gebhart/patrepeval huggingface dataset:
Activity of pemetrexed in pre-clinical chordoma models and humans (2023)

Chordomas are rare slow growing tumors, arising from embryonic remnants of notochord with a close predilection for the axial skeleton. Recurrence is common and no effective standard medical therapy exists. Thymidylate synthase (TS), an intracellular enzyme, is a key rate-limiting enzyme of DNA biosynthesis and repair which is primarily active in proliferating and metabolically active cells. Eighty-four percent of chordoma samples had loss of TS expression which may predict response to anti-folates. Pemetrexed suppresses tumor growth by inhibiting enzymes involved in folate metabolism, resulting in decreased availability of thymidine which is necessary for DNA synthesis. Pemetrexed inhibited growth in a preclinical mouse xenograft model of human chordoma. We report three cases of metastatic chordoma that had been heavily treated previously with a variety of standard therapies with poor response. In two cases, pemetrexed was added and objective responses were observed on imaging with one patient on continuous treatment for > 2 years with continued shrinkage. One case demonstrated tumor growth after treatment with pemetrexed. The two cases which had a favorable response had a loss of TS expression, whereas the one case with progressive disease had TS present. These results demonstrate the activity of pemetrexed in recurrent chordoma and warrant a prospective clinical trial which is ongoing (NCT03955042).
The Aero-Optical Environment of a Helicopter in Forward Flight (2011)

The performance of an optical system mounted in a hemispherical turret can be seriously limited at certain viewing angles due to aero-optical aberrations on the outgoing beam. The strength of these aberrations is related to the density fluctuations in the air immediately surrounding the turret and is proportional to the Mach number squared; helicopters are therefore an attractive platform for optical systems due to their low flight speeds. In this case, aero-optic aberrations can still arise, however, from the wake and especially the tip vortices from the helicopter blades. A simplified model of a rotor tip-vortex system is used to gain insight into the potential aero-optical environment of a helicopter in forward flight. The simplified model allows for the rapid calculation of aero-optic effects at different forward-flight speeds. The results indicate that the largest aero-optic aberration originates from “super vortices” that appear along the lateral edge of the helicopter wake. Estimated aberration amplitudes are presented, as well as an estimate of the undisturbed viewing angle of the optical system as a function of forward-flight speed.
Contraction of the composite skin graft and autograft (2002)

Wound contraction as a result of a delay in grafting or second intention healing in an area that there was no graft take is a serious problem because of the sequela to the burned patient. The objective of the present study was to evaluate the contraction of the cultured keratinocytes and human acellular dermis composite graft by tracing the graft with transparent film after transplantation to the back of athymic mice. The evaluation of the contraction of the composite skin grafts and autografts in relation to the original wound area on the back of the athymic mice demonstrated greater contraction of the grafts after the dressings were removed on the seventh day. The composite skin graft contraction was significantly bigger than the autograft contraction. The experimental data suggested that the contraction appeared after dressing removal, but that the macroscopic aspect of the composite skin graft remained normal with no distortion of the graft or the surrounded murine skin.
Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers (2019)

Chromatin accessibility data can elucidate the developmental origin of cancer cells and reveal the enhancer landscape of key oncogenic transcriptional regulators. We develop a computational strategy called PSIONIC (patient-specific inference of networks informed by chromatin) to combine chromatin accessibility data with large tumor expression data and model the effect of enhancers on transcriptional programs in multiple cancers. We generate a new ATAC-seq data profiling chromatin accessibility in gynecologic and basal breast cancer cell lines and apply PSIONIC to 723 patient and 96 cell line RNA-seq profiles from ovarian, uterine, and basal breast cancers. Our computational framework enables us to share information across tumors to learn patient-specific TF activities, revealing regulatory differences between and within tumor types. PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome. To validate PSIONIC-derived prognostic TFs, we perform immunohistochemical analyses in 31 uterine serous tumors for ETV6 and 45 basal breast tumors for MITF and confirm that the corresponding protein expression patterns are also significantly associated with prognosis.
Characterization of the <i>Drosophila</i> myeloid leukemia factor (2006)

