gebhart/patrepeval huggingface dataset:
Dkk1 Transgenic Mice for the Study of Bone Lesions in Human Multiple Myeloma. (2005)

Abstract Purpose: Extracellular antagonists of the cellular WNT signalling pathway can be divided into two classes depending on the mechanism by which ligand-receptor interactions are inhibited. Members of the first class including SFRP (secreted frizzled-related proteins), WIF1 (WNT inhibitory factor 1) and CER1 (cerberus homolog 1) bind to WNT proteins in the extracellular milieu. Members of the second class including Dickkopf (DKK) proteins bind to the WNT receptor subunits LRP5/6. Reduced WNT signalling may play a role in the natural history of the bone disease that is a hallmark of multiple myeloma (MM). Gene expression profiling of MM plasma cells has shown that over-expression of the Dickkopf family member DKK1 is linked with abundance and size of osteolytic lesions (N Engl J Med 2003, 349:2483–94). The biological mechanism of DKK1-mediated bone destruction is not known. Experimental procedure: To elucidate the mechanism by which DKK1 facilitates osteolysis, we generated transgenic mice in which mouse Dkk1 is expressed under control of the mouse immunoglobulin Eα enhancer. This enhancer is located 3′ of the immunoglobulin heavy-chain locus and comprised of four individual elements that span ~30 kb of genomic DNA. These elements were subcloned into a contiguous stretch of DNA, which we refer to as “reconstituted” Eα enhancer or HS1234 (Int Immunol 2001, 13:1003–12). Here we appended HS1234 to a Dkk1 cDNA whose expression is controlled by a mouse immunoglobulin VH promoter inserted 5′ of the transcriptional start site of Dkk1. Because of an internal ribosome entry site (IRES) 3′ of Dkk1, the gene encoding enhanced green fluorescence protein (EGFP) is co-expressed with Dkk1; i.e., it is a reporter of Dkk1 expression. A scheme of the structure of the Eα-Dkk1 transgene is depicted in Figure 1. Figure 1 Figure 1. Results: We generated 14 founder lines of Eα-Dkk1 transgenic mice that expressed Dkk1 and the EGFP-encoding gene by RT-PCR (Figure 2). Figure 2 Figure 2. The mice contained a variable number of Eα-Dkk1 copies, ranging from 2–3 to more than 100. There was but a loose association of transgene expression (qPCR of Dkk1 mRNA levels) and copy number (qPCR of genomic Ea-Dkk1 fragments); i.e., the high-copy number mice exhibited higher average mRNA levels than the low-copy number mice, although there were outliers in each group. Consistent with Eα-dependent restriction of Dkk1 expression to B/plasma cells, Dkk1 mRNA was readily detectable in lymphoid tissues, such as spleen, mesenteric lymph node and bone marrow, but not in liver. Conclusion: The newly developed Eα-Dkk1 transgenics may provide a valuable model system to elucidate DKK1-dependent bone disease in human MM.
Zinc sulfadiazine for topical therapy of pseudomonas infection in burns (1976)

The Journal of Trauma and Acute Care Surgery® is designed to provide the scientific basis to optimize care of the severely injured and critically ill surgical patient. Thus, the Journal has a high priority for basic and translation research to fulfill this objectives. Additionally, the Journal is enthusiastic to publish randomized prospective clinical studies to establish care predicated on a mechanistic foundation. Finally, the Journal is seeking systematic reviews, guidelines and algorithms that incorporate the best evidence available.The Journal of Trauma and Acute Care Surgery® is designed to provide the scientific basis to optimize care of the severely injured and critically ill surgical patient. Thus, the Journal has a high priority for basic and translation research to fulfill this objectives. Additionally, the Journal is enthusiastic to publish randomized prospective clinical studies to establish care predicated on a mechanistic foundation. Finally, the Journal is seeking systematic reviews, guidelines and algorithms that incorporate the best evidence available.
Comparison of gliding bacteria isolated from fish in North America and other areas of the Pacific rim. (1988)

