gebhart/patrepeval huggingface dataset:
Fluoroquinolones: relationships between structural variations, mammalian cell cytotoxicity and antimicrobial activity (1992)

Fluoroquinolones are potent inhibitors of bacterial topoisomerase II (DNA gyrase). They can also inhibit eukaryotic topoisomerases, which could possibly lead to clastogenicity and/or cellular toxicity. Recent studies have demonstrated a correlation between mammalian cell cytotoxicity of the fluoroquinolones and the potential of these compounds to induce micronuclei, a genetic toxicity endpoint. In an effort to identify potent nontoxic quinolone antibacterials, we have examined the structural features of the fluoroquinolones associated with mammalian cell cytotoxicity. An investigation of a wide variety of substituents at the 1, 5, 7, and 8 positions of a quinolone nucleus was conducted. The results indicate that no one position has a controlling effect on the observed cytotoxicity. Instead, a combination of the various substituents contributes to the effects seen. Certain trends were apparent, such as the fact that compounds with pyrrolidines at the R-7 position were more cytotoxic than those with piperazines, and halogens at R-8 (X-position) were associated with more cytotoxicity relative to hydrogen. A general trend also existed between the cytotoxicity of the compounds and their Gram-positive antibacterial activity. A detailed comparison between the various groups and positional variations as they controlled the cytotoxicity and antibacterial activity is presented.
OmniSLAM: Omnidirectional Localization and Dense Mapping for Wide-baseline Multi-camera Systems (2020)

In this paper, we present an omnidirectional localization and dense mapping system for a wide-baseline multiview stereo setup with ultra-wide field-of-view (FOV) fisheye cameras, which has a 360 degrees coverage of stereo observations of the environment. For more practical and accurate reconstruction, we first introduce improved and light-weighted deep neural networks for the omnidirectional depth estimation, which are faster and more accurate than the existing networks. Second, we integrate our omnidirectional depth estimates into the visual odometry (VO) and add a loop closing module for global consistency. Using the estimated depth map, we reproject keypoints onto each other view, which leads to a better and more efficient feature matching process. Finally, we fuse the omnidirectional depth maps and the estimated rig poses into the truncated signed distance function (TSDF) volume to acquire a 3D map. We evaluate our method on synthetic datasets with ground-truth and real-world sequences of challenging environments, and the extensive experiments show that the proposed system generates excellent reconstruction results in both synthetic and real-world environments.
Efficacy of high-dose leukocytaphereis using extracorporeal circulation through a large leukocyte-removal filter column in patients with refractory asthma (2011)

Leukocytapheresis (LCAP) as well as granulocyte and monocyte adsorptive apheresis (GMA) using extracorporeal circulation through the column has been used to treat inflammatory bowel disease and rheumatoid arthritis in Japan. We previously reported that GMA improved the peek expiratory flow rate (PEFR) in patients with severe asthma. To evaluate the efficacy of high-dose leukocytapheresis (pulse LCAP) using a large leukocyte-removal filter column (Cellsorba® CS-180S, Asahikasei Kuraray Medical, Tokyo, Japan) in patients with refractory asthma, we conducted a clinical trial. Pulse LCAP was performed 2 sessions at 1-week interval and 5 L of blood was filtered per session. The average PEFR during the 4 weeks just after the second LCAP in each patient was compared with that during the 4 weeks just before the first LCAP as a primary end point. The sum total of asthma control test (ACT) score at 4 weeks after the second LCAP was compared with that just before the first LCAP as a secondary end point. We evaluated the change of the fraction of exhaled nitric oxide (FENO) in each patient before and after pulse LCAP as a biomarker of eosinophilic airway inflammation. Five patients fulfilled the ATS criteria for refractory asthma participated in this trial up to now. The morning PEFR and the ACT score were increased in all patients. Although FENO was abnormally increased in four patients in spite of the standard therapy, it was decreased after pulse LCAP. Pulse LCAP might serve as a non-pharmacological strategy to induce clinical improvement in patients with refractory asthma through its unique anti-inflammatory effects.
Cardiac shear-wave elastography using a transesophageal transducer: application to the mapping of thermal lesions in ultrasound transesophageal cardiac ablation (2015)

