gebhart/patrepeval huggingface dataset:
Abstract IA02: The application of integrative sequencing for precision oncology (2015)

Abstract Studies of the genomic landscape of human cancers have demonstrated that most solid cancers have a multitude of mutations, a subset of which may be “actionable” with current drugs. Thus, the personalization of therapy for cancer will require molecular characterization of unique and shared genetic aberrations. Patients who have advanced/refractory cancer and are candidates for clinical trials could potentially benefit by identifying eligibility for “targeted” drugs based on the “actionable” genes in their specific tumor. Growing technological advances in genomic sequencing has now made it possible to consider the use of sequence data in a clinical setting. MI-ONCOSEQ initiative brings together expertise at the University of Michigan including clinical oncology, cancer genetics, bioinformatics, clinical pathology, social and behavioral sciences, and bioethics in order to implement clinical cancer sequencing. Our study identifies patients with advanced or refractory cancers that are eligible for clinical trials, consent them to the study, obtain biospecimens (tumor tissue, germline tissue) and store clinical data. The clinical sequencing team processes biospecimens, performs comprehensive sequencing and analysis of tumors to identify point mutations, copy number changes, rearrangements/gene fusions, and aberrant gene expression. Finally, a multi-disciplinary Sequencing Tumor Board deliberates on return of actionable or incidental genomic results. Citation Format: Arul Chinnaiyan. The application of integrative sequencing for precision oncology. [abstract]. In: Proceedings of the AACR Special Conference on Computational and Systems Biology of Cancer; Feb 8-11 2015; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2015;75(22 Suppl 2):Abstract nr IA02.
Ultrasonic imaging of highly scattering media from local measurements of the diffusion constant: Separation of coherent and incoherent intensities (2007)

As classical imaging fails with diffusive media, one way to image a multiple-scattering medium is to achieve local measurements of the dynamic transport properties of a wave undergoing diffusion. This paper presents a method to obtain local measurements of the diffusion constant D in a multiple-scattering medium. The experimental setup consists in an array of programmable transducers placed in front of the multiple-scattering medium to be imaged. By achieving Gaussian beamforming both at emission and reception, an array of virtual sources and receivers located in the near field is constructed. The time evolution of the incoherent component of the intensity backscattered on this virtual array is shown to represent directly the growth of the diffusive halo as sqrt[Dt]. A matrix treatment is proposed to separate the incoherent intensity from the coherent backscattering peak. Once the incoherent contribution is isolated, a local measurement of the diffusion constant is possible. The technique is applied to image the long-scale variations of D in a random-scattering sample made of two parts with a different concentration of cylindrical scatterers. This experimental result is obtained with ultrasonic waves around 3 MHz. It illustrates the possibility of imaging diffusive media from local measurements of the diffusion constant, based on coherent Gaussian beamforming and a matrix "antisymmetrization," which creates a virtual antireciprocity.
Cyanthiwigin AC and AD, Two Novel Diterpene Skeletons from the Jamaican Sponge Myrmekioderma styx (2003)

[structure: see text] Three novel diterpenes, called cyanthiwigins AB (1), AC (2), and AD (3), were isolated from the Jamaican sponge Myrmekioderma styx. Their structures were elucidated by means of 1D and 2D NMR spectroscopic methods. Cyanthiwigin AC (2) and AD (3) represent novel diterpene-type skeletons.
Effect of Water on Hydrolytic Cleavage of Non-Terminal α-Glycosidic Bonds in Cyclodextrins To Generate Monosaccharides and Their Derivatives in a Dimethyl Sulfoxide–Water Mixture (2014)

