gebhart/patrepeval huggingface dataset:
Utility of a multiple serum biomarker test to monitor remission status and relapse in dogs with lymphoma undergoing treatment with chemotherapy (2014)

A blinded retrospective study was conducted to investigate remission and recurrence of lymphoma in dogs receiving chemotherapy. The objective was to compare clinicians' assessment using palpation and cytology to the results of serum biochemical tests for haptoglobin (Hapt) and C-reactive protein (C-RP). These biochemical test results were combined using a diagnostic algorithm developed using data from 344 individual dogs. This multivariate approach, termed the canine lymphoma blood test (cLBT), was used to follow 57 dogs during and after treatment. cLBT of remission and recurrence compared well with clinicians' assessment and differentiated dogs in remission and those with recurring disease before appearance of lymphadenopathy (P < 0.001). The cLBT demonstrated prognostic potential based on pre-treatment values on dogs with shorter survival times and on those achieving the lowest cLBT score during treatment that showed longer survival times. The test, therefore, demonstrates potential to assist in monitoring treatment of canine lymphoma.
Current standing and future prospects for the technologies proposed to transform toxicity testing in the 21st century (2011)

The National Academy of Sciences publication, Toxicity Testing in the 21st Century: A Vision and a Strategy, proposes a paradigm shift in toxicology from current animal-based testing towards the application of emerging technologies, i.e., assays based on human cells or non-mammalian models, high throughput testing, omics approaches, systems biology, and computational modeling. These technologies should be used to identify how chemicals interact with cellular response networks and alter them to toxicity pathways. According to the authors, such a new paradigm would provide a better scientific understanding and more adequate data to predict the adverse effects of chemicals on human health. As expected from a vision document, the report enthusiastically and optimistically describes a radical transformation of toxicology from current practices to a new approach. Several toxicologists have commented on the report, and although they generally confirm the importance of the vision, they pose critical questions regarding its feasibility. Unlike the theoretical concepts, which are carefully described, many practical aspects of how to establish the vision are less well defined. Today's technologies provide great opportunities, although many challenges remain regarding their development, implementation, and validation to adequately assess human health effects. To bring the envisioned toxicology closer to concrete implementation, it is important to identify the current knowledge gaps in the vision and develop solutions. The goal of this review is to evaluate the technologies proposed as to their maturation to transform toxicity testing in the 21st century. This paper will provide an overview of the current standing by defining advantages, limitations, and developmental needs. In doing so, I do not intend to point out obstacles but, rather, to focus on current opportunities to advance toxicity testing for human risk assessment.
Polyacrylonitrile/graphene composite as a precursor to a sulfur-based cathode material for high-rate rechargeable Li–S batteries (2012)

Polyacrylonitrile/graphene (PAN/GNS) composites have been synthesized via an in situ polymerization method for the first time, which serve as a precursor to prepare a cathode material for high-rate rechargeable Li–S batteries. It is observed from scanning electron microscopy (SEM) and transmission electron microscopy (TEM) that the PAN nanoparticles, less than 100 nm in size, are anchored on the surface of the GNS and this unique structure is maintained in the sulfur composite cathode material. The electrochemical properties of the pyrolyzed PAN-S/GNS (pPAN-S/GNS) composite cathode have been evaluated by cyclic voltammograms, galvanostatic discharge–charge cycling and electrochemical impedance spectroscopy. The results show that the pPAN-S/GNS nanocomposite, with a GNS content of ca. 4 wt.%, exhibits a reversible capacity of ca. 1500 mA hg−1sulfur or 700 mA hg−1composite in the first cycle, corresponding to a sulfur utilization of ca. 90%. The capacity retention is relatively stable at 0.1 C. Even up to 6 C, a competitive capacity of ca. 800 mA hg−1sulfur is obtained. The superior performance of pPAN-S/GNS is attributed to the introduction of the GNS and the even composite structure. The GNS in the composite materials works as a three-dimensional (3-D) nano current collector, which could act not only as an electronically conductive matrix, but also as a framework to improve the electrochemical performance.
Faculty Opinions recommendation of A genetic map of the response to DNA damage in human cells. (2021)

