gebhart/patrepeval huggingface dataset:
SIMON: open-source knowledge discovery platform (2020)

Abstract Data analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of the biological datasets, but necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software SIMON to facilitate the application of 180+ state-of-the-art machine learning algorithms to high-dimensional biomedical data. With an easy to use graphical user interface, standardized pipelines, automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.
Tolerance induction to self antigens by peripheral dendritic cells (2002)

It has been suggested, but not formally demonstrated, that peripheral dendritic cells (DC) alone are capable of tolerance induction by clonal deletion and/or anergy. To resolve such an issue, it is important to develop in vivo systems where DC are the only cells capable of presenting antigen and where a T cell population with a known antigen specificity can be followed. Here we use a transgenic murine model, which expresses the influenza virus hemagglutinin (HA) on B cells and on CD8alpha(+) and CD8alpha(-) DC but not on macrophages. If these mice are on a RAG(-/-) background, one has a model in which only DC present the HA antigen. In these mice, HA-specific T cells are deleted very efficiently in the thymus and those remaining in the periphery cannot respond to further antigenic stimulation in vitro and cannot eliminate antigen in vivo. By performing adoptive transfers, we show for the first time that self-antigen presentation exclusively by peripheral DC results in very efficient clonal deletion of the majority of antigen-specific T cells with the remaining ones in an anergic state. This model will permit us to further address the mechanisms by which DC tolerize or prime T cells and to investigate whether anergy induction by DC is similar to anergy induction by B cells.
Systematic development of bombesin/gastrin-releasing peptide antagonists. (1992)

Several families of very potent bombesin (Bn) receptor antagonist analogues have recently been developed and their biological potencies evaluated in a number of in vitro systems including guinea pig and rat pancreatic acini and Swiss 3T3 cells. These studies showed that analogues can exhibit diverse properties ranging from full antagonists, partial agonists, or full agonists depending on the assay system and animal species employed. We have developed two classes of more potent, shorter chain antagonists based on [psi CH2NH(13-14)]Bn(6-14) and desMet14Bn(6-13)NH2 structures. [D-Phe6 psi Leu13-Leu14] Bn(6-14)NH2 was a potent antagonist (Ki 6nM) in Swiss 3T3 cells and guinea pig acini but exhibited 10% partial agonist activity and lower binding affinity (Ki 60 nM) in rat acini. The partial agonism could be eliminated by using p-Cl-Phe or D-Phe at the C-terminus and partially eliminated using D-4-Cl-Phe in position 6. With the antagonist [D-Phe6]Bn(6-13)NH2 (Ki 96 nM), alkyl substituents on the amide group increased affinity 25-fold with the propylamide being the most potent peptide (Ki 4 nM) in 3T3 cells or guinea pig acini. It did, however, have high 40% partial agonist activity in rat acini. Alkyl esters or hydrazide derivatives were, in contrast, pure antagonists in all systems tested with [D-Phe6]Bn(6-13)OMe having the highest affinity in all systems and also excellent in vivo properties. All of the potent antagonists examined had little affinity for neuromedin B--preferring bombesin receptors, which had entirely new ligand structure-activity relationships.(ABSTRACT TRUNCATED AT 250 WORDS)
Relationship of Serum Antibody to Attachment Level Patterns in Young Adults with Juvenile Periodontitis or Generalized Severe Periodontitis (1987)

The goal of this study was to relate attachment loss patterns in early onset periodontitis subjects (juvenile periodontitis n = 47 and severe (generalized) periodontitis n = 52) with antibody reactivities to 25 bacterial strains which were suspected periodontal pathogens. The 25 antibody reactivities were screened by correlation analysis. Eleven strains were found to be significantly related to attachment loss. Using these 11 reactivities, stepwise multiple linear regression with plaque and age as covariates was used to further relate the reactivities within each subject group. Plaque was significantly related to the number of teeth with slight, moderate, or severe attachment loss. A significant inverse relationship was found between antibody reactivity with Haemophilus actinomycetemcomitans Y4 and the number of teeth having slight or moderate attachment loss. Similarly a significant inverse relationship between antibody reactivity with Bacteroides gingivalis and the number of teeth having moderate or severe attachment loss was found. The inverse relationship between the two antibody reactivities and attachment loss patterns were independent of the positive relationship of plaque. These relationships suggest that the failure to mount a substantial antibody response to these organisms leads to greater and more widespread periodontal disease in early onset periodontitis subjects.
Polymorphonuclear leukocyte responses to monosodium urate crystals: modification by adsorbed serum proteins. (1980)