Heart rhythm disorders, such as atrial fibrillation or ventricular tachycardia can be treated by catheter-based thermal ablation. However, clinically available systems based on radio-frequency or cryothermal ablation suffer from limited energy penetration and the lack of lesion's extent monitoring. An ultrasound-guided transesophageal device has recently successfully been used to perform High-Intensity Focused Ultrasound (HIFU) ablation in targeted regions of the heart in vivo. In this study we investigate the feasibility of a dual therapy and imaging approach on the same transesophageal device. We demonstrate in vivo that quantitative cardiac shear-wave elastography (SWE) can be performed with the device and we show on ex vivo samples that transesophageal SWE can map the extent of the HIFU lesions. First, SWE was validated with the transesophageal endoscope in one sheep in vivo. The stiffness of normal atrial and ventricular tissues has been assessed during the cardiac cycle (n = 11) and mapped (n = 7). Second, HIFU ablation has been performed with the therapy-imaging transesophageal device in ex vivo chicken breast samples (n = 3), then atrial (left, n = 2) and ventricular (left n = 1, right n = 1) porcine heart tissues. SWE provided stiffness maps of the tissues before and after ablation. Areas of the lesions were obtained by tissue color change with gross pathology and compared to SWE. During the cardiac cycle stiffness varied from 0.5 ± 0.1 kPa to 6.0 ± 0.3 kPa in the atrium and from 1.3 ± 0.3 kPa to 13.5 ± 9.1 kPa in the ventricles. The thermal lesions were visible on all SWE maps performed after ablation. Shear modulus of the ablated zones increased to 16.3 ± 5.5 kPa (versus 4.4 ± 1.6 kPa before ablation) in the chicken breast, to 30.3 ± 10.3 kPa (versus 12.2 ± 4.3 kPa) in the atria and to 73.8 ± 13.9 kPa (versus 21.2 ± 3.3 kPa) in the ventricles. On gross pathology, the size of the lesions ranged from 0.1 to 1.5 cm(2) in the imaging plane area. Elasticity-estimated depths and widths of the lesions differed respectively with a median of 0.2 mm (first quartile Q1: -0.8 mm; third quartile Q3: 2.6 mm) for a mean squared error (MSE) of 5.1 mm(2) and a median of 0.2 mm (Q1: -2.7 mm; Q3: 2.7 mm) for a MSE of 11.1 mm(2) from gross pathology. We have demonstrated the feasibility of the HIFU thermal ablation monitoring using a dual therapy and imaging transesophageal device. The combination of HIFU, ultrasound imaging and SWE on the same transesophageal system could lead to a new clinical device for a safer and controlled treatment of a wide variety of cardiac arrhythmias.
Proving Inflation: A Bootstrap Approach (2008)

We note that the essential idea of inflation, that the universe underwent a brief period of accelerated expansion followed by a long period of decelerated expansion, can be encapsulated in a closure which relates the amount of accelerated expansion during inflation to the amount of decelerated expansion afterward. We present a protocol for systematically testing the validity of this condition observationally.
Abstract PO-034: Increased physical activity delays development of obesity-induced pancreatic ductal adenocarcinoma in mice and modulates inflammation (2020)

