantrone and rituximab (BMR) in patients with stage III/IV relapsed or refractory indolent lymphomas and mantle cell lymphoma (MCL) with or without prior rituximab containing chemo-immunotherapy (R-chemo) treatment. Therapy consisted of bendamustine 90 mg/m(2) days 1 + 2, mitoxantrone 10 mg/m(2) day 1, rituximab 375 mg/m(2) day 8. Treatment was repeated on day 29 for a total of four cycles. Between 3 April and 04 July, 57 patients were recruited from 24 participating institutions, 39% of whom had received prior R-chemo therapy. Median age was 66 years (40 - 83). Lymphoma subtypes were 29 follicular (FL), 18 MCL, and 10 other indolent lymphomas. The overall response rate (ORR) was 89% with 35% CR and 54% PR. ORR in R-chemo pretreated patients was 76% (38% CR, 38% PR). After a median observation time of 27 months (1 - 43), the estimated median progression free survival is 19 months. The 2 year overall survival is 60% for patients with FL and MCL. Treatment related toxicities of grade 3/4 comprised a reversible myelosuppression (10% anemia, 78% leukocytopenia, 46% granulocytopenia, 16% thrombocytopenia). However, unexpected hospitalisations were necessary after 4% of BMR-application only. BMR is a very effective new outpatient immuno-chemotherapy with low toxicity for patients with relapsed/refractory FL, MCL and other indolent lymphomas.
Evaluation of Ti Distribution in Zeolite Framework Based on the Catalytic Activity for Alkene Epoxidation (2019)

A method for estimating the location of Ti atoms in zeolite framework has been developed based on the difference in catalytic activity for epoxidation of 1-hexene and 2-methyl-2-pentene. We have fo...
A Physical Law Constrained Deep Learning Model for Vehicle Trajectory Prediction (2023)

Vehicle trajectory prediction is crucial and indispensable for ensuring the safe and efficient operation of autonomous vehicles in complex traffic environments. The application of Internet of Things technology in the collaborative automated driving system (CADS) has established a robust data foundation for vehicle trajectory prediction. Accurate prediction requires not only a substantial amount of high-quality data but also a deep understanding of the vehicle’s driving characteristics and interactions between neighboring vehicles. To enhance the study of vehicle trajectory prediction, this article proposes a novel Social Force-constrained Gated Recurrent Unit (SF-GRU) model, which integrates data-driven and physics-driven models. Specifically, the SF-GRU model is based on the gated recurrent unit encoder–decoder framework and incorporates social force constraints to enhance and supplement the model input based on vehicle time-series trajectory data, which describes the driving and interactive behaviors of vehicles during driving, as well as the interactions between neighboring vehicles and the surrounding environment. The model is trained and validated using the next generation simulation data set. Experimental results demonstrate that the SF-GRU model outperforms existing state-of-the-art models in both longitudinal and lateral motion, and that social force constraints are more effective than spatial variables in improving prediction accuracy. Furthermore, the SF-GRU model can intuitively and accurately consider the interactions between vehicles, and precisely describe the changes of relevant variables in the prediction process, thus enhancing the interpretability of the data-driven model. The SF-GRU model has great potential in vehicle trajectory prediction and can provide important support for the practical implementation of autonomous driving vehicles.
Cytotoxic effector cell granules recognized by the monoclonal antibody TIA-1 are present in CD8+ lymphocytes in lymph nodes of human immunodeficiency virus-1-infected patients. (1993)

A novel monoclonal antibody (mAB) TIA-1, which recognizes a 15-kd granule-associated protein of cytotoxic T lymphocytes and natural killer cells, has been applied to sections of lymph nodes with human immunodeficiency virus (HIV)-induced lymphadenopathy (follicular hyperplasia and lymphocyte depletion). The protein recognized by this mAB induces apoptosis in permeabilized lymphocytes in vitro. While this mAB reacted with approximately 46% of paracortical CD8+ cells in control nodes, it reacted with 75% of such cells in HIV-induced follicular hyperplasia. Germinal centers of the control nodes contained few TIA-1 + cells; in follicular hyperplasia caused by HIV-1, almost all germinal center CD8+ cells were TIA-1 +. Both in the control nodes and in HIV-induced follicular hyperplasia the majority of TIA-1 + cells coexpressed CD45R0. A marked loss of CD8+TIA-1+ cells was seen in lymphocyte-depleted nodes of patients with AIDS. The loss of these cytotoxic T lymphocytes may have a significant impact on the progression of the disease.
Evolution of Surgery for Adolescent Idiopathic Scoliosis Over 20 Years (2017)