Twenty-six isolates of gliding bacteria associated with columnaris disease were collected from different species of fish from a wide geographic range. Although there were three phenotypic variations in colony morphology among the strains observed, the growth and biochemical characteristics, as well as, GC content revealed no differences among these isolates. However, when compared by DNA hybridization, there appeared to be three distinct groups based on the DNA homology. Eighteen of the twenty rhizoid strains represented the first group. They were 81-98% homologous with Pacific Northwest strain DD3 of Flexibacter columnaris and included isolates from Canada, Chile, Japan, Korea, ROC and the USA (Atlantic and Pacific Coasts). The mucoid strain K4m was 95% homologous with strain DD3. Taiwanese strains 4G and 5F belonged to the second group and could be classified into new species of gliding bacteria as a result of low DNA homology (<29%) to the Pacific Northwest strain of F. columnaris. A strain with a honeycomb-like colony morphology which came from the southern portion of the USA represented a third group, was less homologous (73%) with strain DD3 of F. columnaris.
Unique homonuclear multiple bonding in main group compounds (2009)

Significant progress in the chemistry of main group compounds (group 13, 14, and 15) containing homonuclear multiple bonds has been made over the past three decades. This feature article addresses the unique structural and bonding motifs of these compounds, with a particular emphasis on both iconic molecules and recent novel discoveries.
Spreading of a surfactant monolayer on a thin liquid film: Onset and evolution of digitated structures (1999)

We describe the response of an insoluble surfactant monolayer spreading on the surface of a thin liquid film to small disturbances in the film thickness and surfactant concentration. The surface shear stress, which derives from variations in surfactant concentration at the air-liquid interface, rapidly drives liquid and surfactant from the source toward the distal region of higher surface tension. A previous linear stability analysis of a quasi-steady state solution describing the spreading of a finite strip of surfactant on a thin Newtonian film has predicted only stable modes. [Dynamics in Small Confining Systems III, Materials Research Society Symposium Proceedings, edited by J. M. Drake, J. Klafter, and E. R. Kopelman (Materials Research Society, Boston, 1996), Vol. 464, p. 237; Phys. Fluids A 9, 3645 (1997); O. K. Matar Ph.D. thesis, Princeton University, Princeton, NJ, 1998]. A perturbation analysis of the transient behavior, however, has revealed the possibility of significant amplification of disturbances in the film thickness within an order one shear time after the onset of flow [Phys. Fluids A 10, 1234 (1998); "Transient response of a surfactant monolayer spreading on a thin liquid film: Mechanism for amplification of disturbances," submitted to Phys. Fluids]. In this paper we describe the linearized transient behavior and interpret which physical parameters most strongly affect the disturbance amplification ratio. We show how the disturbances localize behind the moving front and how the inclusion of van der Waals forces further enhances their growth and lifetime. We also present numerical solutions to the fully nonlinear 2D governing equations. As time evolves, the nonlinear system sustains disturbances of longer and longer wavelength, consistent with the quasi-steady state and transient linearized descriptions. In addition, for the parameter set investigated, disturbances consisting of several harmonics of a fundamental wavenumber do not couple significantly. The system eventually singles out the smallest wavenumber disturbance in the chosen set. The summary of results to date seems to suggest that the fingering process may be a transient response which nonetheless has a dramatic influence on the spreading process since the digitated structures redirect the flux of liquid and surfactant to produce nonuniform surface coverage. (c) 1999 American Institute of Physics.
O11.1 Decline in genital shedding in the year after first clinical episode genital herpes simplex virus type 1 (2017)

