gebhart/patrepeval huggingface dataset:
Supplementary Video2 from Intraductal Transplantation Models of Human Pancreatic Ductal Adenocarcinoma Reveal Progressive Transition of Molecular Subtypes (2023)

&lt;p&gt;Confocal z-stack imaging of immunofluorescent (IF) images of mStrawberry-hM1A grafts 2 weeks after IGO transplantation&lt;/p&gt;
Technical perspective: DFI: The Data Flow Interface for High-Speed Networks (2022)

Optimizing data movement has always been one of the key ways to get a data processing system to perform efficiently. Appearing under different disguises as computers evolved over the years, the issue is today as relevant as ever. With the advent of the cloud, data movement has become the bottleneck to address in any data processing system. In the cloud, compute and storage are typically disaggregated, with a network in between. In addition, cloud systems are scale-out, i.e., performance is obtained by parallelizing across machines, which also involves network communication. And while it is possible to use machines with large amounts of memory, the pricing models and the virtualized nature of the cloud tends to favor clusters of smaller computing nodes. Nowadays, the problem of optimizing data movement has become the problem of using the network as efficiently as possible.
A tautomeric ligand enables directed C‒H hydroxylation with molecular oxygen (2021)

Hydroxylation of aryl carbon-hydrogen bonds with transition metal catalysts has proven challenging when oxygen is used as the oxidant. Here, we report a palladium complex bearing a bidentate pyridine/pyridone ligand that efficiently catalyzes this reaction at ring positions adjacent to carboxylic acids. Infrared, x-ray, and computational analysis support a possible role of ligand tautomerization from mono-anionic (L,X) to neutral (L,L) coordination in the catalytic cycle of aerobic carbon-hydrogen hydroxylation reaction. The conventional site selectivity dictated by heterocycles is overturned by this catalyst, thus allowing late-stage modification of compounds of pharmaceutical interest at previously inaccessible sites.
Uncertainties in Sampled Data Systems (1989)

The contributions of this paper are threefold. We first explore the differences in uncertainty representations and control designs between continuous time systems and discrete time systems, particularly the high frequency interpretation does not work for discrete time systems. It is shown that uncertainties appeared in sampled data systems may be highly structured, however they do not fall into any category which is currently available in the literature. Secondly, we define a measure on these uncertainties which confines a neighborhood to the nominal model in terms of frequency content, and then we propose a control design method which guarantees the stability of the closed loop system in the face of uncertainties. Last, we consider a generalization of a classical continuous time approach in representing the multiplicative uncertainty to sampled data systems by using a slightly modified sampler and present a method to calculate a frequency bound on the uncertainty in sampled data systems.
Toxicological Profiling of Highly Purified Single‐Walled Carbon Nanotubes with Different Lengths in the Rodent Lung and Escherichia Coli (2018)

Carbon nanotubes (CNTs) exhibit a number of physicochemical properties that contribute to adverse biological outcomes. However, it is difficult to define the independent contribution of individual properties without purified materials. A library of highly purified single-walled carbon nanotubes (SWCNTs) of different lengths is prepared from the same base material by density gradient ultracentrifugation, designated as short (318 nm), medium (789 nm), and long (1215 nm) SWCNTs. In vitro screening shows length-dependent interleukin-1β (IL-1β) production, in order of long > medium > short. However, there are no differences in transforming growth factor-β1 production in BEAS-2B cells. Oropharyngeal aspiration shows that all the SWCNTs induce profibrogenic effects in mouse lung at 21 d postexposure, but there are no differences between tube lengths. In contrast, these SWCNTs demonstrate length-dependent antibacterial effects on Escherichia coli, with the long SWCNT exerting stronger effects than the medium or short tubes. These effects are reduced by Pluronic F108 coating or supplementing with glucose. The data show length-dependent effects on proinflammatory response in macrophage cell line and antibacterial effects, but not on collagen deposition in the lung. These data demonstrate that over the length scale tested, the biological response to highly purified SWCNTs is dependent on the complexity of the nano/bio interface.
AVIS en réponse à la saisine HCB - dossier 2020-172. Paris, le 06 septembre 2021 (2021)