The effects of protein absorption to monosodium urate monohydrate (MSU) crystals on crystal-induced lysosomal enzyme release from human neutrophils were studied. Native crystals produced prompt release of both lysosomal and cytoplasmic enzymes, suggesting that they are directly membranolytic for the neutrophil. When albumin, IgM, or beta-lactoglobulin were adsorbed to MSU crystals, lysis was blocked and lysosomal enzyme release was negligible. Prior incubation of crystals with 20% human serum or adsorption of IgG resulted in inhibition of lysis but enhancement of lysosomal enzyme liberation. This non-cytolytic lysosomal enzyme release induced by IgG-coated crystals may be important in the pathogenesis of acute gouty arthritis.
Recognition and Response in Plant PAMP ‐Triggered Immunity (2012)

Abstract Pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI) describes the first events after pathogen invasion, whereby the plant identifies the presence of an invader and mounts a response. A race ensues in which the pathogen deploys its array of virulence molecules that act in opposition to host defence mechanisms and promote establishment of a pathogenic niche. Since the seminal work identifying the first pathogen receptor, FLAGELLIN‐SENSING 2 (FLS2), the field has worked to define receptor complexes and downstream signalling pathways. This article describes recent progress in this area. In addition, many pathogen effectors target the PTI machinery. Thus, identifying PTI components as effector targets helps to validate those molecules as components of the defence machinery. As such, early molecular interactions are key to the outcome of infection. Indeed it is thought that nonhost resistance, in which most plants species are resistant to most pathogens, is likely to be a result of the PTI system. Key Concepts: Plants have multilayered recognition systems which detect invading pathogens. The first line of recognition involves detection of PAMPs via host pattern‐recognition receptors (PRRs). PRRs are transmembrane receptor‐like kinases or receptor‐like proteins that perceive PAMPs at the cell surface. PRRs act as a major point of control for PTI. Biogenesis and localisation of PRRs to the plasma membrane requires the proteins are processed by the secretory pathway and individual PRRs have varying requirements for endoplasmic reticulum‐quality control pathways. Following PAMP perception, a series of downstream defence responses results in PTI. Attenuation of PRR signalling is necessary to restrict immune responses.
In-vivo MRI Reveals Changes to Intracerebral Vasculature Caliber in HIV Infection (2019)

<b>Objective:</b> To characterize cerebral arterial remodeling in HIV-infected (HIV+) individuals <i>in-vivo</i>, and to study its clinical and immunological associations. <b>Methods:</b> T2<sup>*</sup>-weighted magnetic resonance imagining sequences was used to determine cross-sectional area (vascular caliber) of the anterior (A1 segment) and middle (M1 segment) cerebral arteries in HIV- (control) and HIV+ subjects on antiretroviral therapy. Correlations of A1 caliber with clinical, demographic parameters, and immunological markers in cerebrospinal fluid (CSF) were determined using multivariable analyses. <b>Results:</b> A1 and M1 calibers from 22 HIV- control subjects (age: median 48.5 years, range 22-60 years, 55% male) and 61 HIV+ subjects (age: median 53 years, range 25-60 years, 67% male) were studied. ANCOVA, adjusting for ethnicity and sex (age was not correlated with M1 or A1 caliber in either group), revealed that HIV+ subjects had larger caliber in the A1 segment than HIV- subjects (4.95 ± 0.14 mm<sup>2</sup>, and 4.47 ± 0.21 mm<sup>2</sup> respectively, <i>p</i> = 0.048), but caliber of the M1 segment did not differ among the groups (7.21 ± 0.14 mm<sup>2</sup> and 7.09 ± 0.23 mm<sup>2</sup> respectively, <i>p</i> = 0.65). In the HIV+ cohort, longer disease duration and higher current CD4 T-cell count were associated with reduced A1 caliber (<i>r</i> =-0.42 and -0.33 respectively, <i>p</i> < 0.05). In addition, increase in cardiovascular disease risk (CVD risk) was associated with a decrease in A1 caliber in the HIV group (<i>r</i> = -0.35, <i>p</i> < 0.05). <b>Conclusions:</b> This cross-sectional study reveals an increase in A1 caliber in the HIV+ cohort, compared to control subjects, which is especially prominent in early phase of the disease. This increase in caliber may be associated with acute pathological processes in HIV during the initial stages of infection resulting in loss of compliance or thinning of the arterial wall. At later stages, such changes may be confounded by arteriosclerotic changes that are common in later stages of HIV infection. This study suggests there is extensive vessel remodeling in various stages of infection. Long-term longitudinal follow-up of this cohort is planned to further verify this hypothesis and to better understand this MRI marker of intracranial vascular caliber.
NIMG-47PATHOLOGICALLY CONFIRMED VIABLE TUMOR SURROUNDS REGIONS OF PROGRESSIVELY EXPANDING DIFFUSION-RESTRICTED NECROSIS FOLLOWING BEVACIZUMAB TREATMENT (2015)

