gebhart/patrepeval huggingface dataset:
Transformer as a spatially-aware multi-instance learning framework to predict the risk of death for early-stage non-small cell lung cancer (2023)

In computational pathology, training and inference of conventional deep convolutional neural networks (CNN) are usually limited to patches of small sizes (e.g., 256 × 256) sampled from whole slide images. In practice, however, diagnostic and prognostic information could lie within the context of tumor microenvironment across multiple regions, far beyond the scope of individual patches. For instance, the spatial relationship of tumor-infiltrating lymphocytes (TIL) across regions of interest might be prognostic for non-small cell lung cancer (NSCLC). This poses a multi-instance learning (MIL) problem, and a single-patch-driven CNN typically fails to learn spatial information and context between multiple patches, especially their spatial relationship. In this work, we present a cell graph-based MIL framework to predict the risk of death for early-stage NSCLC by aggregating feature representation of TIL-enclosing patches according to their spatial relationship. Inspired by PATCHY-SAN, a graph-embedding framework for CNNs, we use graph kernel-based approaches to embed a bag of patches into a sequence with their spatial information encoded into the sequence order. A transformer model was then trained to aggregate patch-level features based on spatial information. We demonstrate the capability of this framework to predict the likelihood of the patient with NSCLC in two cohorts (n=240) to survive for more than 5 years. The training cohort (n=195) comprised hematoxylin and eosin (H&E)-stained whole slide images (WSI), while the testing cohort (n=45) comprised H&E-stained tumor microarrays (TMA). We show that, with the spatial context of multiple patches encoded as an ordered patch sequence, the performance in the testing cohort of our approach achieves an area under the receiver operating characteristic curve (AUC) of 0.836 (p=0.009; HR=5.62), as opposed to a baseline conventional CNN with an AUC of 0.542 (p=0.105; HR=1.66). The results suggest that the Transformer is a generic spatial information aware MIL framework that can learn the spatial relationship of multiple TIL-enclosing patches from the graph representation of immune cells.
ChemInform Abstract: Novel Redox Cyclization Products Derived from 2‐Acylpyrroles and trans‐ 3‐Bromo‐3,4‐dihydro‐4‐hydroxy‐2,2‐dimethyl‐2H‐chromene‐6‐carbonitrile. (1992)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Minor Morbidity With Emergency Tourniquet Use to Stop Bleeding in Severe Limb Trauma: Research, History, and Reconciling Advocates and Abolitionists (2011)

We found that morbidity was minor in light of major survival benefits consistent with prior reports.
Measurements of the ϒ(1S), ϒ(2S), and ϒ(3S) differential cross sections in pp collisions at s=7TeV (2015)

Differential cross sections as a function of transverse momentum p T are presented for the production of (nS) (n = 1, 2, 3) states decaying into a pair of muons. Data corresponding to an integrated luminosity of 4.9 fb -1 in pp collisions at s = 7 TeV were collected with the CMS detector at the LHC. The analysis selects events with dimuon rapidity |y| < 1.2 and dimuon transverse momentum in the range 10 < p T < 100 GeV. The measurements show a transition from an exponential to a power-law behavior at p T 20 GeV for the three states. Above that transition, the (3S) spectrum is significantly harder than that of the (1S). The ratios of the (3S) and (2S) differential cross sections to the (1S) cross section show a rise as p T increases at low p T , then become flatter at higher p T .
Positive Curvature of theHc2-versus-TcBoundaries in Layered Superconductors (1974)

We have found what we believe to be a universal characteristic of layered superconductors: A positive curvature of the ${H}_{c2}$-versus-${T}_{c}$ boundary. The origins of the effect are believed to be associated with strong anisotropies of the Fermi surface and electronphonon interaction.
Microparticles for controlled growth differentiation factor 6 delivery to direct adipose stem cell‐based nucleus pulposus regeneration (2019)