Le Haut Conseil des biotechnologies (HCB) a été saisi le 22 juin 2021 par les autorités compétentes françaises (Ministère de l'Agriculture et de l'Alimentation) d'une demande d'avis relative au dossier EFSA-GMO-NL-2020-172 de demande d'autorisation de mise sur le marché du maïs génétiquement modifié DP915635 à des fins d'importation, transformation et alimentation humaine et animale. Ce dossier a été déposé par la société Pioneer Hi-Bred International, Inc. auprès des autorités compétentes néerlandaises sur le fondement du règlement (CE) n° 1829/2003. Dans le cadre de ce règlement, l'évaluation des dossiers de demande de mise sur le marché est confiée à l'Autorité européenne de sécurité des aliments (EFSA). Les Etats membres disposent de trois mois pour envoyer leurs commentaires à l'EFSA en contribution à l'évaluation du dossier. Dans ce contexte, le HCB est invité à proposer des commentaires à destination de l'EFSA au plus tard le 07 septembre 2021.
In Vivo Evaluation of the Nimbus Axial Flow Ventricular Assist System (1993)

Continuing in vivo trials are being conducted at the University of Pittsburgh using the Nimbus axial flow blood pump (AxiPump). To date, 14 sheep experiments have been performed to address several issues related to short-term support. Six acute experiments (< 6 hr) have been performed to assess hemodynamics related to speed regulation and to determine anatomic placement of the pump and cannulae. Eight short-term survival studies lasting up to 6 days have been performed to evaluate biocompatibility and system reliability, and to establish clinical management protocols. The AxiPump has been used as a left ventricular assist device (LVAD), right ventricular assist device (RVAD), and biventricular assist device (BiVAD) with left ventricular and right atrial cannulation. The AxiPump has demonstrated the ability to assume complete support of either the pulmonary or systemic circulation, or both. We have determined that sufficient surgical access may be obtained through left lateral thoracotomy for both LVAD and RVAD insertion. In the absence of post operative anticoagulation therapy, we have detected subclinical renal cortical infarctions in 6 of 8 short-term animals. Thrombus deposition has been observed at the ventricular cannula tip in 4 of 8 cases--necessitating design changes. Two short-term experiments have been terminated because of bleeding--one due to inflow cannula obstruction and one due to cannula failure. Plasma free hemoglobin levels were all below 15 mg/dl, except for one case complicated by inflow obstruction.(ABSTRACT TRUNCATED AT 250 WORDS)
Microstructure of epitaxial SrRuO3 films on Si(001) substrates (2002)

Abstract The microstructure of pulsed-laser-deposited SrRuO3 films on Si(001) with SrO buffer layers has been studied by means of high-resolution electron microscopy and energy-dispersive X-ray spectroscopy. It was found that good epitaxial growths of the SrO buffer layers and the subsequent SrRuO3 films were achieved on the Si(001) substrates. Multiple domains were formed in the SrRuO3 films with domain boundaries nearly perpendicular to the interface between the SrRuO3 films and the SrO buffer layers. A high density of planar defects, such as twins, stacking faults and antiphase boundaries, were formed along the (022) lattice plane of the SrRuO3 films. Lattice strains in the constituting layers were investigated by means of fast Fourier transformation of local regions in the high-resolution images. It was found that, close to the interface between the SrRuO3 films and the SrO buffer layers, both the layers were elastically strained in the opposite sense. The structure of coherent twin boundary in the SrRuO3 films was determined using a computer-aided high-resolution image simulation method. The comparison between the simulated and the experimental images indicated that the Sr-O plane constituted the twin boundary.
Stroke Extraction as a Basis for Structural Analysis of Document Images by Modified MCR Expression (1994)

Since stroke components are the most basic structural featurea of patterns like ch.aracters or linea in im.ages. Prom a tiieui point of bein.g applicable to docum.en.t image understandin.g, it ia necessary to provide a good represen.tation th.at can. express such features, so th,at an interpretation of im.ages can be facilita.ted. Th.is article pre,qen.ta a new tech,n.ique used for ezpressin.g bin.ary doczim.ent im.agea. The proposed technique derieloped from the Minimum. Coverin.g Run (MCR) expression to extract stroke components of patterns in, images accurately. 1
Specifying data availability in multi-device file systems (1990)