Hydrolytic cleavage of the non-terminal α-1,4-glycosidic bonds in α-, β-, and γ-cyclodextrins and the anomeric-terminal one in d-maltose was investigated to examine how the cleavage rate for α-, β-, and γ-cyclodextrins is slower than that for d-maltose. Effects of water and temperature were studied by applying in situ (13)C NMR spectroscopy and using a dimethyl sulfoxide (DMSO)-water mixture over a wide range of water mole fraction, xw = 0.004-1, at temperatures of 120-180 °C. The cleavage rate constant for the non-anomeric glycosidic bond was smaller by a factor of 6-10 than that of the anomeric-terminal one. The glycosidic-bond cleavage is significantly accelerated through the keto-enol tautomerization of the anomeric-terminal d-glucose unit into the d-fructose one. The smaller the size of the cyclodextrin, the easier the bond cleavage due to the ring strain. The remarkable enhancement in the cleavage rate with decreasing water content was observed for the cyclodextrins and d-maltose as well as d-cellobiose. This shows the important effect of the solitary water whose hydrogen bonding to other water molecules is prohibited by the presence of the organic dipolar aprotic solvent, DMSO, and which has more naked partial charges and higher reactivity. A high 5-hydroxymethyl-2-furaldehyde (5-HMF) yield of 64% was attained in a non-catalytic conversion by tuning the water content to xw = 0.30, at which the undesired polymerization by-paths can be most effectively suppressed. This study provides a step toward designing a new optimal, earth-benign generation process of 5-HMF starting from biomass.
Juvenile Chondrocytes May Facilitate Disc Repair~!2010-01-08~!2010-04-08~!2010-08-23~! (2010)

Cell transplantation for disc regeneration is a theoretically-attractive alternative to more invasive surgical procedures to treat discogenic pain. Several cell types have been tried in pre-clinical models for this indication, each with relative merits and limitations. Recently, human chondrocytes from prepubertal donors have been shown to be more synthetically active than their adult counterparts and can form scaffold-independent neocartilage in vitro. These features may also be beneficial in the intervertebral discs' challenging environment including high physical pressure and acidity, and low oxygen tension. To test this, we characterized the in vivo disc regeneration potential of juvenile chondrocytes in caudal rat discs. Human juvenile chondrocytes (JCs) were injected into fifteen rats. Fibrin glue without cells served as a control. Tails were imaged with MRI prior to sacrifice and tail discs were processed for histology. MRI data demonstrates that discs injected with fibrin glue alone degenerated over 12 weeks. By contrast, discs injected with JCs maintained their morphology and MRI signal, and displayed a significantly improved MRI index at 12 weeks post-injection. Transplantation of juvenile chondrocytes results in a significant positive outcome compared to that of fibrin glue alone and may provide an ideal allograft for future human studies.
Unprecedented stereochemistry of the electrophilic arylation at chiral phosphorus (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTUnprecedented stereochemistry of the electrophilic arylation at chiral phosphorusToshiyuki Oshiki and Tsuneo ImamotoCite this: J. Am. Chem. Soc. 1992, 114, 10, 3975–3977Publication Date (Print):May 1, 1992Publication History Published online1 May 2002Published inissue 1 May 1992https://pubs.acs.org/doi/10.1021/ja00036a054https://doi.org/10.1021/ja00036a054research-articleACS PublicationsRequest reuse permissionsArticle Views840Altmetric-Citations98LEARN 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
Negative differential gain due to many body effects in self-assembled quantum dot lasers (2011)

The gain spectrum of a quantum dot laser operating at 1300 nm is studied at high carrier densities, corresponding to dot occupancies of ∼8 e-h pairs per quantum dot. A reduction in peak gain with increasing carrier density is observed, attributed to the saturation of peak gain, yet the continuous increase in dephasing acting to broaden the individual quantum dot transitions.
Membrane Chaperone SecDF Plays a Role in the Secretion of Listeria monocytogenes Major Virulence Factors (2013)