NIMG-47. PATHOLOGICALLY CONFIRMED VIABLE TUMOR SURROUNDS REGIONS OF PROGRESSIVELY EXPANDING DIFFUSION-RESTRICTED NECROSIS FOLLOWING BEVACIZUMAB TREATMENT Peter LaViolette, Nelson Milbach, Jennifer Connelly, Scott Rand, Kathleen Schmainda, and Elizabeth Cochran; Medical College of Wisconsin, Milwaukee, WI, USA INTRODUCTION: In a subset of recurrent glioblastoma patients, bevacizumab has been shown to induce regions of diffusion restriction. Previous conflicting reportshave found that these lesions contain eitherhypercellular tumor or diffusion restricted necrosis. This study uses whole brain samples to determine both the histological characteristics of the diffusion restricted lesions, and the surrounding tissue. METHODS: Seven patients with bevacizumab induced diffusion restricted lesions were recruited for brain donation for this study. The patient’s brains were sectioned in the same axial orientation as their final clinical imaging session using individualized custom 3d-printed slicing jigs. Clinical imagingacquiredprior to death included diffusion weighted imaging (DWI), T1 pre and post gadolinium contrast, and T2 weighted images. Apparent diffusion coefficient (ADC) maps were calculated from the DWI. Diffusion restriction was defined using radiological criteria. All regions were outside of contrast enhancement, yet within T2 hyperintensity. Specimens were acquired from the brain slice and region that co-localized with the diffusion restriction. Samples were then paraffin embedded, H&E stained, and digitized for interpretation. Each sample was the read by our pathologist to differentiate necrotic regions from viable tumor. RESULTS: In six of seven patients, the diffusion-restricted lesions were progressively growingat the time of the patient’s final scan. In all cases, the diffusion restriction was co-localized to necrotic tissue. In the six progressing patients, the diffusionrestricted necrosis was surrounded by viable hypercellular non-enhancing tumor. The patient without progressively growing diffusion restriction had recurrent tumor elsewhere, not directly adjacent to the diffusion restriction. CONCLUSION: We pathologically confirmed that progressively growing diffusion restriction in patients undergoing bevacizumab treatment indicated necrosis surrounded by viable hypercellular tumor. This information should be considered when choosing to continue or withdraw bevacizumab therapy. Neuro-Oncology 17:v153–v171, 2015. doi:10.1093/neuonc/nov225.47 Published by Oxford University Press on behalf of the Society for Neuro-Oncology 2015.
Over-the-Air Computation for Distributed Systems: Something Old and Something New (2022)

Facing the upcoming era of Internet-of-Things and connected intelligence, efficient information processing, computation, and communication design becomes a key challenge in large-scale intelligent systems. Recently, Over-the-Air (OtA) computation has been proposed for data aggregation and distributed computation of functions over a large set of network nodes. Theoretical foundations for this concept exist for a long time, but it was mainly investigated within the context of wireless sensor networks. There are still many open questions when applying OtA computation in different types of distributed systems where modern wireless communication technology is applied. In this article, we provide a comprehensive overview of the OtA computation principle and its applications in distributed learning, control, and inference systems, for both server-coordinated and fully decentralized architectures. Particularly, we highlight the importance of the statistical heterogeneity of data and wireless channels, the temporal evolution of model updates, and the choice of performance metrics, for the communication design in OtA federated learning (FL) systems. Several key challenges in privacy, security, and robustness aspects of OtA FL are also identified for further investigation.
Supplementary Figure 1 from Distinct Subtypes of Gastric Cancer Defined by Molecular Characterization Include Novel Mutational Signatures with Prognostic Capability (2023)