Currently, there is no effective long-term treatment for intervertebral disc (IVD) degeneration, making it an attractive candidate for regenerative therapies. Hydrogel delivery of adipose stem cells (ASCs) in combination with controlled release of bioactive molecules is a promising approach to halt IVD degeneration and promote regeneration. Growth differentiation factor 6 (GDF6) can induce ASC differentiation into anabolic nucleus pulposus (NP) cells and hence holds promise for IVD regeneration. Here, we optimised design of novel poly(DL-lactic acid-co-glycolic acid) (PLGA)-polyethylene glycol-PLGA microparticles to control GDF6 delivery and investigated effect of released GDF6 on human ASCs differentiation to NP cells. Recombinant human (rh)GDF6 was loaded into microparticles and total protein and rhGDF6 release assessed. The effect of microparticle loading density on distribution and gel formation was investigated through scanning electron microscopy. ASC differentiation to NP cells was examined after 14 days in hydrogel culture by quantitative polymerase chain reaction, histological, and immunohistochemical staining in normoxic and IVD-like hypoxic conditions. RhGDF6 microparticles were distributed throughout gels without disrupting gelation and controlled rhGDF6 release over 14 days. Released GDF6 significantly induced NP differentiation of ASCs, with expression comparable with or exceeding media supplemented rhGDF6. Microparticle-delivered rhGDF6 also up-regulated sulphated glycosaminoglycan and aggrecan secretion in comparison with controls. In hypoxia, microparticle-delivered rhGDF6 continued to effectively induce NP gene expression and aggrecan production. This study demonstrates the effective encapsulation and controlled delivery of rhGDF6, which maintained its activity and induced ASC differentiation to NP cells and synthesis of an NP-like matrix suggesting suitability of microparticles for controlled growth factor release in regenerative strategies for treatment of IVD degeneration.
Influenza Gain-of-Function Experiments: Their Role in Vaccine Virus Recommendation and Pandemic Preparedness (2014)

In recent years, controversy has arisen regarding the risks and benefits of certain types of gain-of-function (GOF) studies involving avian influenza viruses. In this article, we provide specific examples of how different types of data, including information garnered from GOF studies, have helped to shape the influenza vaccine production process-from selection of candidate vaccine viruses (CVVs) to the manufacture and stockpiling of safe, high-yield prepandemic vaccines for the global community. The article is not written to support a specific pro- or anti-GOF stance but rather to inform the scientific community about factors involved in vaccine virus selection and the preparation of prepandemic influenza vaccines and the impact that some GOF information has had on this process.
Lazy task creation: A technique for increasing the granularity of parallel programs. Technical report (1991)

Many parallel algorithms are naturally expressed at a fine level of granularity, often finer than a MIMD parallel system can exploit efficiently. Most builders of parallel systems have looked to either the programmer or a parallelizing compiler to increase the granularity of such algorithms. In this paper, the authors explore a third approach to the granularity problem by analyzing two strategies for combining parallel tasks dynamically at run-time. They reject the simpler load-based inlining method, where tasks are combined based on dynamic load level, in favor of the safer and more robust lazy task creation method, where tasks are created only retroactively as processing resources become available. These strategies grew out of work on Mul-T 17, an efficient parallel implementation of Scheme, but could be used with other languages as well. They describe our Mul-T implementations of lazy task creation for two contrasting machines, and present performance statistics which show the method's effectiveness. Lazy task creation allows efficient execution of naturally expressed algorithms of a substantially finer grain than possible with previous parallel Lisp systems.
S-nitrosothiols regulate cell-surface pH buffering by airway epithelial cells during the human immune response to rhinovirus (2006)

