gebhart/patrepeval huggingface dataset:
Observations on electrode-tissue interface temperature and effect on electrical impedance during radiofrequency ablation of ventricular myocardium. (1990)

The purpose of this study was to correlate changes in electrical impedance with the electrode-tissue interface temperature and to characterize the associated events occurring at the catheter tip electrode. In a canine model, lesions were created in vitro (n = 49) and in vivo (n = 31) and radiofrequency power settings were varied. Electrode-tissue interface temperature, delivered current, and voltage were recorded, and impedance was calculated. A sudden rise in electrical impedance was seen in only two of 17 ablations in vitro and in one of 16 ablations in vivo with a peak electrode-tissue interface temperature of less than 100 degrees C compared with 29 of 32 ablations in vitro (p = 0.0001) and 12 of 15 ablations in vivo with a temperature of more than 100 degrees C (p = 0.0001). This phenomenon was associated with the observation of boiling and popping at the tip in in vitro preparations and tissue avulsion and thrombus formation on the catheter tip in in vivo studies. The lesion size was directly proportional to the peak temperature for all ablations but not to the peak power, current, or voltage during radiofrequency catheter ablation in the heart. Maintaining electrode-tissue interface temperature at less than 100 degrees C during radiofrequency catheter ablation in the heart may avoid the complications associated with the sudden rise in electrical impedance.
Detection of differentially expressed genes in synovial fibroblasts by restriction fragment differential display (2004)

Seven genes have been identified with differential expression patterns in terms of disease process (osteoarthritis vs rheumatoid arthritis), state of activation (resting vs cytokine activation) and anatomical location (synovium vs skin). Four of these genes, TFPI2, GRObeta (CXCL2), MnSOD and GCP-2 (CXCL6), were selectively overexpressed in osteoarthritis fibroblasts rather than rheumatoid fibroblasts. While these differences may represent differential behaviour of synovial fibroblasts in in vitro culture, these observations suggest that TFPI2, GRObeta (CXCL2), MnSOD and GCP-2 (CXCL6) may represent new targets for treatments specifically tailored to osteoarthritis.
Computer-based tracking of single sperm (2006)

This paper describes a robust single sperm tracking algorithm (SSTA) that can be used in laser optical trapping and sperm motility studies. The algorithm creates a region of interest (ROI) centered about a sperm selected by the user. SSTA contrast enhances the ROI image and implements a modified four-class thresholding method to extract the tracked sperm as it transitions in and out of focus. The nearest neighbor method is complemented with a speed-check feature to aid tracking in the presence of additional sperm or other particles. SSTA has a collision-detection feature for real or perceived collision or near-miss cases between two sperm. Subsequent postcollision analysis employs three criteria to distinguish the tracked sperm in the image. The efficacy of SSTA is validated through examples and comparisons to commercially available computer-aided sperm tracking systems.
Thrombin Interaction with Human Platelets Potentiation of Thrombin-induced Aggregation and Release by Inactivated Thrombin (1974)

The possibility that thrombin acts on platelets by a mechanism other than proteolysis was investigated. The proteolytic site of thrombin was modified with phenylmethylsulfonyl fluoride (PMSF). This modified enzyme did not induce platelet aggregation or the platelet release reaction. Platelets were then incubated with the inactivated enzyme (PMS-thrombin) and later with active thrombin. In this sequence of incubation, PMS-thrombin enhanced not only platelet aggregation induced by active thrombin but also the thrombin-induced release reaction. Preincubation with PMS-thrombin was essential for this enhancement as the inhibited enzyme did not affect aggregation if added after active thrombin. The effect of PMS-thrombin was limited to thrombin-induced reactions of the platelet. The inhibited enzyme had no effect on aggregation induced by adenosine diphosphate or collagen, or on thrombin-induced coagulation of fibrinogen. These results suggest (1) that both proteolytic and binding sites for thrombin are present on the human platelet plasma membrane; and (2) that interaction of thrombin with the binding site potentiates the activity of the proteolytic site.
Animal models of osteoarthritis. (2001)