Article Free Access Share on Specifying data availability in multi-device file systems Authors: John Wilkes Hewlett-Packard Laboratories, Palo Alto, CA Hewlett-Packard Laboratories, Palo Alto, CAView Profile , Raymie Stata Hewlett-Packard Laboratories, Palo Alto, CA Hewlett-Packard Laboratories, Palo Alto, CAView Profile Authors Info & Claims EW 4: Proceedings of the 4th workshop on ACM SIGOPS European workshopSeptember 1990Pages 1–4https://doi.org/10.1145/504136.504139Published:03 September 1990Publication History 2citation94DownloadsMetricsTotal Citations2Total Downloads94Last 12 Months12Last 6 weeks4 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Publisher SiteeReaderPDF
The Continually Evolving Clostridium difficile Species (2012)

Clostridium difficile is a spore-forming Gram-positive bacterium that causes chronic diarrhea and sometimes life-threatening disease mainly in elderly and hospitalized patients. The reported incidence of C. difficile infection has changed dramatically over the last decade and has been related to the emergence of distinct clonal lineages that appear more transmissible and cause more severe infection. These include PCR ribotypes 027, 017 and more recently 078. Population biology studies using multilocus sequence typing and whole-genome comparisons has helped to define the C. difficile species into four clonal complexes that include PCR ribotypes 027, 017, 078 and 023, as well as a general grouping of most other PCR ribotypes. Further analysis of strains from diverse sources and geographical origins reveal significant microdiversity of clonal complexes and confirms that C. difficile is continuing to evolve. The study of C. difficile represents a real-time global evolutionary experiment where the pathogen is responding to a range of selective pressures created by human activity and practices in healthcare settings. The advent of whole-genome sequencing coupled with phylogeny (phylogeography and phylohistory) will provide unprecedented detail on the local and global emergence and disappearance of C. difficile clones, and facilitate more rational approaches to disease control. This review will highlight the emergence of virulent C. difficile clones and our current understanding of molecular epidemiology of the species.
Abstract IA21: AR is ablated: Now what? Targeting the double-negative phenotype (2018)

Abstract Background/Introduction: Androgen receptor (AR) signaling is a distinctive feature of prostate cancer (PC) and represents the major therapeutic target for treating metastatic prostate cancer (mPC). Though highly effective, AR antagonism can produce tumors that bypass a functional requirement for AR, often through neuroendocrine (NE) transdifferentiation. Through the molecular assessment of mPCs over two decades, we find that a phenotypic shift has occurred in mPC with the emergence of an AR-null NE-null phenotype. We sought to identify drivers of these “double-negative” PCs (DNPC), with the ultimate objective of developing therapeutic strategies. Methods: We used genome-wide profiling of copy number (array CGH), mutations (whole-exome sequencing-WES), and gene expression (RNA-seq) to compare the molecular landscapes of AR-active PC (ARPC), NEPC, and DNPC in tumors obtained from 84 consecutive men with mPC undergoing a rapid autopsy. We developed model systems including DNPC patient-derived xenografts (PDX) and cell lines that are devoid of AR activity and lack NE features. Using these models, we tested therapeutics hypothesized to inhibit the activity of pathways preferentially active in DNPC. Results: In the era prior to the approval of the AR pathway antagonists enzalutamide and abiraterone, most CRPCs were ARPCs (85%) with rare NEPCs (10%) and rarer DNPCs (5%). In the contemporary era (2012-2016), we observed a shift in tumor phenotypes with a higher representation of DNPCs. Gene expression programs of the tumors classified by IHC supported these distinct subtypes. DNPCs did not exhibit GR activity or PI3K/AKT activation but were notable for high MAPK and FGF pathway activity. Models systems recapitulated these findings. FGFR antagonists differentially repressed the growth of DNPC tumors in vitro and in vivo. Conclusions: Though the majority of mPCs that resist AR targeting retain AR signaling, an increasingly common subtype of mPC exhibits a DNPC phenotype. Our results indicate that at least a subset of these DNPCs are driven by FGF signaling and MAPK activation. Targeting the FGF axis may represent a therapeutic approach for those cancers resistant to AR-directed therapies and may circumvent treatment resistance if combined with initial AR pathway blockade. Citation Format: Colm Morrissey, Eric G. Bluemn, Ilsa M. Coleman, Jared M. Lucas, Roger T. Coleman, Robin Tharakan, Daniella Bianchi-Frias, Ruth F. Dumpit, Arja Kaipainen, Alexandra N. Corella, Yu Chi Yang, Michael D. Nyquist, Elahe Mostaghel, Xiaotun Zhang, Eva Corey, Lisha G. Brown, Holly M. Nguyen, Michael Schweizer, Lawrence D. True, Paul S. Rennie, Robert L. Vessella, Peter S. Nelson. AR is ablated: Now what? Targeting the double-negative phenotype [abstract]. In: Proceedings of the AACR Special Conference: Prostate Cancer: Advances in Basic, Translational, and Clinical Research; 2017 Dec 2-5; Orlando, Florida. Philadelphia (PA): AACR; Cancer Res 2018;78(16 Suppl):Abstract nr IA21.
Preparation of ZnO Films by Low-pressure Organometallic Chemical Vapor Deposition (1993)