The response to DNA damage is critical for cellular homeostasis, tumor suppression, immunity, and gametogenesis. In order to provide an unbiased and global view of the DNA damage response in human cells, we undertook 31 CRISPR-Cas9 screens against 27 genotoxic agents in the retinal pigment epithelium-1 (RPE1) cell line. These screens identified 890 genes whose loss causes either sensitivity or resistance to DNA-damaging agents. Mining this dataset, we discovered that ERCC6L2 (which is mutated in a bone-marrow failure syndrome) codes for a canonical non-homologous end-joining pathway factor, that the RNA polymerase II component ELOF1 modulates the response to transcription-blocking agents, and that the cytotoxicity of the G-quadruplex ligand pyridostatin involves trapping topoisomerase II on DNA. This map of the DNA damage response provides a rich resource to study this fundamental cellular system and has implications for the development and use of genotoxic agents in cancer therapy.Copyright © 2020 Elsevier Inc. All rights reserved. PMID: 32649862 Funding information This work was supported by: CIHR, Canada Grant ID: PJT-156330 CIHR, Canada Grant ID: FRN 123518 CIHR, Canada Grant ID: FDN143343 Intramural NIH HHS, United States Grant ID: ZIA ES102765
Lattice-engineered Si<inf>1&#x2212;x</inf>Ge<inf>x</inf>-buffer on Si(001) for GaP integration (2014)

XRD techniques determined that 270 nm GaP grown on 400 nm Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.85</inf> Ge <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.15</inf> /Si(001) substrates by MOCVD is single crystalline and pseudomorphic, but carry a 0.07% tensile strain after cooling down to room temperature due to the bigger thermal expansion coefficient of GaP with respect to Si (Fig. 2). TEM and AFM examinations indicated a closed but defective GaP layer (Fig. 3(a)) with low root mean square of roughness (rms) of 3.0 nm for 1 µm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> surface area (Fig. 3(b)). Although TEM studies confirm the absence of misfit dislocations in the pseudomorphic GaP film, growth defects (e.g. stacking faults, microtwins, and anti-phase domains) are detected, concentrating at the GaP/SiGe interface (Fig. 3(c)-(d), Fig. 4). We interpret these growth defects as a residue of the initial 3D island coalescence phase of the GaP film on the Si <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.85</inf> Ge <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.15</inf> buffer. TEM-EDX studies reveal that the observed growth defects are often correlated with stoichiometric inhomogeneities in the GaP film (not shown here). Finally, ToF-SIMS detects sharp heterointerfaces between GaP and SiGe films with a minor level of Ga diffusion into the SiGe buffer (Fig. 5).
Enabling Cyber Security Data Sharing for Large-scale Enterprises Using Managed Security Services (2018)

Large enterprises and organizations from both private and public sectors typically outsource a platform solution, as part of the Managed Security Services (MSSs), from 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> party providers (MSSPs) to monitor and analyze their data containing cyber security information. Sharing such data among these large entities is believed to improve their effectiveness and efficiency at tackling cybercrimes, via improved analytics and insights. However, MSS platform customers currently are not able or not willing to share data among themselves because of multiple reasons, including privacy and confidentiality concerns, even when they are using the same MSS platform. Therefore any proposed mechanism or technique to address such a challenge need to ensure that sharing is achieved in a secure and controlled way. In this paper, we propose a new architecture and use case driven designs to enable confidential, flexible and collaborative data sharing among such organizations using the same MSS platform. MSS platform is a complex environment where different stakeholders, including authorized MSSP personnel and customers' own users, have access to the same platform but with different types of rights and tasks. Hence we make every effort to improve the usability of the platform supporting sharing while keeping the existing rights and tasks intact. As an innovative and pioneering attempt to address the challenge of data sharing in the MSS platform, we hope to encourage further work to follow so that confidential and collaborative sharing eventually happens among MSS platform customers.
Building extraction and change detection in multitemporal remotely sensed images with multiple birth and death dynamics (2009)

In this paper we introduce a new probabilistic method which integrates building extraction with change detection in remotely sensed image pairs. A global optimization process attempts to find the optimal configuration of buildings, considering the observed data, prior knowledge, and interactions between the neighboring building parts. The accuracy is ensured by a Bayesian object model verification, meanwhile the computational cost is significantly decreased by a non-uniform stochastic object birth process, which proposes relevant objects with higher probability based on low-level image features.
Macromolecular synthesis in oat leaf protoplasts (1976)