Animal models of osteoarthritis are used to study the pathogenesis of cartilage degeneration and to evaluate potential antiarthritic drugs for clinical use. Animal models of naturally occurring osteoarthritis (OA) occur in knee joints of guinea pigs, mice and other laboratory animal species. Transgenic models have been developed in mice. Commonly utilized surgical instability models include medial meniscal tear in guinea pigs and rats, medial or lateral partial meniscectomy in rabbits, medial partial or total meniscectomy or anterior cruciate transection in dogs. Additional models of cartilage degeneration can be induced by intra-articular iodoacetate injection or by administration of oral or parenteral quinolone antibiotics. None of these models have a proven track record of predicting efficacy in human disease since there are no agents that have been proven to provide anything other than symptomatic relief in human OA. However, agents that are active in these models are currently in clinical trials. Methodologies, gross and histopathologic features and comparisons to human disease will be discussed for the various models.
Anatomy and Physiology of Cervical Ripening (1995)

The uterine cervix is a unique organ composed predominately of the extracellular matrix proteins, collagen, elastin, and glycosaminoglycans. During pregnancy and labor, this organ is metabolically active, which is rare in adult tissue. The metabolism is under reproductive hormonal control and is more complex than previously appreciated. Smooth muscle cells, which comprise 10-15% of cervical tissue, undergo programmed cell death and play a role in cervical softening. Apoptosis is a genetically timed event and could explain the species-specific length of gestation. Further research in the next several years will reveal more completely the exciting process of cervical ripening. Only when this phenomenon is understood will rational therapy for preterm labor and post-term pregnancy with an unripe cervix be available. Specific defects in cervical ripening will then be diagnosed and treated. For example, if apoptosis is shown to play an important role in the process of cervical ripening, it could be inhibited. Conversely, it could be induced in the unripe cervix. If we would look for it, we would find that it is probably occurring today in the clinical use of cervical ripening agents. The most important contributor to cervical softening, however, is a rearrangement and realignment of the collagen, elastin, and smooth muscle cells, which occurs due to mechanical forces and to a rearrangement of the collagen that occurs as the content of glycosaminoglycans varies in the cervix with time. One form of dermatan sulfate, decorin, may help to separate the collagen fibrils and then open them up. This rearrangement also involves fiber shortening below the critical length for tensile strength, allowing for extensibility of the cervix. Because of its orientation in the cervix, elastin contributes to the ratchet-like mechanism of dilatation. Finally, the cervix undergoes change in two phases--softening, which involves collagen realignment, and dilatation. The proteolytic enzymes in the cervix degrade cross-linked, newly synthesized collagen, and they help activate other enzymes in a cascade. However, the predominate anatomic and physiologic change in ripening is the rearrangement of collagen.
Electrical Stimulation of the Subthalamic Nucleus in Advanced Parkinson's Disease (1998)

Electrical stimulation of the subthalamic nucleus is an effective treatment for advanced Parkinson's disease. The severity of symptoms off medication decreases, and the dose of levodopa can be reduced with consequent reduction in dyskinesias.
Interactive Medical Image Segmentation Using Deep Learning With Image-Specific Fine Tuning (2018)

Convolutional neural networks (CNNs) have achieved state-of-the-art performance for automatic medical image segmentation. However, they have not demonstrated sufficiently accurate and robust results for clinical use. In addition, they are limited by the lack of image-specific adaptation and the lack of generalizability to previously unseen object classes (a.k.a. zero-shot learning). To address these problems, we propose a novel deep learning-based interactive segmentation framework by incorporating CNNs into a bounding box and scribble-based segmentation pipeline. We propose image-specific fine tuning to make a CNN model adaptive to a specific test image, which can be either unsupervised (without additional user interactions) or supervised (with additional scribbles). We also propose a weighted loss function considering network and interaction-based uncertainty for the fine tuning. We applied this framework to two applications: 2-D segmentation of multiple organs from fetal magnetic resonance (MR) slices, where only two types of these organs were annotated for training and 3-D segmentation of brain tumor core (excluding edema) and whole brain tumor (including edema) from different MR sequences, where only the tumor core in one MR sequence was annotated for training. Experimental results show that: 1) our model is more robust to segment previously unseen objects than state-of-the-art CNNs; 2) image-specific fine tuning with the proposed weighted loss function significantly improves segmentation accuracy; and 3) our method leads to accurate results with fewer user interactions and less user time than traditional interactive segmentation methods.
Coupling of Amino Acids and Amino Sugars with Cyanuric Chloride (2,4,6-Trichloro-s-triazine) (1972)

