gebhart/patrepeval huggingface dataset:
Analysis of fragment ends in plasma DNA from patients with cancer (2021)

Abstract Fragmentation patterns observed in plasma DNA reflect chromatin accessibility in contributing cells. Since DNA shed from cancer cells and blood cells may differ in fragmentation patterns, we investigated whether analysis of genomic positioning and nucleotide sequence at fragment ends can reveal the presence of tumor DNA in blood and aid cancer diagnostics. We analyzed whole genome sequencing data from &gt;2700 plasma DNA samples including healthy individuals and patients with 11 different cancer types. We observed higher fractions of fragments with aberrantly positioned ends in patients with cancer, driven by contribution of tumor DNA into plasma. Genomewide analysis of fragment ends using machine learning showed overall area under the receiver operative characteristic curve of 0.96 for detection of cancer. Our findings remained robust with as few as 1 million fragments analyzed per sample, suggesting that analysis of fragment ends can become a cost-effective and accessible approach for cancer detection and monitoring. One-sentence summary Analyzing the positioning and nucleotide sequence at fragment ends in plasma DNA may enable cancer diagnostics.
Prediction of cancer progression in Barrett’s esophagus patients using miRNA profiling (2014)

Background: Barrett’s esophagus (BE) is a metaplastic disease with risk to develop esophageal adenocarcinoma (EAC). Current screening method for BE patients (endoscopy and biopsy) is discomfort, expensive and relatively risky for patients. Moreover, the procedure is complicated by subjective histopathological examination. Approximately only 2% of BE patients annually progress to adenocarcinoma. The aim of our study was to identify miRNA profiles in order to predict cancer progression in high-risk BE patients. Methods and patients: FFPE samples were obtained from 68 patients (10 EAC, 4 high-grade and 21 low-grade dysplasia of esophagus, and 33 BE). There were 49 males and 19 females; median age was 58 years, range 27 - 97 years. Total RNA was purified from FFPE biopsy samples using Proteinase K treatment followed by RNeasy kit (Qiagen). Microarray analysis was performed using the GeneChip miRNA 3.0 Array (Affymetrix). The data were analyzed using “R” software and the Bioconductor package. Results: In total, 68 GeneChip miRNA 3.0 Arrays were performed in 68 patients (8 poor quality arrays were excluded). Expression profiles of 1733 human miRNAs, 1658 human pre-miRNAs and 2216 human sno-RNAs and sca-RNAs were analyzed. In supervised clustering analysis we found 29 differentially expressed miRNAs, 7 pre-miRNAs and 9 sno-RNAs (p 2) in EAC patients compared to BE patients. One of the dominant findings was decreased expression of miR-22 in EAC samples, which is known to function as a tumor suppressor and histone deacetylase 4 regulator. Conclusion: We have identified miRNA profiles allowing for better diagnostics of cancer progression in BE patients, which, however, will require further validation.
571: ANTIINFLAMMATORY ACTIVITY OF WIN55,212-2, A NONSELECTIVE CANNABINOID CB1/CB2 RECEPTOR AGONIST (2019)

Bradley, Jennifer; Yanyan, Wang; Jankovic, Lazar; Huang, Iris; Sharma, Esha; Moore, Christine; Peberdy, Mary; Ornato, Joseph; Tang, Wanchun; Zhou, Huiping Author Information
In vivo and in vitro cholinesterase inhibitor property of the antitumor agent caracemide. (1990)

The antitumor agent caracemide [N-acetyl-N-(methylcarbamoyloxy)-N'-methylurea] has been observed to induce signs of cholinergic activation in both animal and human studies at high clinical and toxic levels. The present study was designed to further characterize the ability of caracemide to inhibit cholinesterase both in vivo and in vitro. Caracemide produced a time-dependent inhibition of purified acetylcholinesterase, pseudocholinesterase and rat brain homogenate cholinesterase with IC50 values of 0.60, 0.55 and 17.8 microM, respectively, at the maximal time point of inhibition. Analysis of Lineweaver-Burke plots derived from inhibition of brain homogenates revealed predominantly competitive type inhibition at both initial and maximal incubation times. Intravenous administration of caracemide to rats resulted in a dose-dependent inhibition of brain cholinesterase activity, with the greatest inhibition occurring in the cortex.
Non-Singular Kernels for Modelling Power Law Type Long Memory Behaviours and Beyond (2020)

