gebhart/patrepeval huggingface dataset:
Determination of the Size Distribution of Polydisperse Nanoparticles with Single-Particle Mass Spectrometry: The Role of Ion Kinetic Energy (2005)

We develop a method to determine size and size distribution (30–150 nm) of polydisperse nanoparticles using a laser ablation/ ionization time-of-flight single-particle mass spectrometer that extends the work first described by Reents and Ge. We found a composition independent “power law” dependence between the total peak area and original particle volume that enables one to determine particle volume directly from a particles mass spectrum. This power-law relationship suggests that some ions ablated and ionized from a particle are selectively lost during transport from the laser ablation/ionization region to the detector. A numerical calculation of ion trajectories shows that ion loss is highly dependent on the initial kinetic energy of ions. We show that the size-dependent energetic ions formed by the laser-particle interaction lead to power-law relationship between the cube root of peak area and particle diameter. The results demonstrate that particle size distributions measured with the mass spectrometer are in good agreement with those measured with a scanning mobility particle sizer.
Acute Kidney Injury Sensitizes the Brain Vasculature to Ang II (Angiotensin II) Constriction via FGFBP1 (Fibroblast Growth Factor Binding Protein 1) (2020)

Acute kidney injury (AKI) causes multiple organ dysfunction. Here, we identify a possible mechanism that can drive brain vessel injury after AKI. We induced 30-minute bilateral renal ischemia-reperfusion injury in C57Bl/6 mice and isolated brain microvessels and macrovessels 24 hours or 1 week later to test their responses to vasoconstrictors and found that after AKI brain vessels were sensitized to Ang II (angiotensin II). Upregulation of FGF2 (fibroblast growth factor 2) and FGFBP1 (FGF binding protein 1) expression in both serum and kidney tissue after AKI suggested a potential contribution to the vascular sensitization. Administration of FGF2 and FGFBP1 proteins to isolated healthy brain vessels mimicked the sensitization to Ang II after AKI. Brain vessels in <i>Fgfbp1</i><sup>-/-</sup> AKI mice failed to induce Ang II sensitization. Complementary to this, systemic treatment with the clinically used FGF receptor kinase inhibitor BGJ398 (Infigratinib) reversed the AKI-induced brain vascular sensitization to Ang II. All these findings lead to the conclusion that FGFBP1 is especially necessary for AKI-mediated brain vascular sensitization to Ang II and inhibitors of FGFR pathway may be beneficial in preventing AKI-induced brain vessel injury.
Intrasurgical Assessment of Subretinal tPA Injection for Submacular Hemorrhage in the PIONEER Study Utilizing Intraoperative OCT (2015)

iOCT can successfully be performed during pars plana vitrectomy with subretinal tPA injection. Utilizing iOCT, appropriate placement of tPA solution and corresponding retinal architectural changes were visualized.
Supplementary Table S2 from Gain-of-Function <i>RHOA</i> Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer (2023)

&lt;p&gt;RPPA data&lt;/p&gt;
Volume Holographic Data Storage In Photo-organic Media (1993)

Photo-organic media are promising for volume data storage because of low sample costs and easy fabrication of arbitrary sample shapes and sizes. The key disadvantage of volume data storage relative to planar storage is that the space-bandwidth product of the recording fields in a volume system must be large to achieve effective recording. This means that the cost of the data recording and reconstruction systems will be much higher. This problem is alleviated in cylindrical and spherical photo-organic storage media by eliminating the need for imaging optics.
(Invited) Silica Based Ionogels: Raman Study of Protic Vs. non Protic Ionic Liquids, with Lithium Salt Vs. Sodium Salt (2020)