Abstract Background: Obesity is a risk factor for pancreatic ductal adenocarcinoma (PDAC), a deadly disease with no preventive strategies. Lifestyle interventions to decrease obesity might serve to prevent obesity-induced PDAC. We examined whether decreasing obesity via increased physical activity (PA) and/or diet-induced weight loss could prevent PDAC in mice and compared the levels of systemic inflammatory-associated cytokines in human subjects undergoing a PA intervention. Methods: Obesity-induced PDAC mouse models were exposed to various interventions before and after cancer initiation, that included increased PA, diet-induced weight loss, and/or chemotherapy. We evaluated body composition, tumor progression, growth, fibrosis, and inflammation. Circulating inflammatory-associated cytokines of overweight/obese human subjects before and after a PA intervention were also compared. Results: Genetically engineered PDAC mice on a PA intervention while on a HFD, gained less weight, displayed lower grade pancreatic intraepithelial neoplasias lesions, and fewer mice developed PDAC compared to controls. Similar results were observed in PDAC mice given a HFD to induce obesity, prior to a control diet (CD) and PA intervention, compared to mice given a CD after the HFD. PA alone or with a CD intervention decreased body weight but did not prevent tumor growth in an orthotopic mouse model of PDAC. PA combined with chemotherapy increased the percentage of splenic cluster of differentiation 8+ (CD8+) T cells in PDAC mice. Finally, PA prevented the increase of systemic inflammatory-associated cytokines in PDAC mice and in overweight/obese control human subjects. Conclusions: PA alone or with diet-induced weight loss delayed the progression of PDAC in genetically engineered mice and reduced inflammation. While these interventions did not prevent tumor growth in the orthotopic mouse model, it did modulate immune responses. Reducing obesity by increasing PA and decreasing dietary fat intake could be a way of reducing the incidence of PDAC in high-risk obese individuals. Citation Format: Valentina Pita-Grisanti, Kelly Dubay, Ali Lahooti, Niharika Badi, Olivia Ueltschi, Myrriah Chavez-Tomar, Samantha Terhorst, Sue Knoblaugh, Christopher Coss, Thomas Mace, Fouad Choueiry, Alice Hinton, Jennifer M Mitchell, Karen Basen-Engquist, Zobeida Cruz-Monserrate. Increased physical activity delays development of obesity-induced pancreatic ductal adenocarcinoma in mice and modulates inflammation [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2020 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2020;80(22 Suppl):Abstract nr PO-034.
ChemInform Abstract: Ni(II) Salts and 2‐Propanol Effect Catalytic Reductive Coupling of Epoxides and Alkynes. (2011)

Abstract Isopropanol serves not only as a solvent but also as a reducing agent to provide the desired homoallylic alcohol product and regenerate the active Ni(0) catalyst.
Ventricular Stiffening and Chamber Contracture in Heart Failure with Higher Ejection Fraction (2023)

Most pathophysiologic differences in patients with HFpEF and higher EF are related to smaller heart size, increased LV diastolic stiffness, and leftward shift in the EDPVR. These findings may help to explain the absence of efficacy for neurohormonal antagonists in this group and raise a new hypothesis, that interventions to stimulate eccentric LV remodelling and enhance diastolic capacitance may be beneficial for patients with HFpEF and EF in the higher range.
On the Effect of Ti2AlC on the Formation of Thermally Stable Mg Nano Grains (2012)

This chapter contains sections titled: Introduction Experimental Details Summary and Concluding Remarks Acknowledgements
Life Cycle Assessment of Large-scale Piggery for Environmental Assessment (2012)

Life cycle assessment (LCA) methodology was used to establish inventory of energy consumption and pollutant emission and to assess life-cycle environmental impacts of large-scale piggery,and then the way could be found for lessen negative environmental impacts.Four impact categories were investigated,including energy depletion,eutrophication,global warming and acidification,with the impact indices of 8.38×10-3,1.91×10-3,9.80×10-3 and 2.01×10-2,respectively.The life cycle was divided into three stages,i.e.feed ingredients manufacture,swine rearing and wastes disposal,with the environmental impact complex index of 2.52×10-2,1.23×10-2 and 2.71×10-3,respectively.The results showed that manufacture of feed ingredients had the largest environmental impact.Therefore,reducing nitrogenous fertilizer consumption and implementing energy-saving and cleaner production in the production of fertilizers were essential to control the life cycle environmental impacts of large-scale piggery.
ChemInform Abstract: Enantioselective Synthesis of Brinzolamide (AL‐4862), a New Topical Carbonic Anhydrase Inhibitor. The “DCAT Route” to Thiophenesulfonamides. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Sequence of a benzyladenine binding site peptide isolated from a wheat embyro cytokinin-binding protein (1987)