To tackle several limitations recently highlighted in the field of fractional differentiation and fractional models, some authors have proposed new kernels for the definition of fractional integration/differentiation operators. These kernels still have some limitations, however. One goal of this paper is thus to propose other kernels with a power law type behavior that overcome these limitations. All these kernels are nonsingular and have a limited memory. They are then used to define a class of models adapted to capture input-output power law type long memory behaviors. The stability of this class of model is investigated. Finally, the paper shows that the fractional pseudo state space description, a fractional model widely used in the literature, is a special case of Volterra equations, equations introduced nearly a century ago. Volterra equations, whose memory length can be explicitly controlled, can thus be viewed as a serious alternative to fractional pseudo state space descriptions for power law type long memory behavior modeling, as fractional pseudo state space descriptions are known to exhibit serious drawbacks also discussed in the paper.
Diffuse optical tomography with polarized light: a GPU-accelerated polarization-sensitive Monte Carlo simulations for efficient sensitivity kernel computation (2019)

International audience
Common agency contracting and the emergence of \dqopen science\dq institutions (1998)

The Cold War’s ending has brought mounting pressures to recognize national science and technology research systems. Yet, by comparison with what has been learned already concerning institutional arrangements and business strategies affecting corporate RD investments, surprisingly little is known about the economic origins and effects of the corresponding institutional infrastructures shaping the world of “academic” science, and the organization and conduct of publicly supported RD more generally. The desirability of closing this particular lacuna in the economics and economic-history literatures has been just as evident to economists concerned with extending the analysis of modern institutions as to those who have begun to approach the whole area of science and technology studies from the perspectives and methods of industrial-organization economics. [1] Even before the “new economics of science” had begun to direct attention to such a program, Douglass North (1990 p. 75) saw a significant challenge and a promising opportunity in explicit exploration of “the connecting links between institutional structures... and incentives to acquire pure knowledge.” The research reported here has accepted that challenge (see also the other papers in this session: Timothy Lenoir [1998], Christophe Lecuyer [1998], and Marjory S. Blumenthal [1998]). It is focused upon key episodes in the institutional evolution of “public science,” and its complex and changing relationship to the other organizational spheres of contemporaneous scientific activity: those in which research was conducted under “proprietary rules” for industrial profit-goals, and “defense-related” science and engineering knowledge was sought under conditions of restricted access to information concerning methods, findings, and their actual and potential applications.
Association between Intraoperative Hypotension and Myocardial Injury after Vascular Surgery (2015)

In elderly vascular surgery patients, IOH defined as a 40% decrease from the preinduction mean arterial blood pressure with a cumulative duration of more than 30 min was associated with postoperative myocardial injury.
Forward collision warning systems using heads-up displays: Testing usability of two new metaphors (2013)

The incorporation of Augmented Reality (AR) in the windshield of automobiles using heads-up displays (HUD) is starting to be implemented by some manufacturers and is proving to be very useful in some situations, including safety distance keeping. This paper reports on a system that warns the driver via the car's HUD when he violates the predefined safety distance, to avoid a possible forward collision, and proposes two different visualization metaphors based on traffic signals. The metaphors are compared, with and without warning sounds, through computer simulations performed by 22 participants from different age groups and driving experiences. One of the metaphors corresponds to a variant of the traffic sign C10 that forbids circulating from the preceding vehicle shorter than a certain minimum headway, whereas the other corresponds to the road safety marks, which recommend the safety distance to be observed from the vehicle ahead. Results show that the metaphor derived from the safety marks, with warning sounds, is preferred by the participants, and was considered the most useful, intuitive and adequate to a forward collision warning. We also found that this metaphor was preferred by all participants that were 42 or more years old, whereas participants between 28 and 41 years old were divided between the two metaphors, with warning sounds.
PSO-GPU (2011)