Ionogels represent a route to biphasic materials, for the use of ionic liquids (ILs) for all solid devices. Confining ILs within host networks enhances their averaged dynamics, resulting in improved charge transport. Fragility, short relaxation times, low viscosity, and good ionic conductivity, all them appear to be related to the IL / host network interface. The presence of ILs at interface neighborhood leads to the lowering of cation-anion interaction, i.e. to the breakdown of aggregated and structured regions that are systematically found in bulk ILs.[1] This “destructuration”, as well as segregative interactions at interface,[2] coupled with percolation of the bicontinuous solid/liquid interface,[3] make these materials very competitive among the existing solid electrolytes. Herein we will present an in-depth study of coordination of TFSI anion with lithium or with sodium cations, in the presence of protic or non protic pyrrolidinium cations, confined within silica with well-controlled porosities. The coordination number of TFSI-cation is shown to decrease upon confinement, making the lithium of sodium cation more diffusive. Moreover, the cation-anion layering at the interface is studied by DFT and shows striking modifications when a lithium or sodium salt is added, thus highlighting the effect of the chemistry of the host network, similarly with previous study.[4] References 1) A. Guyomard-Lack, P.-E. Delannoy, N. Dupré, C. V. Cerclier, B. Humbert, J. Le Bideau, Phys. Chem. Chem. Phys., 16, (2014) 23639-23645 2) A. Guyomard-Lack, B. Said, N. Dupré, A. Galarneau, J. Le Bideau, New J. Chem., 40, (2016) 4269-4276 3) C. V. Cerclier, J.-M. Zanotti, J. Le Bideau, Phys. Chem. Chem. Phys., 17, (2015) 29707—29713 4) D. Aidoud, D. Guy-Buissou, D. Guyomard, B. Lestriez, J. Le Bideau, J. Electrochem. Soc., 165, (2018) A3179-A3185
Click-Conversion Multi-Task Model with Position Bias Mitigation for Sponsored Search in eCommerce (2023)

Position bias, the phenomenon whereby users tend to focus on higher-ranked items of the search result list regardless of the actual relevance to queries, is prevailing in many ranking systems. Position bias in training data biases the ranking model, leading to increasingly unfair item rankings, click-through-rate (CTR), and conversion rate (CVR) predictions. To jointly mitigate position bias in both item CTR and CVR prediction, we propose two position-bias-free CTR and CVR prediction models: Position-Aware Click-Conversion (PACC) and PACC via Position Embedding (PACC-PE). PACC is built upon probability decomposition and models position information as a probability. PACC-PE utilizes neural networks to model product-specific position information as embedding. Experiments on the E-commerce sponsored product search dataset show that our proposed models have better ranking effectiveness and can greatly alleviate position bias in both CTR and CVR prediction.
Local Definition of Ty1 Target Preference by Long Terminal Repeats and Clustered tRNA Genes (2004)

LTR-containing retrotransposons reverse transcribe their RNA genomes, and the resulting cDNAs are integrated into the genome by the element-encoded integrase protein. The yeast LTR retrotransposon Ty1 preferentially integrates into a target window upstream of tDNAs (tRNA genes) in the yeast genome. We investigated the nature of these insertions and the target window on a genomic scale by analyzing several hundred de novo insertions upstream of tDNAs in two different multicopy gene families. The pattern of insertion upstream of tDNAs was nonrandom and periodic, with peaks separated by approximately 80 bp. Insertions were not distributed equally throughout the genome, as certain tDNAs within a given family received higher frequencies of upstream Ty1 insertions than others. We showed that the presence and relative position of additional tDNAs and LTRs surrounding the target tDNA dramatically influenced the frequency of insertion events upstream of that target.
Integrating Tactile and Force Feedback with Finite Element Models (2006)

Integration of the correct tactile and kinesthetic force feedback response with an accurate computational model of a compliant environment is a formidable challenge. We examine several design issues that arise in the construction of a compliance renderer, specifically the interaction between impedances of tactile displays, impedances of robot arms, and the computational model. We also describe an implementation of a compliance rendering system combining a low-impedance robot arm for large workspace kinesthetic force feedback, a high-impedance shape display for distributed tactile feedback to the finger pad, and a real-time finite element modeler. To determine the efficacy of the integration of tactile and kinesthetic force feedback components, we conducted a study examining the user’s ability to discriminate stiffness. Subjects were able to reliably detect a 20% difference in rendered material stiffness using our compliance rendering system.
Targeting of breast tumors by an HLA A*0201/MIF specific antibody (101.23) (2010)

Abstract We previously utilized secreted HLA technology to identify a Macrophage Migration Inhibitory Factor (MIF19-27) encoded peptide as unique to the HLA-A*0201 molecules of breast cancer derived cell lines. The aims of this study were to (1) generate a mAb specific for the A*0201/MIF complex, (2) to assess A*0201/MIF expression on primary tumors, and (3) to evaluate the cytotoxicity of the antibody to breast cancer cell lines and tumor xenografts. The RL21A mAb specific for A*0201/MIF was generated by immunizing mice with peptide/MHC complexes. Matched tumor and normal cryopreserved breast tissues were HLA typed and A*0201 tissue sections were stained with RL21A. Staining of the normal and primary tumors were compared for HLA A*0201 expression and for A*0201/MIF staining. The RL21A TCRm antibody specifically stained HLA-A*0201 positive breast tumors. This confirms the presentation of the MIF on primary breast cancer tissues and validates cancer epitope discovery using secreted HLA technology and cancer cell lines. RL21A was capable of inducing potent complement mediated (CDC) and cell mediated cytolysis (ADCC) as measured by in vitro lactate dehydrogenase (LDH) release. In addition, RL21A reduced tumor burden in a prophylactic tumor model, employing an aggressive BT20-A2 xenograft. Here we demonstrate that the HLA-based discovery of cancer epitopes can lead to the generation of mAb that specifically recognize and destroy tumors via the A*0201/peptide complex.
Hormonal Influences on Lung Function and Response to Environmental Agents (2012)