Oat mesophyll protoplasts isolated by 2 hr cellulysin treatment of peeled young leaves incorporate tritiated leucine, uridine and thymidine into trichloroacetic acidinsoluble materials. Neither the protoplast-free final supernatant liquid nor protoplasts disrupted by rapid passagethrough the tip of a Pasteur pipette show any incorporation activity, while intact protoplasts incubated in the presence of penicillin and streptomycin are active. Thus, the cycloheximide and actinomycin D inhibitable incorporation processes appear to represent, respectively, synthesis of protein and nucleic acids by intact protoplasts, uncomplicated by organellar or microbial contributions. Net leucine and uridine incorporation by protoplasts continue at a steady rate for about 6 hr, dien abruptly cease, while thymidine incorporation continues linearly for at least 21 hr. Preincubation of protoplasts in leucine-free media for several hours diminishes the duration, but not the initial rate of incorporation. The titer of protoplasts declines progressively with increased time of incubation. Kinetin (10−9 to 10−4 M) progressively inhibits leucine incorporation, 2,4-D at concentrations higher than 10−7 M inhibits uridine incorporation, while gibberellins, abscisic acid and ethylene are without effect on any process studied.
Automatically Inferring Malware Signatures for Anti-Virus Assisted Attacks (2017)

Although anti-virus software has significantly evolved over the last decade, classic signature matching based on byte patterns is still a prevalent concept for identifying security threats. Anti-virus signatures are a simple and fast detection mechanism that can complement more sophisticated analysis strategies. However, if signatures are not designed with care, they can turn from a defensive mechanism into an instrument of attack. In this paper, we present a novel method for automatically deriving signatures from anti-virus software and discuss how the extracted signatures can be used to attack sensible data with the aid of the virus scanner itself. To this end, we study the practicability of our approach using four commercial products and exemplary demonstrate anti-virus assisted attacks in three different scenarios.
Regulation of parathyroid hormone-related protein production by a squamous carcinoma cell line in vitro. (1993)

The results of this study revealed that SCC 2/88 cells spontaneously produced substantial amounts of PTHrP under baseline conditions and that compounds known to affect keratinocyte differentiation/proliferation up-regulated production of PTHrP. These cells will be valuable to investigate the molecular regulation of PTHrP production by squamous cell carcinomas.
Regional pole and zero placement with static output feedback via the Modified Minimum Gain Lemma (2017)

This paper presents static output feedback controller synthesis methods that place closed-loop poles, blocking zeros, and transmission zeros within regions of the complex plane. In particular, closed-loop poles are placed within linear matrix inequality (LMI) regions of the complex plane, while closed-loop blocking and transmission zeros are placed in the open left-half plane (OLHP), and are thus minimum phase. An LMI formulation of the Modified Minimum Gain Lemma is used to ensure that the closed-loop system is minimum phase by forcing a nonzero minimum gain constraint. Two controller synthesis methods are presented, including Method 1, which places the closed-loop poles in the OLHP, and Method 2, which places closed-loop poles in the OLHP and closed-loop poles within a specified LMI region of the complex plane. Numerical examples are provided for both controller synthesis methods, with comparisons to controllers in the literature.
Modeling and 1D Control of a non Contact Magnetic Actuation Platform at the Air/Liquid Interface for Micrometer Scale Applications (2016)

International audience
A proposal for an RLC/MAC protocol for wideband CDMA capable of handling real time and non-real time services (2002)

In this paper we describe a proposal for a radio link control/medium access control (RLC/MAC) protocol for a W-CDMA system. It makes use of the flexibility offered by the physical layer in the sense that it supports variable bit rate services. In addition the RLC/MAC is designed such that multiple services are supported, without the necessity to transmit with multiple spreading codes.
Equipment Aging, Aging Detection, and Aging Management: A Review (2014)

It is becoming increasingly difficult to ignore the importance of equipment aging in critical industries such as power generation plants, oil and gas plants, etc. since many system components are approaching the end of their designed operational lifetime. New installations of system components in these critical industries will be extremely costly whilst any increase in demand will be too small to warrant totally new facilities. Aging management can be an alternative for this aging equipment to ensure its safety and reliability. This review aims to provide a brief understanding of equipment aging, aging detection and recent research into aging management.
Comparison of pharmacokinetic profile of levodopa throughout the day between levodopa/carbidopa/entacapone and levodopa/carbidopa when administered four or five times daily (2009)

The present results on the differences in levodopa PK between LCE and LC provide a basis to evaluate the relationship of levodopa PK and the induction of motor complications in an on-going study in early Parkinson's disease using similar dosing regimens.
Sample collection guidelines for trace elements in blood and urine (Technical Report) (1995)

This paper presents an organized system for element-specific sample collection and handling of human blood (whole blood, serum or plasma, packed cells or erythrocytes) and urine also indicating a proper definition of the subject and sample. Harmonized procedures for collection, preparation, analysis and quality control are suggested. The aim is to assist scientists worldwide to produce comparable data which will be useful on a regional, national and international scale. The guidelines are directed to the elements aluminium, arsenic, cadmium, chromium, cobalt, copper, lead, lithium, manganese, mercury, nickel, selenium and zinc. These include the most important elements measured for their occupational or clinical significance, and serve as examples of principles that will guide development of methods for other elements in the future.
The vectorcardiogram in right bundle branch block: correlation with cardiac failure and pulmonary disease. (1976)