In human, the myeloid leukemia factor 1 (hMLF1) has been shown to be involved in acute leukemia, and mlf related genes are present in many animals. Despite their extensive representation and their good conservation, very little is understood about their function. In Drosophila, dMLF physically interacts with both the transcription regulatory factor DREF and an antagonist of the Hedgehog pathway, Suppressor of Fused, whose over-expression in the fly suppresses the toxicity induced by polyglutamine. No connection between these data has, however, been established. Here, we show that dmlf is widely and dynamically expressed during fly development. We isolated and analyzed the first dmlf mutants: embryos lacking maternal dmlf product have a low viability with no specific defect, and dmlf(-)- adults display weak phenotypes. We monitored dMLF subcellular localization in the fly and cultured cells. We were able to show that, although generally nuclear, dMLF can also be cytoplasmic, depending on the developmental context. Furthermore, two differently spliced variants of dMLF display differential subcellular localization, allowing the identification of regions of dMLF potentially important for its localization. Finally, we demonstrate that dMLF can act developmentally and postdevelopmentally to suppress neurodegeneration and premature aging in a cerebellar ataxia model.
Limits on the efficiency of one-way permutation-based hash functions (2003)

Naor and Yung (1989) show that a one-bit-compressing universal one-way hash function (UOWHF) can be constructed based on a one-way permutation. This construction can be iterated to build a UOWHF which compresses by /spl epsiv/n bits, at the cost of /spl epsiv/n invocations of the one-way permutation. The show that this construction is not far from optimal, in the following sense, there exists an oracle relative to which there exists a one-way permutation with inversion probability 2/sup -p(n)/ (for any p(n)/spl isin//spl omega/(log n)), but any construction of an /spl epsiv/n-bit-compressing UOWHF. Requires /spl Omega/(/spl radic/n/p(n)) invocations of the one-way permutation, on average. (For example, there exists in this relativized world a one-way permutation with inversion probability n/sup -/spl omega/(1)/, but no UOWHF that involves it fewer than /spl Omega/(/spl radic/n/log n) times.) Thus any proof that a more efficient UOWHF can be derived from a one-way permutation is necessarily non-relativizing; in particular, no provable construction of a more efficient UOWHF can exist based solely on a "black box" one-way permutation. This result can be viewed as a partial justification for the practice of building efficient UOWHFs from stronger primitives (such as collision intractable hash functions), rather than from weaker primitives such as one-way permutations.
Prevalence and risk factors of obesity, hypertension, dyslipidemia and diabetes mellitus before and after adult living donor liver transplantation (2014)

The prevalence of hypertension increased after LTx and pretransplant obesity was associated with several post-transplant metabolic abnormalities.
Viral Quantitative Capillary Electrophoresis for Counting and Quality Control of RNA Viruses (2012)

The world of health care has witnessed an explosive boost to its capacity within the past few decades due to the introduction of viral therapeutics to its medicinal arsenal. As a result, a need for new methods of viral quantification has arisen to accommodate this rapid advancement in virology and associated requirements for efficiency, speed, and quality control. In this work, we apply viral quantitative capillary electrophoresis (viral qCE) to determine (i) the number of intact virus particles (ivp) in viral samples, (ii) the amount of DNA contamination, and (iii) the degree of viral degradation after sonication, vortexing, and freeze-thaw cycles. This quantification method is demonstrated on an RNA-based vesicular stomatitis virus (VSV) with oncolytic properties. A virus sample contains intact VSV particles as well as residual DNA from host cells, which is regulated by WHO guidelines, and may include some carried-over RNA. We use capillary zone electrophoresis with laser-induced fluorescent detection to separate intact virus particles from DNA and RNA impurities. YOYO-1 dye is used to stain all DNA and RNA in the sample. After soft lysis of VSV with proteinase K digestion of viral capsid and ribonucleoproteins, viral RNA is released. Therefore, the initial concentration of intact virus is calculated based on the gain of a nucleic acid peak and an RNA calibration curve. After additional NaOH treatment of the virus sample, RNA is hydrolyzed leaving residual DNA only, which is also calculated by a DNA calibration curve made by the same CE instrument. Viral qCE works in a wide dynamic range of virus concentrations from 10(8) to 10(13) ivp/mL. It can be completed in a few hours and requires minimum optimization of CE separation.
Changes in cell cycle‐associated gene expression in a model of impaired liver regeneration (1994)