<h3>Introduction</h3> Herpes simplex virus type 1 (HSV-1) has emerged as the leading cause of first episode genital herpes among adolescents and young adults. The natural history of genital and oral shedding after first episode genital HSV-1 must be described to understand the risk of transmission to sexual partners. <h3>Methods</h3> Persons with laboratory documented first clinical episode genital HSV-1 infection obtained daily self-collected genital and oral swabs for two 30 day sessions starting 2 months and 11 months after the first genital HSV-1 outbreak. HSV was detected in swabs using real-time quantitative HSV-1 PCR. Rates of genital and oral shedding were compared during the first and second swabbing sessions using Poisson regression models. <h3>Results</h3> Of 52 persons who completed the first swabbing session, 27 (52%) were HSV-1 seronegative (primary infection) at presentation and 25 (48%) were HSV-1 seropositive at initial presentation. Twenty-five persons completed both sessions (11–12 months). Genital HSV-1 shedding was detected in 176 (12.2%) of 1438 swabs from the first shedding session, and declined to 46 (7.1%) of 645 swabs in the second session. The rate of genital lesions was 61 of 1595 (3.8%) days in the first session and 12 of 746 (1.6%) days in the second session. Oral shedding was detected infrequently, with 3.6% of swabs HSV-1 positive in the first session, and 3.3% during the second session. Oral lesions were rare in both sessions. <h3>Conclusions</h3> Genital HSV-1 shedding occurs substantially less frequently than genital HSV-2 shedding, and declines in the first year after genital HSV-1 acquisition. These results will inform counselling messages about risk of sexual transmission to persons with first episode genital HSV-1 infection.
Hot Gas Cleaning and Upgrading with a Calcined Dolomite Located Downstream a Biomass Fluidized Bed Gasifier Operating with Steam−Oxygen Mixtures (1997)

Cleaning and upgrading of the hot raw gas from a biomass gasifier, bubbling fluidized bed type, is studied at small pilot plant scale (10 kg biomass fed/h) using a calcined dolomite located downstream from the gasifier. Gasification is made with steam−oxygen mixtures at 800−850 °C and atmospheric pressure. Main variables studied are the gas residence time in the bed of dolomite and the gas atmosphere composition, which depends on the gasifying agent (H2O + O2)-to-biomass and H2O/O2 ratios. H2 and CO content in the flue gas increases by 16−23 vol % and decreases by 15−22 vol % (dry basis), respectively. Although CH4 conversion (elimination) higher than 30 vol % has never been reached, tar conversion (elimination) of 90−95 vol % are obtained with space times of 0.06−0.15 kg calcined dolomite h-1 m-3. A detailed study is here presented on how the calcined dolomite significantly cleans and upgrades the flue gas, increasing also the gas yield by 0.15−0.40 m3(STP)/kg daf biomass fed.
Effect of anterior cruciate ligament graft tensioning direction, magnitude, and flexion angle on knee biomechanics (1993)

The objective of this study was to determine the biomechanical effect of graft tensioning during reconstruction of the anterior cruciate ligament. We evaluated the magnitude of the tensioning force (22 or 67 N), the flexion angle at which the tension was applied (extension or 30 degrees of flexion), and the direction of application of the tensioning force (proximal, distal, or distal with a posterior force simultaneously applied to the tibia) on 10 fresh cadaveric knees. The anterior cruciate ligament was reconstructed using a bone-patellar tendon-bone graft. The graft was then temporarily fixed during the application of each of 12 combinations of tensioning variables listed above. After each fixation, graft force and joint motion were measured during anterior tibial loads. Tensioning direction and the flexion angle significantly affected graft force and joint motion, while the magnitude of the graft tensioning did not. Graft forces were greater when the tensioning was applied at 30 degrees of flexion. Compared with distal tensioning with and without posterior tibial force, graft forces with proximal tensioning were greater in extension and lower in flexion. The position of the tibia relative to the femur was posterior and externally rotated, compared with normal, for all combinations of tensioning variables in both unloaded and anterior load states.
A Gesture-based Tool for Sterile Browsing of Radiology Images (2008)