Numerous studies in humans and experimental animals have identified considerable sex differences in respiratory physiology and in the response of the lung to environmental agents. These differences appear to be mediated, at least in part, by sex hormones and their nuclear receptors. Moreover, animal models are increasingly used to study pathogenic mechanisms and test potential therapies for a variety of human lung diseases, many of which appear to be influenced by sex and sex hormones. In this article, data are summarized from studies of lung function and disease in which sex differences have been observed. Specific attention is paid to animal models of acute lung injury, nonallergic and allergic lung inflammation, and lung fibrosis. It is anticipated that continued investigation of the role of sex and sex hormones in animal models will provide valuable insight into the pathogenesis and potential treatments for a variety of acute and chronic human lung diseases.
Supramolecular Self-Assembly of Multiblock Copolymers in Aqueous Solution (2006)

A unique pH-dependent phase behavior from a copolymer micellar solution to a collapsed hydrogel with micelles ordered in a hexagonal phase was observed. Small-angle neutron scattering (SANS) was used to follow the pH-dependent structural evolution of micelles formed in a solution of a pentablock copolymer consisting of poly((diethylaminoethyl methacrylate)-b-(ethylene oxide)-b-(propylene oxide)-b-(ethylene oxide)-b-(diethylaminoethyl methacrylate)) (PDEAEM25-b-PEO100-b-PPO65-b-PEO100-b-PDEAEM25). Between pH 3.0 and pH 7.4, we observed the presence of charged spherical micelles. Increasing the pH of the micelle solution above pH 7.4 resulted in increasing the size of the micelles due to the increasing hydrophobicity of the PDEAEM blocks above their pKa of 7.6. The increase in size of the spherical micelles resulted in a transition to a cylindrical micelle morphology in the pH range 8.1-10.5, and at pH >11, the copolymer solution undergoes macroscopic phase separation. Indeed, the phase separated copolymer sediments and coalesces into a hydrogel structure that consists of 25-35 wt % water. Small-angle X-ray scattering (SAXS) clearly indicated that the hydrogel has a hexagonal ordered phase. Interestingly, the process is reversible, as lowering of the pH below 7.0 leads to rapid dissolution of the solid into homogeneous solution. We believe that the hexagonal structure in the hydrogel is a result of the organization of the cylindrical micelles due to the increased hydrophobic interactions between the micelles at 70 degrees C and pH 11. Thus we have developed a pH-/temperature-dependent, reversible hierarchically self-assembling block copolymer system with structures spanning nano- to microscale dimensions.
Does Aleutian Disease Occur among Domestic Ferrets in Poland? Results of Preliminary Studies Conducted in Two Regions of Poland (2022)

Although ferrets are becoming increasingly popular as companion animals, their population in households is still far lower compared to cats or dogs. This results in a much smaller number of ferret specialists, and thus poorer diagnosis of various diseases, including the Aleutian disease. Aleutian disease is a slowly progressing viral disease which can cause different symptoms in these animals. The virus can also cause symptoms in different species of animals, but in the case of ferrets, there is relatively less information on about both the prevalence and symptoms of this disease. Therefore, the aim of this study was to determine the presence of antibodies and the virus itself in ferrets from two regions of Poland. Blood samples and rectal swabs were obtained from 61 domestic ferrets from Mazowieckie and Dolnośląskie voivodships. The presence of antibodies was determined using serological methods and real-time PCR analysis was performed to determine presence of viral DNA. Serological analyses demonstrated that 49% (<i>n</i> = 30) of the ferrets had antibodies against Aleutian disease virus (ADV). No relationship was observed between the prevalence of antibodies and age, sex, habitual residence or origin of ferrets. The real-time PCR did not confirm DNA of the ADV in any of the blood and rectal swab samples. Obtained results suggest that ADV circulates in the analyzed population of ferrets, therefore further studies in this direction should be carried out.
A novel selective therapeutic targeting heme oxygenase-1 revealed a potent antimetastatic activity in androgen-refractory human prostate cancer models (2009)