Listeria monocytogenes is a Gram-positive human intracellular pathogen that infects diverse mammalian cells. Upon invasion, L. monocytogenes secretes multiple virulence factors that target host cellular processes and promote infection. It has been presumed, but was not empirically established, that the Sec translocation system is the primary mediator of this secretion. Here, we validate an important role for SecDF, a component of the Sec system, in the secretion of several critical L. monocytogenes virulence factors. A ΔsecDF mutant is demonstrated to exhibit impaired membrane translocation of listeriolysin O (LLO), PlcA, PlcB, and ActA, factors that mediate L. monocytogenes phagosomal escape and spread from cell to cell. This impaired translocation was monitored by accumulation of the factors on the bacterial membrane and by reduced activity upon secretion. This defect in secretion is shown to be associated with a severe intracellular growth defect of the ΔsecDF mutant in macrophages and a less virulent phenotype in mice, despite normal growth in laboratory medium. We further show that SecDF is upregulated when the bacteria reside in macrophage phagosomes and that it is necessary for efficient phagosomal escape. Taken together, these data support the premise that SecDF plays a role as a chaperone that facilitates the translocation of L. monocytogenes virulence factors during infection.
Bandwidth Bandit: Quantitative characterization of memory contention (2013)

On multicore processors, co-executing applications compete for shared resources, such as cache capacity and memory bandwidth. This leads to suboptimal resource allocation and can cause substantial performance loss, which makes it important to effectively manage these shared resources. This, however, requires insights into how the applications are impacted by such resource sharing. While there are several methods to analyze the performance impact of cache contention, less attention has been paid to general, quantitative methods for analyzing the impact of contention for memory bandwidth. To this end we introduce the Bandwidth Bandit, a general, quantitative, profiling method for analyzing the performance impact of contention for memory bandwidth on multicore machines. The profiling data captured by the Bandwidth Bandit is presented in a bandwidth graph. This graph accurately captures the measured application's performance as a function of its available memory bandwidth, and enables us to determine how much the application suffers when its available bandwidth is reduced. To demonstrate the value of this data, we present a case study in which we use the bandwidth graph to analyze the performance impact of memory contention when co-running multiple instances of single threaded application.
A Cryo-Free 10 T High-Field Magnet System for a Novel Superconducting Application (2010)

We present the engineering and design aspects of a cryo-free 10 T high-field magnet system for a completely new type of superconducting application. Design criteria and specifications for the racetrack shaped conduction-cooled magnet and the cryostat are discussed and disclosed.
P-599 The use of serum test to detect the LH surge in ultrasound-monitored intrauterine insemination (IUI) significantly increases pregnancy rates. (2023)

Abstract Study question Could a serum test to detect LH surge in ultrasound-monitored IUI cycle improve pregnancy rates? Summary answer Serum test to detect LH surges with ultrasound monitoring during IUI cycle significantly increased pregnancy rates. What is known already IUI is known as the first line of treatment for infertile couples and is usually administered with human chorionic gonadotropin (hCG) before ovulation with clomiphene citrate (CC) or/and human menopausal gonadotropin (hMG) to ovarian known to stimulate. One of the key factor for IUI is that insemination should be performed close to ovulation time, as there are many reports that sperm injection at the ovulation time has a high pregnancy rates. However, there are still few reports on the optimal timing of ovulation for performing IUI. Study design, size, duration The IUI performed from January 2016 through November 2022 (n = 3187) was included in this study. A total of 875 patients underwent the IUI by inferring LH surge with procedure with serum test, while 2312 patients underwent the procedure IUI without the serum test (control). Participants/materials, setting, methods In this study included 3187 IUI cycle were analyzed. Controlled ovarian hyperstimulation was conducted with CC (100 mg/day) and hMG. Patients were divided into two groups with serum test or not test (control). The serum test group was monitored LH surge by inferring LH peak during IUI cycle. When the sufficient follicular size and endometrial thickness had been reached, hCG was administrated and insemination was performed. Pregnancy rates were compared by Chi-squared test. Main results and the role of chance In each group, there were no significantly difference in age (34.4±3.7 vs. 34.7±3.7 years old) and endometrial thickness (8.8±2.2 vs. 8.9±2.2 mm) for IUI cycle condition. The serum test group was significantly higher clinical pregnancy rates compared to control group (19.0 vs. 15.7 % respectively) during IUI cycle (P &amp;lt; 0.05). In addition, patients were classified according to the history of at least one or more failed IUI cycle. The clinical pregnancy rates was significantly higher in the serum test group than control group (21.6 vs. 10.8 % respectively) who history of at least one or more failed IUI cycle (P &amp;lt; 0.001). Limitations, reasons for caution A limitation of this study has a too small size of the intervention group compared with the control group. Wider implications of the findings In our results, the serum test group had a significantly higher clinical pregnancy rates than the control group. Therefore, detecting a surge in LH with a serum test during the IUI cycle could predict the optimal timing of ovulation and thus increase the pregnancy rates. Trial registration number not applicable
Scaling the Ferroelectric Field Effect Transistor (2005)