Following partial hepatectomy (PH) there is compensatory regeneration of the remnant liver which eventually restores hepatic mass and function. The response to PH was studied in normal BALB/c and athymic nude mice, a model of impaired liver regeneration. Following PH, nude mice demonstrated diminished peak hepatic [3H]thymidine uptake and delayed liver mass restoration through 60 h post-PH. However, between 72-120 h there was no significant difference in mass restoration between the groups. The expression of genes associated with different stages of the cell cycle was evaluated in both models. In nude mice, there was an increase in peak expression of c-jun transcripts, while c-myc transcript expression was moderately attenuated. Thymidine kinase (TK) and cyclin-dependent kinase 1 (CDK1) mRNA expression was also diminished in athymic nude mice. The results suggest that while the defect in the regenerative response of the nude mouse after PH affects events in several phases of the cell cycle, mass restoration of the liver is only delayed and not attenuated.
Degree of Degradation (Biorelated Polymer) (2016)

Like most of the materials used by humans, polymeric materials are proposed in the literature and occasionally exploited clinically, as such, as devices or as part of devices, by surgeons, dentists, and pharmacists to treat traumata and diseases. Applications have in common the fact that polymers function in contact with animal and human cells, tissues, and/or organs. More recently, people have realized that polymers that are used as plastics in packaging, as colloidal suspension in paints, and under many other forms in the environment, are also in contact with living systems and raise problems related to sustainability, delivery of chemicals or pollutants, and elimination of wastes. These problems are basically comparable to those found in therapy. Last but not least, biotechnology and renewable resources are regarded as attractive sources of polymers. In all cases, water, ions, biopolymers, cells, and tissues are involved. Polymer scientists, therapists, biologists, and ecologists should thus use the same terminology to reflect similar properties, phenomena, and mechanisms. Of particular interest is the domain of the so-called “degradable or biodegradable polymers” that are aimed at providing materials with specific time-limited applications in medicine and in the environment where the respect of living systems, the elimination, and/or the bio-recycling are mandatory, at least ideally.
Lipoate Ester Multifunctional Lubricant Additives (2015)

Seven lipoate esters were synthesized by esterification of lipoic acid with different structures of alcohols in the presence of a solid acid catalyst and without solvent. The esters were obtained in good yield, characterized using 1H NMR and GPC; and their physical properties investigated. Four of the seven lipoate esters, with good solubility in high oleic sunflower oil (HOSuO) and polyalphaolefin (PAO6) base oils, were further investigated for their lubricant additive property. Additive properties were investigated in HOSuO base oil by varying the additive concentrations in the range 0–20 (w/w %). Properties investigated include: density; kinematic and dynamic viscosity; viscosity index (VI); oxidation stability from onset and peak oxidation temperatures on a PDSC; 4-ball antiwear (AW); and 4-ball extreme pressure (EP). Neat lipoate esters displayed high oxidation stability and high VI. As additives to HOSuO base oil, lipoate esters displayed good viscosity index improver (VII), good antioxidant, good extreme pressure (EP), but poor AW properties. The VI and VII properties were attributed to the presence of low concentrations of polymeric byproducts in the ester product mixtures. This work demonstrates that lipoate esters can be developed into effective multifunctional biobased lubricant additives with excellent VII, AO and EP properties.
FABRICATION OF SUPERCONDUCTING CAVITIES FOR SNS (2004)