The use of doctor-computer interaction devices in the operation room (OR) requires new modalities that support medical imaging manipulation while allowing doctors' hands to remain sterile, supporting their focus of attention, and providing fast response times. This paper presents "Gestix," a vision-based hand gesture capture and recognition system that interprets in real-time the user's gestures for navigation and manipulation of images in an electronic medical record (EMR) database. Navigation and other gestures are translated to commands based on their temporal trajectories, through video capture. "Gestix" was tested during a brain biopsy procedure. In the in vivo experiment, this interface prevented the surgeon's focus shift and change of location while achieving a rapid intuitive reaction and easy interaction. Data from two usability tests provide insights and implications regarding human-computer interaction based on nonverbal conversational modalities.
Hemothorax in 2 Horses (1999)

This report documents the successful conservative medical management of hemothorax in 2 horses. Hemothorax occurred after a lung biopsy procedure (horse 1) and strenuous exercise on a treadmill (horse 2). The horses had tachypnea, tachycardia, nostril flaring, hemoptysis, and pawing. Hemothorax was suspected based upon absence of auscultable ventral lung sounds; development of cool extremities and pale, tacky mucous membranes; the ultrasonographic appearance of moderate to severe amounts of pleural fluid; and a concurrent decrease in hematocrit and total plasma protein. Both horses were treated successfully by intranasal administration of oxygen, intravenous administration of balanced polyionic solutions, and treatment with antibiotics, nonsteroidal anti-inflammatory drugs, and analgesics. In neither case was pleural blood removed. The hemothorax resolved in both horses without lasting abnormalities. Hemothorax does not require drainage for successful resolution.
Evaluation of synthetic and agro-industrial carriers for immobilization of Aureobasidium pullulans cells for fructo-oligosaccharides production (2015)

Fructooligosaccharides (FOS) are prebiotic oligosaccharides with increased commercial interest [1]. FOS can be produced from sucrose by free or immobilized microorganisms with transfructosylating enzymes [2]. Cells immobilization can be applied to improve FOS yields and percentage in the medium as it increases cells stability and concentration in the medium [3]. Nevertheless, a good performance of the system depends on the right selection of the suitable carrier to adhere cells [4]. In this work, selected agro-industrial carriers to immobilize Aureobasidium pullulans fungi cells were compared to synthetic and mineral materials. Agro- industrial carriers include mandarin and banana peels, and nut, almond, pistachio and chestnut shells; synthetic carriers include foams, vegetal and synthetic fibers, porous clay and glass wool; and mineral carriers include pumice and porous stone. Cells were immobilized in situ by adhesion, through direct contact to the carrier at the beginning of the batch fermentations. The cells immobilization capacity was evaluated based on the biomass amount free and adhered to the carrier and by the water absorption index (WAI) and the critical humidity point (CHP) values determined for each carrier.
Ion mobility mass spectrometry of proteins and proteinassemblies (2009)

Traditionally, mass spectrometry has been a powerful analytical method enabling the structural analysis of small molecules, and later on peptides and proteins. With the advent of native mass spectrometry, using a combination of electrospray ionisation and time of flight analysis, mass spectrometry could also be applied to the mass determination of large protein complexes such as ribosomes and whole viruses. More recently, ion mobility has been coupled to mass spectrometry providing a new dimension in the analysis of biomolecules, with ion mobility separating ions according to differences in size and shape. In the context of native mass spectrometry, ion mobility mass spectrometry opens up avenues for the detailed structural analysis of large and heterogeneous protein complexes, providing information on the stoichiometry, topology and cross section of these assemblies and their composite subunits. With these characteristics, ion mobility mass spectrometry offers a complementary tool in the context of structural biology. Here, we critically review the development, instrumentation, approaches and applications of ion mobility in combination with mass spectrometry, focusing on the analysis of larger proteins and protein assemblies (185 references).
(Sensor Division Outstanding Achievement Award Presentation) Ceramic Gas Sensors to Oxide Nanostructures: Opportunities and Challenges (2013)