Human rhinovirus infection is a common trigger for asthma exacerbations. Asthma exacerbations and rhinovirus infections are both associated with markedly decreased pH and ammonium levels in exhaled breath condensates. This observation is thought to be related, in part, to decreased activity of airway epithelial glutaminase. We studied whether direct rhinovirus infection and/or the host immune response to the infection decreased airway epithelial cell surface pH in vitro. Interferon-gamma and tumor necrosis factor-alpha, but not direct rhinovirus infection, decreased pH, an effect partly associated with decreased ammonium concentrations. This effect was 1) prevented by nitric oxide synthase inhibition; 2) independent of cyclic GMP; 3) associated with an increase in endogenous airway epithelial cell S-nitrosothiol concentration; 4) mimicked by the exogenous S-nitrosothiol, S-nitroso-N-acetyl cysteine; and 5) independent of glutaminase expression and activity. We then confirmed that decreased epithelial pH inhibits human rhinovirus replication in airway epithelial cells. These data suggest that a nitric oxide synthase-dependent host response to viral infection mediated by S-nitrosothiols, rather than direct infection itself, plays a role in decreased airway surface pH during human rhinovirus infection. This host immune response may serve to protect the lower airways from direct infection in the normal host. In patients with asthma, however, this fall in pH could be associated with the increased mucus production, augmented inflammatory cell degranulation, bronchoconstriction, and cough characteristic of an asthma exacerbation.
Erratum: Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis (2016)

Nature Communications 7: Article number: 12460 (2016); Published: 23 August 2016; Updated: 10 October 2016. The HTML version of this Article incorrectly duplicated the authors S. Louis Bridges, Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan and Lara M.
Tunable 503 ns optical delay of 40 Gbit/s RZ-OOK and RZ-DPSK using a wavelength scheme for phase conjugation to reduce residual dispersion and increase delay (2009)

We demonstrate a method for a tunable optical delay element that allows for minimal residual dispersion and double the relative delay. A tunable delay of 503 ns for 40 Gbit/s return-to-zero on-off keying and return-to-zero differential phase-shift keying is shown with a reduction in residual dispersion of approximately 95%.
Dynamical Isometry and a Mean Field Theory of CNNs: How to Train\n 10,000-Layer Vanilla Convolutional Neural Networks (2018)

In recent years, state-of-the-art methods in computer vision have utilized\nincreasingly deep convolutional neural network architectures (CNNs), with some\nof the most successful models employing hundreds or even thousands of layers. A\nvariety of pathologies such as vanishing/exploding gradients make training such\ndeep networks challenging. While residual connections and batch normalization\ndo enable training at these depths, it has remained unclear whether such\nspecialized architecture designs are truly necessary to train deep CNNs. In\nthis work, we demonstrate that it is possible to train vanilla CNNs with ten\nthousand layers or more simply by using an appropriate initialization scheme.\nWe derive this initialization scheme theoretically by developing a mean field\ntheory for signal propagation and by characterizing the conditions for\ndynamical isometry, the equilibration of singular values of the input-output\nJacobian matrix. These conditions require that the convolution operator be an\northogonal transformation in the sense that it is norm-preserving. We present\nan algorithm for generating such random initial orthogonal convolution kernels\nand demonstrate empirically that they enable efficient training of extremely\ndeep architectures.\n
AXOR12, a Novel Human G Protein-coupled Receptor, Activated by the Peptide KiSS-1 (2001)

A novel human G protein-coupled receptor named AXOR12, exhibiting 81% homology to the rat orphan receptor GPR54, was cloned from a human brain cDNA library. Heterologous expression of AXOR12 in mammalian cells permitted the identification of three surrogate agonist peptides, all with a common C-terminal amidated motif. High potency agonism, indicative of a cognate ligand, was evident from peptides derived from the gene KiSS-1, the expression of which prevents metastasis in melanoma cells. Quantitative reverse transcriptase-polymerase chain reaction was used to study the expression of AXOR12 and KiSS-1 in a variety of tissues. The highest levels of expression of AXOR12 mRNA were observed in brain, pituitary gland, and placenta. The highest levels of KiSS-1 gene expression were observed in placenta and brain. A polyclonal antibody raised to the C terminus of AXOR12 was generated and used to show localization of the receptor to neurons in the cerebellum, cerebral cortex, and brainstem. The biological significance of these expression patterns and the nature of the putative cognate ligand for AXOR12 are discussed.
An array of fully-integrated quadrature TX/RX NMR field probes for MRI trajectory mapping (2016)