e16090 Prostate cancer is a highly prevalent disease. Despite a significant improvement in the overall survival attributed in part to early detection and introduction of novel therapeutic modalities, many cancer patients at primary diagnosis present advanced disease or experience recurrence of the cancer. The progression of prostate cancer (PCA) to hormone-refractory phenotype (HRPCA) and to metastasis is an ominous event in patients with advanced PCA. Currently, clinically available drugs for hormone refractory PCA have only marginal efficacy. In this study, we identified heme oxygenase 1 (HO-1) to be significantly upregulated in epithelial PCA cells, but not in surrounding stromal cells, from hormone refractory prostate cancer cases compared to hormone-responsive prostate cancer and to benign tissues. We validated HO-1 as a novel therapeutic target for HRPCA. Specifically, inhibition of HO-1 gene in androgen-independent and highly invasive prostate cancer cells, PC3M, decreased HO-1 activity, oxidative stress, MAPKs activation, cell proliferation, and cell migration and invasion in vitro, as well as inhibition of prostate tumor growth and lymph nodes and lung metastases in vivo. The impact of HO-1 silencing on these oncogenic features was mimicked by exposure of cells to a novel selective small-molecule HO-1 inhibitor referred to as OB-24. OB-24 selectively downregulates HO-1 activity, oxidative stress, and significantly inhibits cell proliferation in vitro and tumor growth and lymph node/lung metastases in vivo. A potent synergistic activity in inhibiting HRPCA metastasis formation was observed when OB-24 was combined with the chemotherapy drug taxol. The molecular and potential clinical impact of OB-24 alone and in combination with taxanes on HRPCA will be discussed. [Table: see text]
F-18 FDG PET/CT, breast MRI and mammography: Can breast cancer be reliably detected? (2006)

1642 Objectives: F-18 FDG PET/CT is a powerful imaging modality for cancer diagnosis, staging and establishing response to therapy, including breast cancer (BC). Breast MRI (BMRI) is gaining a major role in the management of high risk BC patients, adding information when mammography findings are equivocal. The role of PET/CT in addition to mammography and BMRI in BC diagnosis is not completely elucidated. Therefore, we were prompted to review our experience with mammography, BMRI and PET/CT in BC. Methods: This is a retrospective study of 101 women with BC, 30-82 years-old (average: 56.1±12.1), who had F-18 FDG PET/CT at our institution from Jan 2003 to Jun 2005. Of these, 27 patients also had mammography and BMRI. Reinterpretation of the studies for accuracy and data analysis from medical records were performed. Sensitivity and specificity were calculated using a 2 x 2 table with pathology results (84.1% of the patients) or clinical follow-up (15.9% of the cases) as the gold standard. Results: The tumor types in the 85 patients with available pathology reports were: 68 ductal (41 infiltrative, 22 invasive, 5 in situ), 11 lobular (5 infiltrative, 6 invasive), 4 adenocarcinomas and 2 mucinous carcinomas. Tumor size at cancer presentation ranged 0.8-10.0 cm (average: 2.8±1.9) for all the patients and 1.9-9.0 cm (average: 3.72±1.8) for the patients that had PET/CT at initial presentation. PET/CT sensitivity was 79.2 % (95% CI: 59.5-90.7) for breast disease, 68.2% (95% CI: 47.3-83.6) for axilla and 94.1% (95% CI: 80.9-93.3) for distant metastases. Specificities were 98.7% (95% CI: 93-99.8), 100% (95% CI: 95.3-100) and 91% (95% CI: 81.8-95.8), respectively. For the 27 patients with all 3 exams, sensitivities and specificities for BC detection were 69.2% (95% CI: 42.3-87.3) and 77.8% (95% CI: 45.3-93.7) for mammography, 80% (95% CI: 54.8-92.9) and 91.7% (95% CI: 64.6-98.5) for BMRI, and 71.4% (95% CI: 45.3-88.3) and 92.3% (95% CI: 66.7-98.6) for PET/CT. Conclusions: Our results suggest a good performance for PET/CT in identification of BC and distant metastases in this patient population. However, the sensitivity of PET/CT for axillary staging is limited, despite excellent specificity. BMRI appears more sensitive than PET/CT and mammography in the detection of breast lesions, probably due to higher resolution. The specificities of BMRI and PET/CT are similar, outperforming mammography. In addition, PET/CT as a whole body examination detected axillary and distant metastases in 9 (33.3%) of the 27 patients. Thus, PET/CT should be used as a complimentary imaging tool in the evaluation of patients with locally advanced BC, since a whole body staging can be achieved in a single exam.
Highly Anisotropic Mechanical and Optical Properties of 2D Layered As2S3 Membranes (2019)