This work presents a PSO implemention in CUDA architecture, aiming to speed up the algorithm on problems which has large amounts of data. PSO-GPU algorithm was designed to customization, in order to adapt for any problem that can be solved by a PSO algorithm. By implementing PSO using CUDA architecture, each processing core of the GPU will be responsible for a portion of the overall processing operation, where each one of these pieces are handled and executed in a massive parallel enviroment, opening the possibility for solving problems that require a large processing load in considerably less time. In order to evaluate the performance of PSO-GPU algorithm two functions were used, both global optimization problems, where without constraints (Griewank function) and other considering constraints, the Welded Beam Design (WBD).
Seven-Tesla Proton Magnetic Resonance Spectroscopic Imaging in Adult X-Linked Adrenoleukodystrophy (2008)

Seven-Tesla proton magnetic resonance spectroscopic imaging reveals differences in the neurochemistry of adult cerebral ALD but cannot distinguish AMN patients from female heterozygotes. Myo-inositol to creatine ratio correlates with the severity of the symptoms and may be a meaningful biomarker in adult X-ALD.
An adaptive doctor-recommender system (2019)

Recommender systems use machine-learning techniques to make predictions about resources. The medical field is one where much research is currently being conducted on recommender system utility. In the last few years, the amount of information available online that relates to healthcare has increased tremendously. Patients nowadays are more aware and look for answers to healthcare problems online. This has resulted in a dire need of an effective reliable online system to recommend the physician that is best suited to a particular patient in a limited time. In this article, a hybrid doctor-recommender system is proposed, by combining different recommendation approaches: content base, collaborative and demographic filtering to effectively tackle the issue of doctor recommendation. The proposed system addresses the issue of personalization through analysing patient's interest towards selecting a doctor. It uses a novel adoptive algorithm to construct a doctor's ranking function. Moreover, this ranking function is used to translate patients’ criteria for selecting a doctor into a numerical base rating, which will eventually be used in the recommendation of doctors. The system has been evaluated thoroughly, and result show that recommendations are reasonable and can fulfil patient's demand for reliable doctor's selection effectively.
Attractiveness of chemicals toGlossina tachinoidesWestwood (Diptera, Glossinidae) in Côte d'Ivoire (1991)

Abstract Studies on the use of 22 chemical attractants for Glossina tachinoides were undertaken in Côte d'Ivoire following earlier work on G. m. morsitans and G. pallidipes in Zimbabwe. While catches of G. m. morsitans and G. pallidipes increased by several times when traps were baited with some of these substances, catches of G. tachinoides were only marginally increased. G. tachinoides is slightly attracted by octenol and acetone, alone or in combination, and its response to CO2 is much weaker than that of the species tested in Zimbabwe. Phenol and indol mixtures both showed dose‐response relationships with catch. The indols were more potent in the lowest of the tested dosages (catch increase of 52%, P < 0001) whereas the phenols showed better attractiveness in their higher concentrations (catch increase of 42%, P < 0.05). Odour is probably less important in host finding for the riverine species G. tachinoides than it is for the savanna species studied in Zimbabwe.
The oxidation of ethane-1,2-diol resulting from molecular oxygen activation by copper: formation of an oxoethanoate complex precedes carbon–carbon bond cleavage (1993)

The aerial oxidation of ethane-1,2-diol in the presence of copper metal and pyridine (py) at room temperature and atmospheric pressure produces [Cu(py)2(HCO2)2]·H2O and [Cu2(py)4(OCH2CO2)2]·(CH2OH)2; the structure of the latter has been fully elucidated by an X-ray study.
Role of the Pilot Protein YscW in the Biogenesis of the YscC Secretin in Yersinia enterocolitica (2004)