2,4,6-Trichloro-s-triazine (cyanuric chloride) has been used to couple glycine ethyl ester with seven carbohydrate derivatives that contain amino groups. The reactions proceed in high yield under mild conditions. The compounds serve as models for the coupling of carbohydrates to proteins by well-defined linkages through amino groups.
Analysis of quorum sensing-deficient clinical isolates of Pseudomonas aeruginosa (2004)

Pseudomonas aeruginosa produces multiple virulence factors and causes different types of infections. Previous clinical studies identified P. aeruginosa isolates that lack individual virulence factors. However, the impact of losing several virulence factors simultaneously on the in vivo virulence of P. aeruginosa is not completely understood. The P. aeruginosa cell-to-cell communication system, or quorum sensing (QS), controls the production of several virulence factors. Animal studies using constructed QS mutants indicated that loss of the QS system severely impacts the virulence of P. aeruginosa. In this study, we tried to determine if deficiency within the QS system compromises the ability of P. aeruginosa to establish infections in humans. We have identified five QS-deficient strains through screening 200 isolates from patients with urinary tract, lower respiratory tract and wound infections. These strains lacked LasB and LasA activities and produced either no or very low levels of the autoinducers N-(3-oxododecanoyl) homoserine lactone and N-butyryl homoserine lactone. PCR analysis revealed that three isolates contained all four QS genes (lasI, lasR, rhlI and rhlR) while two isolates lacked both the lasR and rhlR genes. We also examined the five isolates for other virulence factors. The isolates produced variable levels of exotoxin A and, with one exception, were deficient in pyocyanin production. One isolate produced the type III secretion system (TTSS) effector proteins ExoS and ExoT, two isolates produced ExoT only and two isolates produced no TTSS proteins. The isolates produced weak to moderate biofilms on abiotic surfaces. Analysis of the patients' data revealed that two of the isolates represented a single strain that was isolated twice from the same patient within a 1 month interval. One QS-deficient clinical isolate (CI-1) lacked all tested virulence factors and produced a weak biofilm. These results suggest that naturally occurring QS-deficient strains of P. aeruginosa do occur and are capable of causing infections; and, that besides the known virulence factors, additional factors may contribute to the ability of certain strains such as CI-1 to establish an infection.
Chosen-Ciphertext Secure Proxy Re-Encryption without Pairings. (2008)

Proxy re-encryption (PRE), introduced by Blaze, Bleumer and Strauss, allows a semi-trusted proxy to convert a ciphertext originally intended for Alice into an encryption of the same message intended for Bob. Proxy re-encryption has found many practical applications, such as encrypted email forwarding, secure distributed file systems, and outsourced filtering of encrypted spam. In ACM CCS’07, Canetti and Hohenberger presented a bidirectional PRE scheme with chosen-ciphertext security, and left an important open problem to construct a chosen-ciphertext secure proxy reencryption scheme without pairings. In this paper, we propose a bidirectional PRE scheme with chosen-ciphertext security. The proposed scheme is fairly efficient due to two distinguished features: (i) it does not use the costly bilinear pairings; (ii) the computational cost and the ciphertext length decrease with re-encryption.
The partial purification and properties of pig brain glycogen synthase. (1975)