Two-dimensional (2D) materials with strong in-plane anisotropy are of interest for enabling orientation-dependent, frequency-tunable, optomechanical devices. However, black phosphorus (bP), the 2D material with the largest anisotropy to date, is unstable as it degrades in air. In this work we show that As<sub>2</sub>S<sub>3</sub> is an interesting alternative, with a similar anisotropy to bP, while at the same time having a much higher chemical stability. We probe the mechanical and optical anisotropy in As<sub>2</sub>S<sub>3</sub> by three distinct angular-resolved experimental methods: Raman spectroscopy, atomic force microscopy (AFM), and resonance frequency analysis. Using a dedicated angle-resolved AFM force-deflection method, an in-plane anisotropy factor of [Formula: see text] is found in the Young's modulus of As<sub>2</sub>S<sub>3</sub> with <i>E</i><sub><i>a</i>-axis</sub> = 79.1 ± 10.1 GPa and <i>E</i><sub><i>c</i>-axis</sub> = 47.2 ± 7.9 GPa. The high mechanical anisotropy is also shown to cause up to 65% difference in the resonance frequency, depending on crystal orientation and aspect ratio of membranes.
Solution-processable 2,1,3-benzothiadiazole containing compound based on the novel 1-dodecyl-6-dodecoxynaphthyridine-2-one unit for organic field-effect transistors (2017)

Small molecule organic semiconductors have well-defined structures and can be used in place of polymers which often show batch-to-batch variation. Many different electron-rich donor and electrondeficient acceptor units have been used to design materials with reduced HOMO-LUMO gaps and improved mobilities. Here we introduce a novel acceptor unit, 1-dodecyl-6-dodecoxynaphthyridine-2one. This acceptor unit has been used in the synthesis of two novel compounds, with thiophene and 2,1,3-benzothiadiazole (BT) cores. The BT-containing compound shows a narrower HOMO-LUMO gap, broad solid-state absorption and has been applied to organic field-effect transistors, showing a mobility of 0.022 cm 2 V 1 s 1 after optimisation of devices using self-assembled monolayers.
Vitamin K deficiency and covid-19 (2020)

Summarizing, the results of this study suggest that vitamin K deficiency is frequently observed in COVID-19 patients and that the deficit is greater in males than in females. In addition, in male patients, vitamin K deficiency is associated with a greater IL-6 level in the general circulation. In conclusion, we propose that vitamin K deficiency could support both cytokine storm Th2 by increasing proinflammatory cytokines such as IL-6, which is involved in the building up of the inflammatory response recruiting both cellular and humoral components. Besides, it can also contribute to those events involved in vascular calcification\nleading to thrombosis and disseminate intravascular coagulation (DIC), which feature the microvascular damage observed in COVID patients The results of this study highlight the role of Vitamin K as a possible modifiable risk factor for a more severe evolution of COVID-19 in infected patients with clinical symptoms. While a cause-effect relationship has not be established, our findings support further investigating the\nrole of vitamin K in this clinical setting.
Modulation of keratinocyte growth factor and its receptor in reepithelializing human skin. (1995)

We investigated the expression and distribution of keratinocyte growth factor (KGF) (FGF-7) and its receptor (KGFR) during reepithelialization of human skin. KGF mRNA levels increased rapidly by 8-10-fold and remained elevated for several days. In contrast, KGFR transcript levels decreased early but were significantly elevated by 8-9 d. A KGF-immunoglobulin G fusion protein (KGF-HFc), which specifically and sensitively detects the KGFR, localized the receptor to differentiating keratinocytes of control epidermis, but revealed a striking decrease in receptor protein expression during the intermediate period of reepithelization. Suramin, which blocked KGF binding and stripped already bound KGF from its receptor, failed to unmask KGFRs in tissue sections from the intermediate phase of wound repair. The absence of KGFR protein despite increased KGFR transcript levels implies functional receptor downregulation in the presence of increased KGF. This temporal modulation of KGF and KGFRs provides strong evidence for the functional involvement of KGF in human skin reepithelialization.