Abstract Using zinc acetate as a precursor, ZnO films have been prepared on sapphire () substrates at pressures of 2.7 × 10−2 and 6.7 × 10−3 Pa. The deposition rate increased with substrate temperature. The crystal structure of ZnO film was dependent on the substrate temperature and H2O partial pressure. In particular, oriented () ZnO films have been formed at 350 °C at 2.7 × 10−2 Pa.
Designing for ubiquity: the perception of privacy (2003)

Ubicomp researchers have long argued that privacy is a design issue, and it goes without saying that successful design requires that we understand the desires, concerns, and awareness of the technology's users. Yet, because ubicomp systems are relatively unusual, too little empirical research exists to inform designers about potential users. Complicating design further is the fact that ubicomp systems are typically embedded or invisible, making it difficult for users to know when invisible devices are present and functioning. As early as 1993, ubicomp researchers recognized that embedded technology's unobtrusiveness both belies and contributes to its potential for supporting potentially invasive applications. Not surprisingly, users' inability to see a technology makes it difficult for them to understand how it might affect their privacy. Unobtrusiveness, nevertheless, is a reasonable goal because such systems must minimize the demands on users. To investigate these issues further, I conducted an ethnographic study of what I believe is the first US eldercare facility to use a sensor-rich environment. Our subjects were normal civilians (rather than ubicomp researchers) who lived or worked in a ubiquitous computing environment. We interviewed residents, their family members, and the facility's caregivers and managers. Our questions focused on how people understood both the ubiquitous technology and its effect on their privacy. Although the embedded technology played a central role in how people viewed the environment, they had a limited understanding of the technology, thus raising several privacy, design, and safety issues.
The role of the 2-methyl substituent in governing stereoselective formation of the E isomer in the synthesis of 4-hydroxy-2-methyltamoxifen (1-{4-[2-(di-methylamino)ethoxy]phenyl}-1-(4-hydroxy-2-methylphenyl)-phenylbut-1-ene) (1988)

Syntheses of 4-hydroxy-2-methyltamoxifen (1-{4-[2-(dimethylamino)ethoxy]phenyl}-1-(4-hydroxy-2methylphenyl)-2-phenylbut-1-ene) by dehydration of diastereoisomeric triphenylbutan-1-ol precursors were compared. Crystal structures of these diastereoisomers have now both been determined. Acid treatment of either diastereoisomer gave predominantly the E olefin (8:1 trans–cis), consistent with a mechanism proceedings by way of a common carbenium ion intermediate whereby the 2-methyl group destabilises the transition state that would lead to Z-olefin. A synthesis of 4-hydroxy-2,3,5-trimethyltamoxifen proceeded similarly. The (E)-4-hydroxy-2-methyltamoxifen was more resistant to isomerisation into a Z–E mixture than was 4-hydroxytamoxifen but a 3:1 trans–cis equilibirum mixture could be obtained. The 4-hydroxy-2,3,5-trimethyltamoxifen gave the same ratio of isomers at equilibrium as did the 4-hydroxy-2-methyl compound but it isomerised at a faster rate. It was shown from the 1H n.m.r. spectrum of the carbenium ion derived by trifluoromethanesulphonic acid treatment of the model compound 1-(4-methoxy-2-methylphenyl)-1-(4-methoxyphenyl)-2-phenylbut-1-ene that, in these systems, the aryl ring that is best able to stabilise the positively charged carbon atom is preferred cis to the 2-phenyl ring in the alkene product.
Social media as a measurement tool of depression in populations (2013)

