gebhart/patrepeval huggingface dataset:
Bioreduction of Trichloroethene Using a Hydrogen-Based Membrane Biofilm Reactor (2007)

A H2-based, denitrifying membrane-biofilm reactor (MBfR) was effective for removing trichloroethene (TCE) by reductive dechlorination. When TCE was first added to the MBfR, reductive dechlorination took place immediately and then increased over 18 weeks, and TCE was completely dechlorinated to ethene by about 120 days. These results indicate that TCE-dechlorinating bacteria were present naturally in the H2-based biofilm, and that enrichment for TCE-dechlorinating bacteria occurred. Dehalococcoides were documented in the MBfR biofilm before and after TCE feeding. Their proportion, quantified using the 16S rRNA gene, increased from 2.9 to 12% after TCE addition. This is the first report in which Dehalococcoides are proven to be present as part of an autotrophic biofilm community active in reductive dechlorination of TCE to ethene in a laboratory controlled experiment. Based on the complete reduction of TCE to ethene, the 16S rRNA clone libraries results, and the amount of tceA and bvcA, it appears that at least two Dehalococcoides strains were present in the enriched biofilm. One of them seems to be a new strain that is unique for having tceA and bvcA reductive dehalogenases.
Growth Inhibition of Cotton (Gossypium hirsutum) and Soybean (Glycine max) Roots and Shoots by Three Dinitroaniline Herbicides (1979)

Environmental control chamber experiments showed that cotton ( Gossypium hirsutum L. ‘Stoneville 213′) and soybean [ Glycine max (L.) Merr. ‘Bragg’] root and shoot growth were reduced when treated with increasing rates of dinitramine ( N 4 , N 4 -diethyl-α,α,α-tri-fluoro-3,5-dinitrotoluene-2,4-diamine), profluralin [ N -(cyclopropylmethyl)-α,αα-trifluoro-2,6-dinitro- N -propyl- p -toluidine], and trifluralin (α,α,α-trifluoro-2,6-dintrio- N,N -dipropyl- p -toluidine). Viusal root ratings, dry root weights, and fresh and dry herbage weights were used to evaluate plant response to herbicide treatments in environmental chambers. The order of increasing GR 50 values for cotton on two soils and with all response measurements, except dry root weights on one soil, was trifluralin, dinitramine, and profluralin. The order of increasing GR 50 values for soybeans on two soils and with all response measurements was dinitramine, trifluralin, and profluralin.
Effects of high-frequency oscillating pressures on upper airway muscles in humans (1993)

We examined the effects of high-frequency- (30-Hz) low-pressure oscillations (< 1 cmH2O) applied to the upper airway, via a nose mask, on genioglossus (EMGgg), sternomastoid (EMGsm), and diaphragm electromyogram (EMGdia) activity in sleeping humans. Ten patients with sleep apnea and six normal subjects were studied. The pressure oscillations were applied through the mask for a single breath. The subjects were studied in non-rapid-eye-movement (NREM) and rapid-eye-movement (REM) sleep. In the normal subjects, during NREM sleep, peak EMGgg, EMGsm, and EMGdia activity increased significantly in response to the oscillations in 63, 51, and 46%, respectively, of all trials. During REM sleep, significant increases occurred in 73, 88, and 13%, respectively, of all trials. Similar responses were observed in the patients with obstructive sleep apnea. Peak EMGgg, EMGsm, and EMGdia activity increased significantly in 74, 50, and 67%, respectively, of all NREM sleep trials and in 55, 81, and 76%, respectively, of all REM sleep trials. An important finding was that in 46% of the trials in the patients with sleep apnea the oscillation-induced increase in EMGgg activity was associated with a partial or complete reversal of the upper airway obstruction with an increase in tidal volume. This was observed in NREM and REM sleep. We conclude that there are upper airway receptors that respond to low-pressure-high-frequency oscillations applied to the upper airway that have input to the genioglossus and other muscles of respiration. These responses may be utilized in future treatment for sleep apnea.
Non-negative Matrix Factorization under sparsity constraints to unmix in vivo spectrally resolved acquisitions (2010)

International audience
A platform-agnostic, function first-based antibody discovery strategy using plasmid-free mammalian expression of antibodies (2021)