Both the I (independent of glucose 6-phosphate) and D (dependent on glucose 6-phosphate) forms of glycogen synthase (UDP-glucose:glycogen alpha-4-glucosyltransferase EG 2.4.1.11) have been partially purified from pig brain and the kinetic constants of the enzymes have been examined. The Km for UDP-glucose for the I form increased from 0.11 to 0.5 mM when the temperature was raised from 25 to 37 degrees. When glucose 6-phosphate was present, the Km for UDP-glucose was decreased to 0.03 and 0.08 mM at 25 and 37 degrees, respectively. The amount of glucose 6-phosphate required to produce half-maximal stimulation decreased with increasing UDP-glucose concentration at both temperatures but increased with increasing temperature. The Km for glucose 6-phosphate at 0.03 and 0.20 mM UDP-glucose was 0.13 and 0.10 mM, respectively, at 25 degrees. At 37 degrees and 0.125 and 4.0 mM UDP-glucose the Km for glucose 6-phosphate was 0.32 and 0.04 mM, respectively. The Km for UDP-glucose for the D form at 0.75, 2.0, and 10 mM glucose 6-phosphate was 0.71, 0.50, and 0.42 mM at 25 degrees. At higher temperatures the apparent affinity for the substrate was decreased; at 37 degrees, the Km for UDP-glucose at 0.75 and 2.0 nM glucose 6-phosphate was 5.75 and 1.42 mM, respectively. The requirement for glucose 6-phosphate was decreased when UDP-glucose concentrations were increased; at 0.5 and 5.0 mM UDP-glucose concentrations, the Km for glucose 6-phosphate was 22.7 and 1.82 mM at 25 degrees. As was the case with the I form, the apparent Km for glucose 6-phosphate increased at higher temperatures. At 37 degrees, the Km for glucose 6-phosphate at 0.5 and 5.0 mM UDP-glucose was 43.5 and 6.15 mM. The temperature coefficient for the maximum velocity was 10.1% per degree for synthase I and 8.5% per degree for synthase D between 25 and 37 degrees. The D form of synthase was calculated to be virtually inactive under normal physiological conditions with the substrate concentrations found in the brain. The enzymatic activity calculated for synthase I correlates well with the observed rate of incorporation of UDP-[U-14C]glucose into brain glycogen.
A Placebo- and Midazolam-Controlled Phase I Single Ascending-Dose Study Evaluating the Safety, Pharmacokinetics, and Pharmacodynamics of Remimazolam (CNS 7056) (2012)

Population pharmacokinetic and pharmacodynamic models developed for remimazolam and midazolam fitted the observed data well. Simulations based on these models show that remimazolam delivers extremely rapid sedation, with maximal effect being reached within 3 minutes of the start of treatment. This property will enable maintenance doses to be given more accurately than with slower-acting drugs. No covariate effects considered to be clinically relevant were observed, suggesting that dosing by body weight may offer no advantage over fixed doses in terms of consistency of exposure to remimazolam within the weight range studied (65-90 kg).
Fast, Sensitive Hydrogen Gas Detection Using Single Palladium Nanowires That Resist Fracture (2009)

Two types of pure palladium (Pd) nanowires, differentiated by microstructure, were electrodeposited: (1) nanocrystalline Pd nanowires (grain diameter approximately 5 nm, henceforth nc5-Pd) and (2) nanocrystalline Pd nanowires with a grain diameter of 15 nm (nc15-Pd). These nanowires were evaluated for the detection of hydrogen gas (H(2)). Despite their fundamental similarities, the behavior of these nanowires upon exposure to H(2) was dramatically and reproducibly different: nc5-Pd nanowires spontaneously fractured upon exposure to H(2) above 1-2%. Fractured nanowires continued to function as sensors for H(2) concentrations above 2%, actuated by the volume change associated with the alpha to beta phase transition of PdH(x). nc15-Pd nanowires, in contrast, withstood repeated exposures to H(2) up to 10% without fracturing. nc15-Pd nanowires showed a rapid (2 s at 10%) increase in resistance in the presence of H(2) and a response that scaled smoothly with [H(2)] spanning 5 orders of magnitude down to 2 ppm.
The Mitochondrial Permeability Transition, Release of Cytochrome c and Cell Death (2001)