In this paper we present fully-integrated field probes for real-time trajectory mapping during magnetic resonance imaging (MRI) experiments. The field probes co-integrate an NMR microcoil and the required transceiver electronics on a single ASIC manufactured in a 0.13μm CMOS technology. Thanks to an on-chip PLL, power amplifier and low-IF quadrature receiver, all connections to and from the chip carry only low frequency signals allowing for an effective reduction of the magnetic coupling between the field probes and the MRI scanner during imaging. The small form factor and low power consumption of 16.5mW allows for the realization of arrays of field probes, which in contrast to single probes enable the correction of higher order field imperfections. Measured trajectory maps acquired with a prototype array consisting of four probes demonstrate the excellent sensor performance achievable using the proposed approach.
RSVP-TE Signaling Extension for LSP Handover from the Management Plane to the Control Plane in a GMPLS-Enabled Transport Network (2010)

In a transport network scenario, Data Plane connections controlled by either a Generalized Multiprotocol Label Switching (GMPLS) Control Plane (Soft Permanent Connections -SPC) or a Management System (Permanent Connections -PC) may independently coexist.The ability of transforming an existing PC into an SPC and vice versa --without actually affecting Data Plane traffic being carried over it --is a requirement.The requirements for the conversion between permanent connections and switched connections in a GMPLS Network are defined in RFC 5493.This memo describes an extension to GMPLS Resource Reservation Protocol -Traffic Engineering (RSVP-TE) signaling that enables the transfer of connection ownership between the Management and the Control Planes.Such a transfer is referred to as a Handover.This document defines all Handover-related procedures.This includes the handling of failure conditions and subsequent reversion to original state.A basic premise of the extension is that the Handover procedures must never impact an already established Data Plane connection.
Characterization of [Nphe1]nociceptin(1‐13)NH2, a new selective nociceptin receptor antagonist (2000)

1.. Nociceptin (orphanin FQ) is a novel neuropeptide capable of inducing a variety of biological actions via activation of a specific G-protein coupled receptor. However, the lack of a selective nociceptin receptor antagonist has hampered our understanding of nociceptin actions and the role of this peptide in pathophysiological states. As part of a broader programme of research, geared to the identification and characterization of nociceptin receptor ligands, we report that the novel peptide [Nphe(1)]nociceptin(1-13)NH(2) acts as the first truly selective and competitive nociceptin receptor antagonist and is devoid of any residual agonist activity. 2. [Nphe(1)]nociceptin(1-13)NH(2) binds selectively to recombinant nociceptin receptors expressed in Chinese hamster ovary (CHO) cells (pK(i) 8.4) and competitively antagonizes the inhibitory effects of nociceptin (i) on cyclic AMP accumulation in CHO cells (pA(2) 6.0) and (ii) on electrically evoked contractions in isolated tissues of the mouse, rat and guinea-pig with pA(2) values ranging from 6.0 to 6.4. 3. [Nphe(1)]nociceptin(1-13)NH(2) is also active in vivo, where it prevents the pronociceptive and antimorphine actions of intracerebroventricularly applied nociceptin, measured in the mouse tail withdrawal assay. Moreover, [Nphe(1)]nociceptin(1-13)NH(2) produces per se a dose dependent, naloxone resistant antinociceptive action and, at relatively low doses, potentiates morphine-induced analgesia. 4. Collectively our data indicate that [Nphe(1)]nociceptin(1-13)NH(2), acting as a nociceptin receptor antagonist, may be the prototype of a new class of analgesics.
Ischaemic myocardial injury and ventricular remodelling (1993)