A wheat embryo cytokinin-binding protein (CBF-1) was covalently modified with the radiolabeled photoaffinity ligand (/sup 14/C)-2-azido-N/sup 6/-benzyladenine (AzBA). A single labeled peptide was obtained after proteolytic digestion and isolation by reversed-phase and anion exchange HPLC. Sequencing by Edman degradation identified 11 of the 12 residues, but failed to identify the labeled amino acid. Amino acid analysis and sequencing by laser photodissociation-Fourier transform mass spectrometry conclusively identified the labeled residue as the histidine: Ala-Phe-Leu-Gln-Pro-Ser-His-His*-Asp-Ala-Asp-Glu. Comparison of this sequence with the known partial primary sequence of CBF-1 (determined by tandem quadrupole mass spectrometry) showed that there were two homologous sequences in CBF-1. One exactly matched the above AzBA labeled peptide and the other differed by a substitution of tyrosine for the second histidine. The possibility of binding and non-binding CBF-1 isomers will be discussed along with a proposed model for BA binding.
Quantum Dot Targeting with Lipoic Acid Ligase and HaloTag for Single-Molecule Imaging on Living Cells (2012)

We present a methodology for targeting quantum dots to specific proteins on living cells in two steps. In the first step, Escherichia coli lipoic acid ligase (LplA) site-specifically attaches 10-bromodecanoic acid onto a 13 amino acid recognition sequence that is genetically fused to a protein of interest. In the second step, quantum dots derivatized with HaloTag, a modified haloalkane dehalogenase, react with the ligated bromodecanoic acid to form a covalent adduct. We found this targeting method to be specific, fast, and fully orthogonal to a previously reported and analogous quantum dot targeting method using E. coli biotin ligase and streptavidin. We used these two methods in combination for two-color quantum dot visualization of different proteins expressed on the same cell or on neighboring cells. Both methods were also used to track single molecules of neurexin, a synaptic adhesion protein, to measure its lateral diffusion in the presence of neuroligin, its trans-synaptic adhesion partner.
CCDC 890165: Experimental Crystal Structure Determination (2013)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Chemical encoding of risk perception and predator detection among estuarine invertebrates (2018)

An effective strategy for prey to survive in habitats rich in predators is to avoid being noticed. Thus, prey are under selection pressure to recognize predators and adjust their behavior, which can impact numerous community-wide interactions. Many animals in murky and turbulent aquatic environments rely on waterborne chemical cues. Previous research showed that the mud crab, <i>Panopeus herbstii</i>, recognizes the predatory blue crab, <i>Callinectus sapidus</i>, via a cue in blue crab urine. This cue is strongest if blue crabs recently preyed upon mud crabs. Subsequently, mud crabs suppress their foraging activity, reducing predation by blue crabs. Using NMR spectroscopy- and mass spectrometry-based metabolomics, chemical variation in urine from blue crabs fed different diets was related to prey behavior. We identified the urinary metabolites trigonelline and homarine as components of the cue that mud crabs use to detect blue crabs, with concentrations of each metabolite dependent on the blue crab's diet. At concentrations found naturally in blue crab urine, trigonelline and homarine, alone as well as in a mixture, alerted mud crabs to the presence of blue crabs, leading to decreased foraging by mud crabs. Risk perception by waterborne cues has been widely observed by ecologists, but the molecular nature of these cues has not been previously identified. Metabolomics provides an opportunity to study waterborne cues where other approaches have historically failed, advancing our understanding of the chemical nature of a wide range of ecological interactions.
Generation and characterization of CSSi016-A (9938) human pluripotent stem cell line carrying two biallelic variants in MTMR5/SBF1 gene resulting in a case of severe CMT4B3 (2022)