Hybridoma technology has been valuable in the development of therapeutic antibodies. More recently, antigen-specific B-cell selection and display technologies are also gaining importance. A major limitation of these approaches used for antibody discovery is the extensive process of cloning and expression involved in transitioning from antibody identification to validating the function, which compromises the throughput of antibody discovery. In this study, we describe a process to identify and rapidly re-format and express antibodies for functional characterization. We used two different approaches to isolate antibodies to five different targets: 1) flow cytometry to identify antigen-specific single B cells from the spleen of immunized human immunoglobulin transgenic mice; and 2) panning of phage libraries. PCR amplification allowed recovery of paired V(H) and V(L) sequences from 79% to 96% of antigen-specific B cells. All cognate V(H) and V(L) transcripts were formatted into transcription and translation compatible linear DNA expression cassettes (LEC) encoding whole IgG or Fab. Between 92% and 100% of paired V(H) and V(L) transcripts could be converted to LECs, and nearly 100% of them expressed as antibodies when transfected into Expi293F cells. The concentration of IgG in the cell culture supernatants ranged from 0.05 µg/ml to 145.8 µg/ml (mean = 18.4 µg/ml). Antigen-specific binding was displayed by 78–100% of antibodies. High throughput functional screening allowed the rapid identification of several functional antibodies. In summary, we describe a plasmid-free system for cloning and expressing antibodies isolated by different approaches, in any format of choice for deep functional screening that can be applied in any research setting during antibody discovery.
Synthesis of ZnO tetrapods for flexible and transparent UV sensors (2012)

ZnO tetrapods (ZnO-Ts) were synthesized in a vertical flow reactor by gas phase oxidation of Zn vapor in an air atmosphere. The morphology of the product was varied from nearly spherical nanoparticles to ZnO-Ts, together with the partial pressure of Zn and reaction temperature. MgO introduced during synthesis, increased the band gap, the optical transparency in the visible range, and also changed the ZnO-T structure. Fabricated flexible transparent UV sensors showed a 45-fold current increase under UV irradiation with an intensity of 30 μW cm(-2) at a wavelength of 365 nm and response time of 0.9 s.
Modelling the MYC-driven normal-to-tumour switch in breast cancer (2019)

The potent MYC oncoprotein is deregulated in many human cancers, including breast carcinoma, and is associated with aggressive disease. To understand the mechanisms and vulnerabilities of MYC-driven breast cancer, we have generated an <i>in vivo</i> model that mimics human disease in response to MYC deregulation. MCF10A cells ectopically expressing a common breast cancer mutation in the phosphoinositide 3 kinase pathway (PIK3CA<sup>H1047R</sup>) led to the development of organised acinar structures in mice. Expressing both PIK3CA<sup>H1047R</sup> and deregulated MYC led to the development of invasive ductal carcinoma. Therefore, the deregulation of MYC expression in this setting creates a MYC-dependent normal-to-tumour switch that can be measured <i>in vivo</i> These MYC-driven tumours exhibit classic hallmarks of human breast cancer at both the pathological and molecular level. Moreover, tumour growth is dependent upon sustained deregulated MYC expression, further demonstrating addiction to this potent oncogene and regulator of gene transcription. We therefore provide a MYC-dependent model of breast cancer, which can be used to assay <i>in</i><i>vivo</i> tumour signalling pathways, proliferation and transformation from normal breast acini to invasive breast carcinoma. We anticipate that this novel MYC-driven transformation model will be a useful research tool to better understand the oncogenic function of MYC and for the identification of therapeutic vulnerabilities.
WEAK-CONSISTENCY GROUP COMMUNICATION AND MEMBERSHIP (Ph.D. dissertation) (1992)

Many distributed systems for wide-area networks can be built conveniently, and operate efficiently and correctly, using a *weak consistency group communication* mechanism. This mechanism organizes a set of *principals* into a single logical entity, and provides methods to multicast messages to the members. A weak consistency distributed system allows the principals in the group to differ on the value of shared state at any given instant, as long as they will eventually converge to a single, consistent value. A group containing many principals and using weak consistency can provide the reliability, performance, and scalability necessary for wide-area systems. I have developed a framework for constructing group communication systems, for classifying existing distributed system tools, and for constructing and reasoning about a particular group communication model. It has four components: message delivery, message ordering, group membership, and the application. Each component may have a different implementation, so that the group mechanism can be tailored to application requirements. The framework supports a new message delivery protocol, called *timestamped anti-entropy*, which provides reliable, eventual message delivery; is efficient; and tolerates most transient processor and network failures. It can be combined with message ordering implementations that provide ordering guarantees ranging from unordered to total, causal delivery. A new group membership protocol completes the set, providing temporarily inconsistent membership views resilient to up to k simultaneous principal failures. The Refdbms distributed bibliographic database system, which has been constructed using this framework, is used as an example. Refdbms databases can be replicated on many different sites, using the group communication system described here.
Ultra-efficient N-junction photovoltaic cells with V<inf>OC</inf> > 14V at high optical input powers (2016)