The YscC secretin is a major component of the type III protein secretion system of Yersinia enterocolitica and forms an oligomeric structure in the outer membrane. In a mutant lacking the outer membrane lipoprotein YscW, secretion is strongly reduced, and it has been proposed that YscW plays a role in the biogenesis of the secretin. To study the interaction between the secretin and this putative pilot protein, YscC and YscW were produced in trans in a Y. enterocolitica strain lacking all other components of the secretion machinery. YscW expression increased the yield of oligomeric YscC and was required for its outer membrane localization, confirming the function of YscW as a pilot protein. Whereas the pilot-binding site of other members of the secretin family has been identified in the C terminus, a truncated YscC derivative lacking the C-terminal 96 amino acid residues was functional and stabilized by YscW. Pulse-chase experiments revealed that approximately 30 min were required before YscC oligomerization was completed. In the absence of YscW, oligomerization was delayed and the yield of YscC oligomers was strongly reduced. An unlipidated form of the YscW protein was not functional, although it still interacted with the secretin and caused mislocalization of YscC even in the presence of wild-type YscW. Hence, YscW interacts with the unassembled YscC protein and facilitates efficient oligomerization, likely at the outer membrane.
VibEmoji: Exploring User-authoring Multi-modal Emoticons in Social Communication (2022)

Emoticons are indispensable in online communications. With users’ growing needs for more customized and expressive emoticons, recent messaging applications begin to support (limited) multi-modal emoticons:, enhancing emoticons with animations or vibrotactile feedback. However, little empirical knowledge has been accumulated concerning how people create, share and experience multi-modal emoticons in everyday communication, and how to better support them through design. To tackle this, we developed VibEmoji, a user-authoring multi-modal emoticon interface for mobile messaging. Extending existing designs, VibEmoji grants users greater flexibility to combine various emoticons, vibrations, and animations on-the-fly, and offers non-aggressive recommendations based on these components’ emotional relevance. Using VibEmoji as a probe, we conducted a four-week field study with 20 participants, to gain new understandings from in-the-wild usage and experience, and extract implications for design. We thereby contribute to both a novel system and various insights for supporting users’ creation and communication of multi-modal emoticons.
Influence of soybean management decisions on the subsequent rice crop's response to nitrogen (2020)

Abstract Little is known about the effects of soybean [ Glycine max (L.) Merr.] management practices on the success of the subsequent rice ( Oryza sativa L.) crop. A study was initiated to determine how rice was affected by the preceding soybean crop's maturity group (MG) and planting date when grown in rotation on silt loam and clay soils. Optimum and late soybean planting dates and MGs (3.5, 4.7, 5.4, and 5.6) were followed by a rice crop. The results differed by soil texture, with the planting date and MG selection of the previous soybean crop more influential to the rice crop produced on a silt loam soil than a clay soil. Rice grown on a clay soil produced a higher grain yield when following a 5.4 MG soybean, whereas the planting date of a previous soybean crop influenced the soil‐N credits measured at rice emergence. On a silt loam soil, the interaction of both planting date and MG of the previous soybean crop influenced the maximal grain yield achieved by the rice crop. When soybean is planted during an optimum planting date, soybean MG has little effect on the successive rice crop. However, when the soybean crop is planted late, a determinate MG should be selected to achieve the highest rice crop total N uptake, maximal grain yield, and reduce the rate of fertilizer‐N needed to achieve 95% relative grain yield. Management techniques should be considered when implementing a soybean–rice rotation to maximize rice grain yield and overall farm profitability.
Direct‐Write Optical Patterning of P3HT Films Beyond the Diffraction Limit (2016)