Journal Article Ischaemic myocardial injury and ventricular remodelling Get access Piero Anversa, Piero Anversa Department of Medicine, New York Medical College, Vosburgh Pavilion – room 302, Valhalla, New York 10595, USA: P Anversa, P Li, X Zhang, G Olivetti, J M Capasso. Correspondence to Dr Anversa. Search for other works by this author on: Oxford Academic PubMed Google Scholar Peng Li, Peng Li Department of Medicine, New York Medical College, Vosburgh Pavilion – room 302, Valhalla, New York 10595, USA: P Anversa, P Li, X Zhang, G Olivetti, J M Capasso. Correspondence to Dr Anversa. Search for other works by this author on: Oxford Academic PubMed Google Scholar Xun Zhang, Xun Zhang Department of Medicine, New York Medical College, Vosburgh Pavilion – room 302, Valhalla, New York 10595, USA: P Anversa, P Li, X Zhang, G Olivetti, J M Capasso. Correspondence to Dr Anversa. Search for other works by this author on: Oxford Academic PubMed Google Scholar Giorgio Olivetti, Giorgio Olivetti Department of Medicine, New York Medical College, Vosburgh Pavilion – room 302, Valhalla, New York 10595, USA: P Anversa, P Li, X Zhang, G Olivetti, J M Capasso. Correspondence to Dr Anversa. Search for other works by this author on: Oxford Academic PubMed Google Scholar Joseph M Capasso Joseph M Capasso Department of Medicine, New York Medical College, Vosburgh Pavilion – room 302, Valhalla, New York 10595, USA: P Anversa, P Li, X Zhang, G Olivetti, J M Capasso. Correspondence to Dr Anversa. Search for other works by this author on: Oxford Academic PubMed Google Scholar Cardiovascular Research, Volume 27, Issue 2, February 1993, Pages 145–157, https://doi.org/10.1093/cvr/27.2.145 Published: 01 February 1993 Article history Received: 11 May 1992 Accepted: 21 July 1992 Published: 01 February 1993
Molecular Flexibility and Bend in Semi‐Rigid Liquid Crystals: Implications for the Heliconical Nematic Ground State (2019)

The N<sub>TB</sub> phase phases possess a local helical structure with a pitch length of a few nanometers and is typically exhibited by materials consisting of two rigid mesogenic units linked by a flexible oligomethylene spacer of odd parity, giving a bent shape. We report the synthesis and characterisation of two novel dimeric liquid crystals, and perform a computational study on 10 cyanobiphenyl dimers with varying linking groups, generating a large library of conformers for each compound; this allows us to present molecular bend angles as probability weighted averages of many conformers, rather than use a single conformer. We validate conformer libraries by comparison of interproton distances with those obtained from solution-based 1D <sup>1</sup> H NOESY NMR, finding good agreement between experiment and computational work. Conversely, we find that using any single conformer fails to reproduce experimental interproton distances. We find the use of a single conformer significantly overestimates the molecular bend angle while also ignoring flexibility; in addition, we show that the average bend angle and flexibility are both linked to the relative stability of the N<sub>TB</sub> phase.
A Study on Acoustical Characteristics of Ear Canal by Earphones (A Derivation of Resonance Correction Filter by Using Transfer Matrix Method) (2012)

This paper attempts to improve the performance of ear-plug type earphones. The transmission characteristics of the ear canal with/without earphones are different. Therefore, the sound quality of the earphone is a little poor compared with audio speaker. In addition, it is well-known that the acoustical characteristics of ear canal vary among individuals. Therefore, we are studying to predict the acoustical characteristics of ear canal with ear-plug type earphones by using transfer matrix method and are studying how to improve the transmission characteristics of the ear canal. In this paper, a method for adjusting the resonance characteristic of the ear canal with earphones to the characteristic of the ear canal of AV speakers without earphones using digital filtering technique is proposed. With this method, the improvement of the sound reproduction performance was verified on the basis of experiments.
Transverse flux permanent magnet motor with double-C stator hoops and flux-concentrated rotor for in-wheel drive electric vehicle (2014)

This paper proposes a novel transverse flux permanent magnet motor (TFPMM) with double-C stator hoops. The proposed TFPMM carries significantly increased power density due to higher coefficient of utilization of the volume compared with the traditional double-side counterparts. The topology, principle and parametric calculation of the TFPMM are described elaborately. The magnetic field and characteristics analysis are conducted by three-dimensional finite element method (3D FEM) including flux density, EMF and winding inductance, and cogging torque are obtained to verify the feasibility of proposed TFPMM design. The mechanism of cogging torque of the proposed double-C stator hoops TFPMM is also analyzed. The results of transient simulation of power density well align with the theoretical analysis, which confirm that the power density is significantly increased due to its higher volumetric utilization ratio.