Charcot-Marie-Tooth type 4B3 (CMT4B3) is a rare subtype of hereditary neuropathy associated with variants in the MTMR5/SBF1 gene. Herein, we report the generation and characterization of a hiPSC line from a 12-year-old Italian girl with early onset severe polyneuropathy with motor and axonal involvement, harboring biallelic variants in the MTMR5/SBF1 gene. Fibroblasts were reprogrammed using non-integrating episomal plasmids, and iPSCs successfully passed the stemness and pluripotency tests. Patient-specific hiPSCs were produced to obtain a disease model for the study of this rare condition.
Development of Singlet Oxygen Luminescence Kinetics during the Photodynamic Inactivation of Green Algae (2016)

Recent studies show the feasibility of photodynamic inactivation of green algae as a vital step towards an effective photodynamic suppression of biofilms by using functionalized surfaces. The investigation of the intrinsic mechanisms of photodynamic inactivation in green algae represents the next step in order to determine optimization parameters. The observation of singlet oxygen luminescence kinetics proved to be a very effective approach towards understanding mechanisms on a cellular level. In this study, the first two-dimensional measurement of singlet oxygen kinetics in phototrophic microorganisms on surfaces during photodynamic inactivation is presented. We established a system of reproducible algae samples on surfaces, incubated with two different cationic, antimicrobial potent photosensitizers. Fluorescence microscopy images indicate that one photosensitizer localizes inside the green algae while the other accumulates along the outer algae cell wall. A newly developed setup allows for the measurement of singlet oxygen luminescence on the green algae sample surfaces over several days. The kinetics of the singlet oxygen luminescence of both photosensitizers show different developments and a distinct change over time, corresponding with the differences in their localization as well as their photosensitization potential. While the complexity of the signal reveals a challenge for the future, this study incontrovertibly marks a crucial, inevitable step in the investigation of photodynamic inactivation of biofilms: it shows the feasibility of using the singlet oxygen luminescence kinetics to investigate photodynamic effects on surfaces and thus opens a field for numerous investigations.
WIRE AND MAGNET SEPTOTOME, A NEW METHOD FOR ENDOSCOPIC LEAK-FREE SECTION OF SEPTA IN THE GI TRACT: PRELIMINARY RESULT OF A PILOT ANIMAL STUDY (2019)

Treatment of symptomatic mid- or distal- esophageal diverticulum is challenging. The rationale of the endoscopic treatment is its marsupialisation into the esophagus and/or treatment of underlying motility disorders. Section of the septum carries the risk of bleeding and perforation, the latter being potentially prevented by the use of magnets or sutures endoscopically performed at the bottom of the diverticulum.
A framework for selective recompilation in the presence of complex intermodule dependencies (1995)

Article Free Access Share on A framework for selective recompilation in the presence of complex intermodule dependencies Authors: Craig Chambers Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WashingtonView Profile , Jeffrey Dean Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WashingtonView Profile , David Grove Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, Washington Department of Computer Science and Engineering, Box 352350, University of Washington, Seattle, WashingtonView Profile Authors Info & Claims ICSE '95: Proceedings of the 17th international conference on Software engineeringApril 1995Pages 221–230https://doi.org/10.1145/225014.225035Published:23 April 1995Publication History 20citation336DownloadsMetricsTotal Citations20Total Downloads336Last 12 Months21Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Cornea Findings of Spectral Domain Anterior Segment Optical Coherence Tomography in Uveitic Eyes of Various Etiologies (2019)

AS-OCT images showed characteristic and specific morphological patterns. AS-OCT examination is a noninvasive and repeatable method for the diagnosis of uveitis by evaluating the morphologies of KPs and treatment effectiveness.
Supplementary Table 2 from Emergence of Enzalutamide Resistance in Prostate Cancer is Associated with BCL-2 and IKKB Dependencies (2023)

&lt;p&gt;List of primers used for qPCR analyses&lt;/p&gt;