The scaling of the ferroelectric field effect transistor (FeFET) is studied by utilizing transistor model simulation (BSIM3v3) and analytic expressions, and is compared to the scaling of the MOSFET. Two scaling approaches are discussed—"variable gate stack scaling," that requires changing the gate stack, and "constant gate stack scaling," that leaves the gate stack unchanged. The material parameters were assumed fixed throughout the scaling procedure.
Leveraging Behavioral Data to Improve Workplace Productivity (2020)

Information workers spend significant amounts of their time managing personal information such as communications, documents and tasks. A recent study reported that the average information worker spends an estimated 28 percent of the workweek managing e-mail and nearly 20 percent looking for internal information or tracking down colleagues who can help with specific tasks. This highlights the potential value intelligent technologies could provide by realizing faster and more effective collaboration and information sharing. The use of artificial intelligence in online services has been steadily increasing. Over the past couple of years, we have worked on techniques for understanding user interaction in communication, information sharing and task management to create new intelligence experiences that can help us be more productive. In this talk, I will present an overview of this line of research.
Ensemble Learning Methods for Binary Classification with Multi-modality within the Classes (2015)

We consider binary classification problems where each of the two classes show multi-modal distribution in the feature space. Inspired by existing ensemble learning methods for multi-class classification, we develop ensemble learning methods for binary classification that make use of the bipartite nature of the positive and negative modes in the data. By constructing ensembles that make use of the multi-modal structure within the two classes, as opposed to using random samples, we are able to ensure sufficient diversity among the classifiers and adequate representation of the modes in the learning of the classifiers. We demonstrate the effectiveness of the proposed ensemble learning methods in comparison with existing approaches over a synthetic dataset and a real-world application involving global lake monitoring, over a broad range of base classifiers.
Experimental verifications of offshore marine substation for grid-connection of wave energy farm (2013)

An offshore marine substation has been designed and constructed for grid-connection of a wave energy farm. The substation will be deployed 2 km off the Swedish West coast, on the seabed at a depth of 25 m. Before the deployment, the substation electrical circuit has been tested in the laboratory. The functionality and total substation efficiency have been evaluated at different voltage levels. A synchronous generator with variable speed control has been programmed to generate a similar voltage output as a single wave energy converter. The generator output has been connected to the substation and power transferred to the local grid at unity power factor. The impact on the total efficiency by adding a DC/DC boost converter is also discussed. The conducted experiments verify the functionality of the marine substation before deployment.
Stereospecific styrene polymerization and ethylene–styrene copolymerization with titanocenes containing a pendant amine donor (2010)