GaAs phototransducers with 5 to 12 p/n junctions are shown to demonstrate breakthrough performance in optical conversion efficiency ranging from 65% to just under 70%. In particular, for a current-matched 12 junction device we have recorded an efficiency of 66.5% at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">oc</sub> = 14.46V (open circuit voltage) with an approximately 650 suns / 841 nm monochromatic source. Our simulations reproduce the PV characteristics of the physical devices with good (~ %) accuracy for V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">oc</sub> and I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">sc</sub> (short circuit current), which allows us to numerically study the influence of experimental conditions and design factors on device performance. Moreover, our simulations suggest that measured efficiencies are very close to the theoretical limits of the heterostructures under consideration. Our focus in these proceedings is twofold: a) to present an overview of the results of these experiments as well as b) study the factors which limit simulated device performance with the objective of attaining monochromatic conversions efficiencies exceeding 70%.
Induced Laminar Flow due to a Rotating Sphere. (1993)

A non-iterative finite-difference scheme has been developed to solve the boundary layer equations governing the laminar flow engendered by the rotation of a sphere about its diameter in a stagnant fluid. Advantages of the developed numerical scheme are simplicity, low required computer core storage, and less computational time. No points of zero meridional velocity gradient normal to the wall (separation points) could be detected in the domain of solution (from the pole to the equator). The obtained numerical results for the meridional, azimuthal and radial velocity components and for the torque are presented and compared with the results of other investigators.
The effect of pressure-induced conformational changes on the longitudinal acoustic mode in perfluoro-n-alkanes (1991)

An investigation of the longitudinal acoustic mode (LAM) in a series perfluoro-n-alkanes under pressure has been carried out using Raman spectroscopy in conjunction with a diamond anvil cell. Perfluoro-n-alkanes are shown to undergo a phase transition from a helical to a planar zigzag structure at 5 kbar. This conformational change with pressure results in an abrupt increase in the LAM frequency. Since the chain axis elastic modulus of a planar zigzag molecule is larger than that of a helical one, such a conformational change leads to stiffening of the backbone giving rise to the observed change in the LAM frequency.
Device Prototype for Vaginal Delivery of Extremely Preterm Fetuses in the Breech Presentation (2020)

Vaginal delivery is typically avoided in the extremely preterm breech population due to the concern of entrapment by the cervix of the aftercoming head. A mechanical device concept is presented to enable vaginal delivery by preventing retraction of the cervix against the fetus during delivery. The two-part device was designed to dilate the cervix, prevent prolapse of small fetal parts and maintain sufficient dilation during delivery. The two-part device was designed and manufactured with the following modules: an inflatable saline-filled cervical balloon for dilation and a cervical retractor composed of semirigid beams to stabilize the cervix and maintain adequate dilation. The device was tested using a cervical phantom designed to simulate the compressive force the cervix exerts. The cervical balloon reached a maximum dilation of 8.5 cm, after which there was leakage of saline from the balloon. While this dilation was less than the target goal of 10 cm, the leaking was attributed to prototype manufacturing defects, which could be resolved with further development. The cervical retractor was able to withstand between 1-3 kPa. Although estimates of cervical pressure values can be upward of 30 kPa, there are no in vivo measurements to formally identify the pressure values for patients in preterm labor. This device serves as a viable proof-of-concept for utilizing an inflatable balloon device to prevent cervical retraction in the setting of extremely preterm vaginal breech delivery. Further manufacturing improvements and design changes could improve the device for continued development and testing.
High-Density Regular Arrays of Nanometer-Scale Rods Formed on Silicon Surfaces via Femtosecond Laser Irradiation in Water (2008)

We report on the formation of high-density regular arrays of nanometer-scale rods using femtosecond laser irradiation of a silicon surface immersed in water. The resulting surface exhibits both micrometer-scale and nanometer-scale structures. The micrometer-scale structure consists of spikes of 5-10 mum width, which are entirely covered by nanometer-scale rods that are roughly 50 nm wide and normal to the surface of the micrometer-scale spikes. The formation of the nanometer-scale rods involves several processes: refraction of laser light in highly excited silicon, interference of scattered and refracted light, rapid cooling in water, roughness-enhanced optical absorptance, and capillary instabilities.
Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CLpro) (2021)

Starting from the MLPCN probe compound ML300, a structure-based optimization campaign was initiated against the recent severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CL<sup>pro</sup>). X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CL<sup>pro</sup> enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound <b>41</b> (CCF0058981). The disclosed inhibitors utilize a noncovalent mode of action and complex in a noncanonical binding mode not observed by peptidic 3CL<sup>pro</sup> inhibitors. <i>In vitro</i> DMPK profiling highlights key areas where further optimization in the series is required to obtain useful <i>in vivo</i> probes. Antiviral activity was established using a SARS-CoV-2-infected Vero E6 cell viability assay and a plaque formation assay. Compound <b>41</b> demonstrates nanomolar activity in these respective assays, comparable in potency to remdesivir. These findings have implications for antiviral development to combat current and future SARS-like zoonotic coronavirus outbreaks.
Synthesis of hydrogen-carbon clathrate material and hydrogen evolution therefrom at moderate temperatures and pressures (2023)