During the last three years ACCEL fabricated almost all 109 superconducting cavities for the Spallation Neutron Source (SNS) in Oak Ridge, Tennessee. Two series of 35 medium beta (beta=0.61) and 74 high beta (beta=0.81) cavities will be delivered until October 2004. Besides cavity manufacturing ACCEL also performed RF tuning and chemical surface preparation. We give an outline on the current manufacturing experience and comment on future developments for industrial cavity production.
Nitrous oxide versus carbon dioxide for supercritical-fluid extraction and chromatography of amines (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNitrous oxide versus carbon dioxide for supercritical-fluid extraction and chromatography of aminesM. Ashraf-Khorassani, L. T. Taylor, and P. ZimmermanCite this: Anal. Chem. 1990, 62, 11, 1177–1180Publication Date (Print):June 1, 1990Publication History Published online1 May 2002Published inissue 1 June 1990https://pubs.acs.org/doi/10.1021/ac00210a016https://doi.org/10.1021/ac00210a016research-articleACS PublicationsRequest reuse permissionsArticle Views357Altmetric-Citations47LEARN 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-Alertsclose Get e-Alerts
Occurrence of Mycotoxins in Feed as Analyzed by a Multi-Mycotoxin LC-MS/MS Method (2009)

Crops used for animal feed can be easily contaminated by fungi during growth, harvest, or storage, resulting in the occurrence of mycotoxins. Because animal feed plays an important role in the food safety chain, the European Commission has set maximum levels for aflatoxin B1 and recommended maximum levels for deoxynivalenol, zearalenone, ochratoxin A, and the sum of fumonisin B1 and B2. A multimycotoxin LC-MS/MS method was developed, validated according to Commission Decision 2002/657/EC and EN ISO 17025 accredited for the simultaneous detection of 23 mycotoxins (aflatoxin-B1, aflatoxin-B2, aflatoxin-G1, aflatoxin-G2, ochratoxin A, deoxynivalenol, zearalenone, fumonisin B1, fumonisin B2, fumonisin B3, T2-toxin, HT2-toxin, nivalenol, 3-acetyldeoxynivalenol, 15-acetyldeoxynivalenol, diacetoxyscirpenol, fusarenon-X, neosolaniol, altenuene, alternariol, alternariol methyl ether, roquefortine-C, and sterigmatocystin) in feed. The decision limits of the multimycotoxin method varied from 0.7 to 60.6 microg/kg. The apparent recovery and the results of the precision study fulfilled the performance criteria as set in Commission Decision 2002/657/EC. The analysis of three different feed matrices (sow feed, wheat, and maize) provided a good basis for the evaluation of the toxin exposure in animal production. In total, 67 samples out of 82 (82%) were contaminated; type B-trichothecenes and fumonisins occurred most often. The majority of the infected feed samples (75%) were contaminated with more than one type of mycotoxin.
ChemInform Abstract: pH‐Sensitive Ni(OH)2‐Based Microelectrochemical Transistors. (1987)

Abstract The electrochemical properties of pH‐sensitive Ni(OH) 2 ‐based microelectrochemical transistors, prepared by cathodic electrochemical deposition of Ni(OH) 2 onto Au or Pt microelectrode arrays, have been investigated.
Temperature dependence of on–off ratio and reverse recovery time in NiO/β-Ga2O3 heterojunction rectifiers (2022)