&lt;p&gt;Fig. S1: Optimization of number of molecular subtypes and assessment of batch effects.&lt;/p&gt;
Enhanced Features for Design of Traveling Wave Tubes Using CHRISTINE-1D (2007)

Traveling wave tubes (TWTs) are vacuum devices invented in the early 1940s for amplification of radio frequency power. These devices are critical for radar, communications, and electronic warfare missions in the military, as well as in commercial applications. The physics-based design and simulation code CHRISTINE-1D was used in the past to explore different TWT circuit designs and to automate the process of parameter estimation. However, the current capability of CHRISTINE-1D allows optimization of only helix TWT designs and includes a limited number of optimization goal functions. In addition, the current optimizer in CHRISTINE-1D employs a modified steepest descent method to carry out the optimization process. The objectives of this paper are threefold: (1) to investigate optimization techniques that may be better suited for this problem (for example, simplex type methods such as Nelder-Mead and Dividing Rectangles); (2) to allow optimization of nonhelix TWTs; and (3) to implement new optimization goal functions. Finally, to show the feasibility of our approach, we apply our optimization algorithms to the problem of designing a folded waveguide slow-wave circuit.
Transactional event profiling in a best-effort hardware transactional memory system (2012)

Blue Gene/Q's (BG/Q) unique transactional memory system provides hardware isolation, atomicity and consistency for memory locations while leaving the details of the transactional programming system to software layers above the hardware [3]. This design allows for complex systems implemented as part of the software runtime. Here a profiling extension to the software runtime is presented.
Editorial: improvement of cardiovascular risk factor control in patients with type 2 diabetes and nonalcoholic fatty liver disease—time for action! Authors' reply (2023)

LINKED CONTENT This article is linked to Zhang et al papers. To view these articles, visit https://doi.org/10.1111/apt.17428 and https://doi.org/10.1111/apt.17467
PCR detection of metallo-beta-lactamase gene (blaIMP) in gram-negative rods resistant to broad-spectrum beta-lactams (1996)

We applied PCR to the rapid detection of the metallo-beta-lactamase gene, blaIMP, in clinically isolated gram-negative rods. A total of 54 high-level ceftazidime-resistant strains (MICs, > 128 micrograms/ml) were subjected to PCR analyses with the blaIMP-specific primers, since the blaIMP-bearing clinical isolates tested in our previous study always demonstrated high-level resistance to ceftazidime. Twenty-two blaIMP-positive strains including 9 Pseudomonas aeruginosa, 9 Serratia marcescens, 2 Alcaligenes xylosoxidans, 1 Pseudomonas putida, and 1 Klebsiella pneumoniae strains were newly identified from 18 different hospitals in Japan. These strains were mostly isolated from urine samples and showed high-level resistance to almost every cephem, while their levels of resistance to carbapenems were diverse. The PCR analyses with novel integrase gene-specific (intI3) and acc(6')-Ib gene-specific primers suggested that the integron structure found in a large plasmid harbored by S. marcescens AK9373 was also well conserved among blaIMP-positive strains. These results imply that the blaIMP gene cassettes have been dispersing into various gram-negative rods with the help of the newly identified integron element. Thus, the PCR-aided rapid detection will be helpful for the early recognition of emerging blaIMP-positive clinical isolates which demonstrate consistent resistance to beta-lactams.
On the Degrees of Freedom of Full-Duplex Cellular Networks. (2016)