Abstract A series of monocyclopentadienyl titanium complexes containing a pendant amine donor on a Cp group ( A = CpTiCl 3 , B = Cp N TiCl 3 , C = Cp N TiCl 2 TEMPO, for Cp = C 5 H 5 , Cp N = C 5 H 4 CH 2 CH 2 N(CH 3 ) 2 , and TEMPO = 2,2,6,6‐tetramethylpiperidine‐ N ‐oxyl) are investigated for styrene homopolymerization and ethylene–styrene (ES) copolymerization. When activated by methylaluminoxane at 70 °C, complexes with the amine group ( B and C ) are active for styrene homopolymerization and afford syndiotactic polystyrene (sPS). The copolymerizations of ethylene and styrene with B and C yield high‐molecular weight ES copolymer, whereas complex A yields mixtures of sPS and polyethylene, revealing the critical role that the pendant amine has on the polymerization behavior of the complexes. Fractionation, NMR, and DSC analyses of the ES copolymers generated from B and C suggest that they contain sPS. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 1579–1585, 2010
Gate capacitance of cylindrical nanowires with elliptical cross-sections (2011)

We investigate gate capacitance of cylindrical nanowires with elliptical cross-sections because most fabricated Si nanowires have elliptical cross-sections. We derive an exact result for the capacitance of confocal elliptical capacitors and an approximate expression for the capacitance of conformal elliptical capacitors. Using numerical simulations for conformal elliptical capacitors, we show that the analytical results for the confocal and conformal elliptical capacitors are within 5% of the numerical values for eccentricity &amp;lt;0.85. We also provide correction factors to the analytical results that match the numerical conformal elliptical capacitances to within 5% for all values of eccentricity.
An Expansible Aortic Ring For A Physiological Approach Of Aortic Valve Repair (2008)

status: Published
Supplementary Figure 1 from Direct Metabolic Interrogation of Dihydrotestosterone Biosynthesis from Adrenal Precursors in Primary Prostatectomy Tissues (2023)

&lt;p&gt;Figure S1. Validation of a mixed substrate approach to track 5α-reductase activity by LC-MS/MS.&lt;/p&gt;
Real-time continuous action detection and recognition using depth images and inertial signals (2017)

This paper presents an approach to detect and recognize actions of interest in real-time from a continuous stream of data that are captured simultaneously from a Kinect depth camera and a wearable inertial sensor. Actions of interest are considered to appear continuously and in a random order among actions of non-interest. Skeleton depth images are first used to separate actions of interest from actions of non-interest based on pause and motion segments. Inertial signals from a wearable inertial sensor are then used to improve the recognition outcome. A dataset consisting of simultaneous depth and inertial data for the smart TV actions of interest occurring continuously and in a random order among actions of non-interest is studied and made publicly available. The results obtained indicate the effectiveness of the developed approach in coping with actions that are performed realistically in a continuous manner.
Total Synthesis of Altohyrtin A (Spongistatin 1): Part 1 (1998)

The most active compound of the extraordinarily cytotoxic spongipyrans, spongistatin 1, isolated from marine sponges, appeared to be identical to altohyrtin A. The total synthesis of this macrolide has now firmly established the relative and absolute stereochemistry proposed by Kitagawa (see picture below), and has also verified that altohyrtin A and spongistatin 1 are identical.
Cardiac MR elastography using reduced‐FOV, single‐shot, spin‐echo EPI (2017)

This pilot volunteer study demonstrated that rFOV cardiac MRE has the capability to reduce ghosting and to improve image quality in both MRE magnitude images and stiffness maps. Magn Reson Med 80:231-238, 2018. © 2017 The Authors Magnetic Resonance in Medicine published by Wiley Periodicals, Inc. on behalf of International Society for Magnetic Resonance in Medicine. This is an open access article under the terms of the Creative Commons Attribution NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.
Deducing trip related information from flickr (2009)

Uploading tourist photos is a popular activity on photo sharing platforms. These photographs and their associated metadata (tags, geo-tags, and temporal information) should be useful for mining information about the sites visited. However, user-supplied metadata are often noisy and efficient filtering methods are needed before extracting useful knowledge. We focus here on exploiting temporal information, associated with tourist sites that appear in Flickr. From automatically filtered sets of geo-tagged photos, we deduce answers to questions like "how long does it take to visit a tourist attraction?" or "what can I visit in one day in this city?" Our method is evaluated and validated by comparing the automatically obtained visit duration times to manual estimations.