Doping-induced solubility control is a patterning technique for semiconducting polymers, which utilizes the reduction in polymer solubility upon p-type doping to provide direct, optical control of film topography and doping level. In situ direct-write patterning and imaging are demonstrated, revealing sub-diffraction-limited topographic features. Photoinduced force microscopy shows that doping level can be optically modulated with similar resolution.
Staar Collamer posterior chamber phakic intraocular lens to correct myopia and hyperopia (1998)

In this short-term study, the posterior chamber phakic IOL was predictable, safe, and efficacious in the correction of myopic and hyperopic refractive errors, with good refractive stability. Long-term follow-up is required to validate that the absence of significant complications in most patients is a lasting phenomenon.
Accurate simulation of hip joint range of motion (2003)

This paper presents a hip joint motion simulation method using accurate hip joint center (HJC) and hip range of motion. We calculate the extreme hip joint range of motion centered on the HJC that is located by an automatic calculation algorithm on 3D reconstructed surface models. We make 3D bone surface models from computer tomography or magnetic resonance imaging. The medical objective is to quantify hip kinematics in the function of hip morphology. Since only extreme ranges of motions are evaluated from bones, we can estimate the motions that are restricted by bones impingements by comparing the computed values with real extreme range of motion.
Introduction (2005)

Henry James's fiction is full of death. It drives the plot, colours the mood, and heightens the climaxes of his novels and tales. Among the cast of James's characters are suicidal artists, murderous lovers, adventurous heiresses, romantic consumptives, fallen soldiers, intrusive biographers, and faithful keepers of the flame. Death comes violently by poison, drowning, gunshot, fall, and execution, peacefully at home, or as a gothic spectacle. James gives us some of the most famous hauntings in literature, and by the end of his long career has explored again and again the relationships between the living and the dead. Jamesian death is varied and complex. It is not a passenger, contributing nothing of interest to his novels and tales — how could it be, as if separate from everything else that makes James one of the most critically contested of writers? Death informs James's narrative structures and strategies, his characteristic subjects and styles, and thereby invites the full range of critical approaches that have made James studies such a rich field.KeywordsFinal PageLiterary RealismLate StylePhysical DeathNorth American LiteratureThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
A Brief Description of the NMP ISA and Benchmarks (2005)

The Near Memory Processor (NMP) is a multithreaded vector processor integrated with the memory controller. The NMP works subordinately upon requests from the main processors. The NMP is complementary to the conventional superscalar processors and it is optimized for the bandwidth bounded applications and bit manipulation workloads. A program addressable memory in the NMP, Scratchpad provides an effectively large register set to hold vectors, streams and frequently accessed values. Avoiding saving and restoring the vector registers during context switch, the scratchpad reduces the overhead of the multithreading and enables a simple NMP architectural design. We design an instruction set that includes vector, streaming and bit manipulation instructions. We present the instruction set architecture of the NMP in this report, including register sets, addressing mode and instruction formats. A brief description of the benchmarks is also included. 1 The Near-Memory Processor This doucument briefly describes the ISA of the Near-Memory Processor[3]. Figure 1 presents the NMP in the base line environment of a shared memory multiprocessor. Each memory controller is integrated with one NMP. All address space, including the NMP storage (scratchpad) is shared and can be accessed both by the main (commodity) processors and by the NMPs. The threads that the NMPs execute are called Memory Threads (MT). An MT context includes a set of registers that are described below. Not all these registers need to be saved and restored on context switching. ∗ This work is supported by DARPA Contract NBCHC-02-0056 and NBCH30390004. 1 2
Applying a submicron mismatch model to practical IC design (2002)

A model of the mismatch effect in IC devices is presented that extends the validity of existing models to the sub-micron region. Unlike in previous studies the effect of a finite two dimensional correlation length is taken into account, thus allowing a good reproduction of the differences in device variance that occur for different aspect ratios. The model has been characterized on a 0.75 /spl mu/ CMOS technology and has been implemented in a powerful CAD system for statistical design analysis, thus being of practical utility for IC designers when making critical design considerations and trade-offs. >