Frank vectorcardiograms (VCG) and clinical records of 243 patients with right bundle branch block (RBBB) were compared. The patients were classified into three categories on the basis of VCG criteria. The first category included 100 patients with a normal frontal axis, and the second category included 44 patients with concomitant left anterior hemiblock. The third category consisted of 99 patients with RBBB and myocardial infarction. The VCGs were classified into three types accoriding to the QRS configuration in the transverse plane. In type I the initial forces were anterior and counterclockwise and the afferent limb crossed the midline posterior to E point; in type II the initial forces were anterior and counterclockwise and the afferent limb crossed the midline posterior to E point; in type II the initial forces were anterior and counterclockwise and the afferent limb crossed the midline anterior to or through E point; and in type III the entire transverse loop was clockwise and anterior to E point. The patients were further classified according to the presence or absence of cardic failure or severe pulmonary disease. In patients with RBBB and a normal axis, cardiac failure or severe pulmonary disease was found in five of 49 patients wtih type I, 17 of 31 with type II, and 18 of 20 with type III pattern. In patients with RBBB and left anterior hemiblock, significant disease was found in one of 17 with type I, five of 16 with type II, and eight of 11 with type III pattern. These data show that, in patients with RBBB, the position of the afferent limb in the transverse plane can be used to predict cardiac failure or severe pulmonary disease.
Algorithms for Combining Airspace Sectors (2009)

A heuristic algorithm for combining under-utilized airspace sectors to conserve air traffic control resources is described and analyzed. Simulations and analysis using historical air traffic data and operational sector combination data suggest that systematically combining under-utilized sectors can lead to fewer sectors and therefore a more efficient utilization of resources. Currently, sector combinations are restricted to occur within groups of sectors called areas of specialization. A second heuristic algorithm is proposed that defines new groups of sectors that may be combined. These new groups allow more sector combinations and could be building blocks for new areas of specialization. An analysis of the new groups of sectors suggests that they allow for more frequent sector combinations than existing areas of specialization, and therefore even further efficiencies. Feedback from managers at the Cleveland Air Route Traffic Control Center suggests that both of these algorithms would be useful in Center operations.
Alkynyl-Enrichable Carboxyl-Selective Crosslinkers to Increase the Crosslinking Coverage for Deciphering Protein Structures (2022)

The coverage of chemical crosslinking coupled with mass spectrometry (CXMS) is of great importance to determine its ability for deciphering protein structures. At present, <i>N</i>-hydroxysuccinimidyl (NHS) ester-based crosslinkers targeting lysines have been predominantly used in CXMS. However, they are not always effective for some proteins with few lysines. Other amino acid residues such as carboxyl could be crosslinked to complement lysines and improve the crosslinking coverage of CXMS, but the low intrinsic chemical reactivity of carboxyl compromises the application of carboxyl-selective crosslinkers for complex samples. To enhance the crosslinking efficiency targeting acidic residues and realize in-depth crosslinking analysis of complex samples, we developed three new alkynyl-enrichable carboxyl-selective crosslinkers with different reactive groups such as hydrazide, amino, and aminooxy. The crosslinking efficiencies of the three crosslinkers were systematically evaluated, giving the best reactivity of the amino-functionalized crosslinker BAP. Furthermore, BAP was extended to the crosslinking analysis of <i>Escherichia coli</i> lysate in combination with efficient crosslink enrichment. A total of 1291 D/E-D/E crosslinks involved in 392 proteins were identified under a false discovery rate (FDR) of ≤1%. Obvious structural complementarity of BAP was exhibited to the lysine-targeting crosslinker, facilitating the capability of CXMS for protein structure elucidation. To the best of our knowledge, this was the first time for the carboxyl-selective crosslinker to achieve proteome-wide crosslinking analysis of the whole cell lysate. Collectively, we believe that this work not only expands on a promising toolkit of CXMS targeting acidic residues but also provides a valuable guideline to advance the performance of carboxyl-selective crosslinkers.
Phenotypic subpopulations of metastatic colon cancer stem cells: genomic analysis. (2009)

The proposed approaches allow for reliable isolation and propagation of highly tumorigenic and clonogenic cells of different phenotypes. Genomic analysis of several candidate CSC phenotypic populations may contribute to the identification of novel targets for colon cancer stem cell-targeted drug development and treatment.