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Targeting Binding Function-3 of the Androgen Receptor Blocks Its Co-Chaperone Interactions, Nuclear Translocation, and Activation (2016)

The development of new antiandrogens, such as enzalutamide, or androgen synthesis inhibitors like abiraterone has improved patient outcomes in the treatment of advanced prostate cancer. However, due to the development of drug resistance and tumor cell survival, a majority of these patients progress to the refractory state of castration-resistant prostate cancer (CRPC). Thus, newer therapeutic agents and a better understanding of their mode of action are needed for treating these CRPC patients. We demonstrated previously that targeting the Binding Function 3 (BF3) pocket of the androgen receptor (AR) has great potential for treating patients with CRPC. Here, we explore the functional activity of this site by using an advanced BF3-specific small molecule (VPC-13566) that was previously reported to effectively inhibit AR transcriptional activity and to displace the BAG1L peptide from the BF3 pocket. We show that VPC-13566 inhibits the growth of various prostate cancer cell lines, including an enzalutamide-resistant cell line, and reduces the growth of AR-dependent prostate cancer xenograft tumors in mice. Importantly, we have used this AR-BF3 binder as a chemical probe and identified a co-chaperone, small glutamine-rich tetratricopeptide repeat (TPR)-containing protein alpha (SGTA), as an important AR-BF3 interacting partner. Furthermore, we used this AR-BF3-directed small molecule to demonstrate that inhibition of AR activity through the BF3 functionality can block translocation of the receptor into the nucleus. These findings suggest that targeting the BF3 site has potential clinical importance, especially in the treatment of CRPC and provide novel insights on the functional role of the BF3 pocket. Mol Cancer Ther; 15(12); 2936-45. ©2016 AACR.
MSK1 and MSK2 Are Required for the Mitogen- and Stress-Induced Phosphorylation of CREB and ATF1 in Fibroblasts (2002)

Using mouse knockouts for mitogen- and stress-activated protein kinase 1 (MSK1) and MSK2 and a double knockout of both MSK1 and MSK2, we show that these protein kinases are required for the stress-induced phosphorylation of transcription factors CREB and ATF1 in primary embryonic fibroblasts. In contrast mitogen-induced phosphorylation of CREB and ATF1 is greatly reduced but not totally abolished. The mitogen- and stress-induced phosphorylation of CREB at Ser133 has been linked to the transcription of several immediate early genes, including c-fos, junB, and egr1. The knockout of both MSK1 and MSK2 resulted in a 50% reduction in c-fos and junB gene transcription in response to anisomycin or UV-C radiation but only a small reduction in response to tetradecanoyl phorbol acetate or epidermal growth factor in fibroblasts. The transcription of egr1 in response to both mitogenic and stress stimuli, as well as stress-induced apoptosis, was unaffected in the MSK1/MSK2 double knockout.
Ultrasensitive and Selective Gas Sensor Based on a Channel Plasmonic Structure with an Enormous Hot Spot Region (2019)

We present experimental and theoretical studies of a metamaterial-based plasmonic structure to build a plasmonic-molecular coupling detection system. High molecular sensitivity is realized only when molecules are located in the vicinity of the enhanced field (hot spot region); thus, introducing target molecules in the hot spot region to maximize plasmonic-molecular coupling is crucial to developing the sensing technology. We design a metamaterial consisting of a vertically oriented metal insulator metal (MIM) structure with a 25 nm channel sandwiched between two metal films, which enables the delivery of molecules into the large ravinelike hot spot region, offering an ultrasensitive platform for molecular sensing. This metamaterial is applied to carbon dioxide and butane detection. We design the structure to exhibit resonances at 4033 and 2945 cm<sup>-1</sup>, which overlap with the C═O and -CH<sub>2</sub> vibration modes, respectively. The mutual coupling of these two resonance modes creates a Fano resonance, and their distinct peaks are clearly observed in the corresponding transmission dips. In addition, owing to its small footprint, such a vertical-oriented MIM structure enables us to increase the integration density and allows the detection of a 20 ppm concentration with negligible background noise and high selectivity in the mid-infrared region.