This article summarizes R&amp;D efforts in the author's laboratory starting with the development of ceramic-based gas sensors to the fabrication of ordered/oriented oxide nanostructures exploiting intrinsic material properties. Over the past twenty years, our focus has been on the development of a series of high-temperature gas sensors specifically for combustion processes. We have developed both the resistive and electrochemical sensors and the underlying theme of our work has been the use of materials science and chemistry to promote high-temperature performance with selectivity. Our recent work has led to the development of surface modification techniques for the fabrication of oxide nanostructures that are inexpensive, highly scalable and do not require use of lithography. These nano-structures can be used as platforms for chemical sensing, photocatalysis, electroemission and biomedical applications. This article is concluded with preliminary results on chemical sensing along with future directions.
Preparation of Ionic Liquids of Fluorocomplex and Oxofluorocomplex Anions by Fluoroacid–Base Reactions (2012)

This chapter contains sections titled: Preparation of 1-Ethyl-3-Methylimidazolium Tetrafluoroborate ([EMIm][BF 4 ]) Preparation of 1-Ethyl-3-Methylimidazolium Hexafluoroniobate ([EMIm)[NbF 6 ]) References
Zeolite-supported ultra-small nickel as catalyst for selective oxidation of methane to syngas (2020)

The development of simple catalysts with high performance in the selective oxidation of methane to syngas at low temperature has attracted much attention. Here we report a nickel-based solid catalyst for the oxidation of methane, synthesised by a facile impregnation method. Highly dispersed ultra-small NiO particles of 1.6 nm in size are successfully formed on the MOR-type zeolite. The zeolite-supported nickel catalyst gives continuously 97-98% methane conversion, 91-92% of CO yield with a H<sub>2</sub>/CO ratio of 2.0, and high durability without serious carbon deposition onto the catalyst at 973 K. DFT calculations demonstrate the effect of NiO particle size on the C-H dissociation process of CH<sub>4</sub>. A decrease in the NiO particle size enhances the production of oxygen originating from the NiO nanoparticles, which contributes to the oxidation of methane under a reductive environment, effectively producing syngas.
Catalysis at the Interface of Ruthenium Carbene and Ruthenium Hydride Chemistry: Organometallic Aspects and Applications to Organic Synthesis (2004)

Abstract Soon after the introduction of stable and defined ruthenium precatalysts for olefin metathesis it was discovered that double bond migrations may interfere with the metathesis reaction. This undesired side reaction has been attributed to the formation of ruthenium hydride species from metathesis‐active ruthenium carbene species in situ. Over the past few years, several studies have indeed revealed the existence of pathways leading from ruthenium carbene to ruthenium hydride complexes. Furthermore, a number of examples have been published recently where typical precatalysts for olefin metathesis were found to promote non‐metathesis transformations efficiently in preparatively useful yields and selectivities, presumably via the in situ formation of ruthenium hydride species. These results open up a pathway to the development of novel catalyzed reaction sequences that combine ruthenium carbene‐ and ruthenium‐hydride‐mediated steps. This paper provides an overview of the field and covers organometallic aspects as well as synthetic applications. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2004)
The synthesis of 2‐(1‐Pentenyl) furan and its relationship to the reversion flavor of soybean oil (1978)

Abstract Cis and trans ‐2‐(1‐pentenyl) furan were postulated as possible contributors to the reversion flavor of soybean oil. These compounds were synthesized, and structures were confirmed by infrared, nuclear magnetic resonance, and mass spectroscopy. Organoleptic evaluation of them in oil suggested that they could contribute to the beany and grassy note of the reverted soybean oil. This approach to flavor problems of food was given a new name — reverse phase flavor chemistry.
Design and synthesis of organic chromophores for imaging, lithography and organic electronics (2011)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2011
Identifying the Ultra-High Risk (Prodromal) Population: Evaluation of Training Workshops with Mental Health Services (2008)

UHR training workshops are a valuable means of increasing mental health workers' confidence in identifying UHR patients. Future UHR training programmes with experienced mental health professionals should pay particular attention to the correct identification of UHR-negative cases.