We investigated the relationship between opening of the permeability transition pore (PTP), mitochondrial depolarization, cytochrome c release, and occurrence of cell death in rat hepatoma MH1C1 cells. Treatment with arachidonic acid or induces PTP opening in situ with similar kinetics, as assessed by the calcein loading-Co(2+) quenching technique (Petronilli, V., Miotto, G., Canton, M., Colonna, R., Bernardi, P., and Di Lisa, F. (1999) Biophys. J. 76, 725-734). Yet depolarization, as assessed from the changes of mitochondrial tetramethylrhodamine methyl ester (TMRM) fluorescence, is rapid and extensive with arachidonic acid and slow and partial with. Cyclosporin A-inhibitable release of cytochrome c and cell death correlate with the changes of TMRM fluorescence but not with those of calcein fluorescence. Since pore opening must be accompanied by depolarization, we conclude that short PTP openings are detected only by trapped calcein and may have little impact on cell viability, while changes of TMRM distribution require longer PTP openings, which cause release of cytochrome c and may result in cell death. Modulation of the open time appears to be the key element in determining the outcome of stimuli that converge on the PTP.
A micromethod for the screening of individual seeds and cotyledons of Brassica napus and brassica campestris (rapeseed) for low sinapine content (1979)

Abstract The association of sinapine with the fishy or crabby odour present in eggs laid by certain brown egg laying hens when fed diets containing rapeseed meal indicates the desirability of removing sinapine from the original rapeseed. A method is presented whereby seeds and cotyledons of Brassica napus and B. campestris may be selected for low levels of sinapine. The method, based on microextraction, rapid chromatographic separation of sinapine and visual estimation of its fluorescence allows detection of 0.025 μg sinapine and enables 300‐400 seed samples to be screened daily.
Agrobacterium rhizogenes as a vector for transforming higher plants. (1987)

Agrobacterium rhizogenes is a natural vector for genetically transforming higher plants. A protocol is given for using this system to insert foreign genes into host plants. Improvements currently being developed in several laboratories are also discussed.
Effects of Intravenously Administered Recombinant Vesicular Stomatitis Virus (VSV ΔM51 ) on Multifocal and Invasive Gliomas (2006)

Systemically delivered VSV(deltaM51) was an effective and safe oncolytic agent against laboratory models of multifocal and invasive malignant gliomas, the most challenging clinical manifestations of this disease.
Hematopoietic Expression of Hoxb4 Is Regulated in Normal and Leukemic Stem Cells through Transcriptional Activation of the Hoxb4 Promoter by Upstream Stimulating Factor (Usf)-1 and Usf-2 (2000)

The homeobox genes encode a family of transcription factors that regulate development and postnatal tissue homeostasis. Since HOXB4 plays a key role in regulating the balance between hematopoietic stem cell renewal and differentiation, we studied the molecular regulation of HOXB4 expression in human hematopoietic stem cells. HOXB4 expression in K562 cells is regulated at the level of transcription, and transient transfection defines primary HOXB4 regulatory sequences within a 99-bp 5' promoter. Culture of highly purified human CD34(+) bone marrow cells in thrombopoietin/Flt-3 ligand/stem cell factor induced HOXB4 3-10-fold, whereas culture in granulocyte/macrophage colony-stimulating factor, only increased HOXB4/luciferase expression 20-50%. Mutations within the HOXB4 promoter identified a potential E box binding site (HOX response element [HXRE]-2) as the most critical regulatory sequence, and yeast one hybrid assays evaluating bone marrow and K562 libraries for HXRE-2 interaction identified upstream stimulating factor (USF)-2 and micropthalmia transcription factor (MITF). Electrophoretic mobility shift assay with K562 extracts confirmed that these proteins, along with USF-1, bind to the HOXB4 promoter in vitro. Cotransfection assays in both K562 and CD34(+) cells showed that USF-1 and USF-2, but not MITF, induce the HOXB4 promoter in response to signals stimulating stem cell self-renewal, through activation of the mitogen-activated protein kinase pathway. Thus hematopoietic expression of the human HOXB4 gene is regulated by the binding of USF-1 and USF-2, and this process may be favored by cytokines promoting stem cell self-renewal versus differentiation.
Multiple Sclerosis (1993)

Central nervous system (CNS) remyelination has been found by light and electron microscopy and immunocytochemistry within fresh lesions from four cases of acute and chronic progressive multiple sclerosis (MS). The remyelination was sparse and existed in an edematous parenchyma containing oligodendrocytes, macrophages, hypertrophic astrocytes and inflammatory components, but no fibrillary astrogliosis. It is suggested that this type of CNS remyelination in MS is a transient event. Possible underlying factors are discussed.