A process for making a hydrogenated carbon material is provided which includes forming a mixture of a carbon source, particularly a carbonaceous material, and a hydrogen source. The mixture is reacted under reaction conditions such that hydrogen is generated and/or released from the hydrogen source, an amorphous diamond-like carbon is formed, and at least a portion of the generated and/or released hydrogen associates with the amorphous diamond-like carbon, thereby forming a hydrogenated carbon material. A hydrogenated carbon material including a hydrogen carbon clathrate is characterized by evolution of molecular hydrogen at room temperature at atmospheric pressure in particular embodiments of methods and compositions according to the present invention.
Automated Treatment Planning Using a Database of Prior Patient Treatment Plans (2012)

• Objectives: – To develop an analytical database and infrastructure to store clinical information for personalized medicine and future analysis • Project 1: Integration of Data Collection with Clinical Workflow • Project 2: Database Design: Security and Distributed Web-Access • Project 3: Tools for Query, Analysis, Navigation and Decision Support • Project 4: Data Mining, Decision Support and Biostatistic Research,
Selective Hydrodeoxygenation of Cyclic Vicinal Diols to Cyclic Alcohols over Tungsten Oxide–Palladium Catalysts (2014)

Hydrodeoxygenation of cyclic vicinal diols such as 1,4-anhydroerythritol was conducted over catalysts containing both a noble metal and a group 5-7 transition-metal oxide. The combination of Pd and WOx allowed the removal of one of the two OH groups selectively. 3-Hydroxytetrahydrofuran was obtained from 1,4-anhydroerythritol in 72 and 74% yield over WOx -Pd/C and WOx -Pd/ZrO2 , respectively. The WOx -Pd/ZrO2 catalyst was reusable without significant loss of activity if the catalyst was calcined as a method of regeneration. Characterization of WOx -Pd/C with temperature-programmed reduction, X-ray diffraction, and transmission electron microscopy/energy-dispersive X-ray spectroscopy suggested that Pd metal particles approximately 9 nm in size were formed on amorphous tungsten oxide particles. A reaction mechanism was proposed on the basis of kinetics, reaction results with tungsten oxides under an atmosphere of Ar, and density functional theory calculations. A tetravalent tungsten center (W(IV) ) was formed by reduction of WO3 with the Pd catalyst and H2 , and this center served as the reductant for partial hydrodeoxygenation.
Technical and clinical evaluation of a new polyamide hollow fiber hemofilter for CAVH (1988)

We carried out an in-vivo and in-vitro evaluation of a new polyamide hollow fiber hemofilter especially designed to operate under conditions of low pressure and low blood flow, such as in continuous arteriovenous hemofiltration (CAVH). The results obtained suggest that this filter is a prototype of a new generation of hemofilters especially designed for CAVH. Its low resistance permits its use even in patients with severe hypotension. The high blood flows achieved at a given pressure reduce the risk of clotting and increase the ultrafiltration rate. When an average ultrafiltration of 20-25 ml/min is achieved in 24 hours CAVH becomes very efficient, and alternative techniques to increase its efficiency are no longer required.
Diphosphines with natural bite angles near 120.degree. increase selectivity for n-aldehyde formation in rhodium-catalyzed hydroformylation (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTDiphosphines with natural bite angles near 120.degree. increase selectivity for n-aldehyde formation in rhodium-catalyzed hydroformylationCharles P. Casey, Gregory T. Whiteker, Margaret G. Melville, Lori M. Petrovich, James A. Gavney Jr., and Douglas R. PowellCite this: J. Am. Chem. Soc. 1992, 114, 14, 5535–5543Publication Date (Print):July 1, 1992Publication History Published online1 May 2002Published inissue 1 July 1992https://pubs.acs.org/doi/10.1021/ja00040a008https://doi.org/10.1021/ja00040a008research-articleACS PublicationsRequest reuse permissionsArticle Views3322Altmetric-Citations340LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Studies on the constituents of Marsdenia formosana Masamune. III. Isolation and structural elucidation of some new steroidal glycosides. (1978)

From the methanolic extracts of Marsdenia formosana MASAMUNE (Asclepiadaceae), three new steroidal glycosides, MF-A, MF-C and MF-D, together with β-sitosterol-3β-D-glucoside (VIII) and dehydrotomentosin (I) were isolated. As the results of spectroscopic and chemical investigations, it has been demonstrated that the stereostructures of MF-A, MF-C and MF-D were represented, respectively, by the formulas II, IV and VI.