Depression is a serious and widespread public health challenge. We examine the potential for leveraging social media postings as a new type of lens in understanding depression in populations. Information gleaned from social media bears potential to complement traditional survey techniques in its ability to provide finer grained measurements over time while radically expanding population sample sizes. We present work on using a crowdsourcing methodology to build a large corpus of postings on Twitter that have been shared by individuals diagnosed with clinical depression. Next, we develop a probabilistic model trained on this corpus to determine if posts could indicate depression. The model leverages signals of social activity, emotion, and language manifested on Twitter. Using the model, we introduce a social media depression index that may serve to characterize levels of depression in populations. Geographical, demographic and seasonal patterns of depression given by the measure confirm psychiatric findings and correlate highly with depression statistics reported by the Centers for Disease Control and Prevention (CDC).
Infrared spectroscopic method for uranium isotopic analysis (2020)

A high performance infrared (HPIR) system was developed and demonstrated for the infrared absorption analysis of <sup>235</sup>U and <sup>238</sup>U isotopes in uranium hexafluoride gas samples. Sweeping the quantum cascade laser light source over the spectral range and sampling via a high-rate analog-to-digital converter provided 0.0005 cm<sup>-1</sup> spectral resolution, which allowed for high-precision measurements of the isotopic peak shift. A data analysis method was developed using principal component analysis to predict the isotope weight % content of 235U. The HPIR precision, accuracy, and error were evaluated for a wide range of isotopic ratio samples (0.287 – 93.7 weight % <sup>235</sup>U), and the results were compared to the International Target Values (ITVS) set forth by the International Atomic Energy Agency (IAEA) for non-destructive and destructive analytical techniques. The method meets or surpasses the IAEA ITVs for non-destructive analysis of samples with isotopic content of depleted to highly enriched. The results also demonstrated the capability of the HPIR system to correctly predict the <sup>235</sup>U weight % content of a mislabeled sample whose isotopic distribution was validated by mass spectroscopic measurements. The HPIR measurement is nondestructive and, thus, allows for confirmatory analyses of the exact sample at a designated IAEA lab if higher-resolution or a certified analysis is needed.
Pose-conditioned joint angle limits for 3D human pose reconstruction (2015)

Estimating 3D human pose from 2D joint locations is central to the analysis of people in images and video. To address the fact that the problem is inherently ill posed, many methods impose a prior over human poses. Unfortunately these priors admit invalid poses because they do not model how joint-limits vary with pose. Here we make two key contributions. First, we collect a motion capture dataset that explores a wide range of human poses. From this we learn a pose-dependent model of joint limits that forms our prior. Both dataset and prior are available for research purposes. Second, we define a general parametrization of body pose and a new, multi-stage, method to estimate 3D pose from 2D joint locations using an over-complete dictionary of poses. Our method shows good generalization while avoiding impossible poses. We quantitatively compare our method with recent work and show state-of-the-art results on 2D to 3D pose estimation using the CMU mocap dataset. We also show superior results using manual annotations on real images and automatic detections on the Leeds sports pose dataset.
Identifying Cellular Targets of Small-Molecule Probes and Drugs with Biochemical Enrichment and SILAC (2011)

Sequencing of the human genome in the last decade has not yet led to a concomitant increase in the numbers of novel drug targets. While the pharmaceutical industry has invested heavily in improving drugs for existing protein targets, it has not tended toward a similar investment in experimental approaches to identify cellular targets of drugs. It is striking that the targets of numerous widely used FDA-approved drugs remain unknown. The development of robust, unbiased methods for target identification would greatly enhance our understanding the mechanisms-of-action of small molecules. Cell-based phenotypic screens followed by unbiased target identification have the potential to identify novel combinations of small molecules and their protein targets, shed light on drug polypharmacology, and enable unbiased screening approaches to drug discovery. Classical biochemical enrichment with immobilized small molecules has been used for over four decades but has been limited by issues concerning specificity and sensitivity. The application of mass spectrometry-based quantitative proteomics in combination with these affinity reagents has proven to be especially useful in addressing these common issues in affinity purification experiments. We describe the use of SILAC in identifying proteins that bind small-molecule probes and drugs in a cellular context.
Planning sequences of squeeze-grasps to orient and grasp polygonal objects (2018)

Computer Science Department