The temperature-dependent behavior of on/off ratio and reverse recovery time in vertical heterojunction p-NiO/β n-Ga2O/n+ Ga2O3 rectifiers was investigated over the temperature range of 25–300 °C. The device characteristics in forward bias showed evidence of multiple current transport mechanisms and were found to be dependent on the applied bias voltages and temperatures. The on–off ratio decreased from 3 × 106 at 25 °C to 2.5 × 104 at 300 °C for switching to 100 V reverse bias. For 200 μm diameter rectifiers, the reverse recovery time of ∼21 ns was independent of temperature, with the Irr monotonically increasing from 15.1 mA at 25 °C to 25.6 mA at 250 °C and dropping at 300 °C. The dI/dt increased from 4.2 to 4.6 A/μs over this temperature range. The turn-on voltage decreased from 2.9 V at 25 °C to 1.7 V at 300 °C. The temperature coefficient of breakdown voltage was negative and does not support the presence of avalanche breakdown in NiO/β-Ga2O3 rectifiers. The energy loss during switching from 100 V was in the range 23–31 μJ over the temperature range investigated.
Extraction of Neural Activity from In Vivo Optical Recordings Using Multiple Independent Component Analysis (2007)

A multiple independent component analysis (ICA) method based on the noisy time-delayed decorrelation algorithm is described that overcomes the problems and improves the usefulness of conventional ICA, which is commonly used for extracting the actual neural activity from data measured using optical recording with a voltage-sensitive dye to visualize neural activities in cortical areas as two-dimensional images. The problems with conventional ICA extraction include the lack of an a priori guarantee that the solution will be appropriate, the linear mixing of mutually independent random variables although the mixtures are not random variables but time signals in many applications, and the general requirement for repetitive calculation of large matrices. Application of multiple ICA to the extraction of neural activities in the guinea pig auditory cortex evoked by both click sounds and pure tones from optical recordings made using a voltage sensitive dye demonstrated that it effectively removes pulsatile and respiratory components from the measurement data and extracts neural activities from the optical recordings.
Network assisted rate adaptation for conversational video over LTE, concept and performance evaluation (2014)

This work investigates rate adaptation of conversational video in a mobile system using Long Term Evolution, LTE, and where the adaptation is assisted by the radio network. The conventional way to do rate adaptation is through adaptation in the end-points where the transmission rate is selected based on measurements of received packets.
Dynamic light scattering in localized coherence volumes (2001)

We introduce a novel light-scattering technique for investigating the dynamics of random media with a broad range of optical densities. By use of the spatial coherence properties of a single-mode optical fiber and the temporal coherence of a broadband source, the measurement volume is isolated at the end of the optical waveguide. Optical mixing between the fluctuating scattered light and the Fresnel-reflected field at the fiber-medium interface is analyzed directly in the frequency domain. The unique characteristics of this new technique are discussed in the context of simultaneous measurement of average scatterer size and concentration in dense colloidal suspensions.
MIMO Radar: A Multi-Sensor Spatially Diverse Radar Architecture (2008)

Abstract : The research supported by this grant: (a) provides an in depth analysis of the localization accuracy gain attainable with the MIMO radar systems by means of the Cramer-Rao Lower bound (b) introduces the geometric dilution of precision (GDOP) metric and the contour mapping, providing an insight into the relative performance accuracy for a given layout of radars over a given geographic area. These plots offer a clear understanding of the collaboration effect of different sensor scheme on the resulting accuracy. Furthermore, target localization estimators were developed and evaluated (c) presents the analysis on the ambiguity arising in the high resolution localization due to side-lobe characteristics of the MIMO system and viable solutions to the problem. This report documents our work on MIMO radar with widely separated antennas thus called distributed MIMO radar. Widely separated transmit/receive antennas capture the spatial diversity of the target's radar cross section (RCS). For target location, it is shown that coherent processing can provide a resolution far exceeding that supported by the radar's waveform.
Joint Power and Channel Resource Allocation for F/TDMA Decode and Forward Relay Networks (2009)

In this paper, we study the joint power and channel resource allocation problem for a multiuser F/TDMA decode-and-forward (DF) relay network under per-node power constraints and a total channel resource constraint. Our goal is to maximize the total throughput achieved by the systems. To that end, we formulate a joint power and channel resource allocation problem. We develop an iterative optimization algorithm to solve this problem, whose convergence and optimality are guaranteed. Due to the per-node power constraints, more than one relay node may be needed for a single data stream. Our solution also provides a way of finding the optimal relays among the assisting relay nodes.