Full-duplex (FD) cellular networks are considered in which a FD base station (BS) simultaneously supports a set of half-duplex (HD) downlink (DL) users and a set of HD uplink (UL) users. The transmitter and the receiver of the BS are equipped with reconfigurable antennas, each of which can choose its transmit or receive mode from several preset modes. Under the no self-interference assumption arisen from FD operation at the BS, the sum degrees of freedom (DoF) of FD cellular networks is investigated for both no channel state information at the transmit side (CSIT) and partial CSIT. In particular, the sum DoF is completely characterized for the no CSIT model and an achievable sum DoF is established for the partial CSIT model, which improves the sum DoF of the conventional HD cellular networks. For both the no CSIT and partial CSIT models, the results show that the FD BS with reconfigurable antennas can double the sum DoF even in the presence of user-to-user interference as both the numbers of DL and UL users and preset modes increase. It is further demonstrated that such DoF improvement indeed yields the sum rate improvement at the finite and operational signal-to-noise ratio regime.
Subband autocorrelation features for video soundtrack classification (2013)

Inspired by the system presented in [1], we have developed novel auditory-model-based features that preserve the fine time structure lost in conventional frame-based features. While the original auditory model is computationally intense, we present a simpler system that runs about ten times faster but achieves equivalent performance. We use these features for video soundtrack classification with the Columbia Consumer Video dataset, showing that the new features alone are roughly comparable to traditional MFCCs, but combining classifiers based on both features achieves a substantial mean Average Precision improvement of 15% over the MFCC baseline.
4Pi Microscopy (2012)

Optical microscopy has become a key technology in the life sciences today. Its noninvasive nature provides access to the interior of intact and even living cells, where specific molecules can be precisely localized by fluorescent tagging. However, the attainable 3D resolution of an optical microscope has long been hampered by a comparatively poor resolution along the optic axis. By coherent focusing through two objective lenses, 4Pi microscopy improves the axial resolution by three- to fivefold. This primer is intended as a starting point for the design and operation of a 4Pi microscope of type A.
A Simple Transmission-Line Model to Distinguish the Q-Factor Responses among Various Kinds of Integrated Inductors (2007)

This paper presents a novel transmission-line model for integrated inductors to derive their quality (Q) factors in terms of the well-known transmission-line parameters in closed forms. The derived formulas are general and suitable for all kinds of integrated inductors when used to account for the frequency dependence of Q factors. The presented formulas can also uniquely distinguish the improvement in Q-factor responses between the reduction of conductor loss and dielectric loss.
ChemInform Abstract: Catalytic Antioxidant Therapy by Metallodrugs: Lessons from Metallocorroles (2015)

Abstract Review: [106 refs.
Rapidly Alternating COPP/ABV/IMEP Is Not Superior to Conventional Alternating COPP/ABVD in Combination With Extended-Field Radiotherapy in Intermediate-Stage Hodgkin’s Lymphoma: Final Results of the German Hodgkin’s Lymphoma Study Group Trial HD5 (2002)

PURPOSE: To investigate whether treatment results in intermediate-stage Hodgkin’s lymphoma can be improved by rapid application of non–cross-resistant drugs, the 10-drug regimen cyclophosphamide, vincristine, procarbazine, and prednisone (COPP), doxorubicin, bleomycin, and vinblastine (ABV), and ifosfamide, methotrexate, etoposide, and prednisone (IMEP), repeated every 6 weeks, was compared with conventional alternating COPP/doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) administered every 8 weeks. PATIENTS AND METHODS: From January 1988 to January 1993, 996 patients in stage I or II Hodgkin’s lymphoma with at least one risk factor (massive mediastinal tumor, massive spleen involvement, extranodal disease, elevated ESR, or more than two lymph node areas involved) and all patients in stage IIIA Hodgkin’s lymphoma were randomized to receive two cycles of COPP/ABVD or COPP/ABV/IMEP followed by extended-field radiotherapy. RESULTS: Both regimens produced similar rates for treatment responses (complete remission, 93% v 94%), freedom from treatment failure (80% v 79%), and overall survival (88% for both regimens) at a median follow-up time of 7 years. Most serious toxicities during chemotherapy were similar in both regimens. However, World Health Organization grade 3 and 4 leukocytopenia occurred significantly more frequently in the COPP/ABV/IMEP arm (53% v 44% of patients; P = .010). There were no differences in the number of serious infections and toxic deaths during therapy. The number of second malignancies was also the same in both arms (22 each). CONCLUSION: Alternating COPP/ABVD and rapid alternating COPP/ABV/IMEP in combination with extended-field radiotherapy are equally effective in intermediate-stage Hodgkin’s lymphoma and produce excellent long-term treatment results.