gebhart/patrepeval huggingface dataset:
Appendiceal Adenocarcinoma Presenting as a Rectal Polyp (2016)

Appendiceal adenocarcinoma typically presents as an incidentally noted appendiceal mass, or with symptoms of right lower quadrant pain that can mimic appendicitis, but local involvement of adjacent organs is uncommon, particularly as the presenting sign. We report on a case of a primary appendiceal cancer initially diagnosed as a rectal polyp based on its appearance in the rectal lumen. The management of the patient was in keeping with standard practice for a rectal polyp, and the diagnosis of appendiceal adenocarcinoma was made intraoperatively. The operative strategy had to be adjusted due to this unexpected finding. Although there are published cases of appendiceal adenocarcinoma inducing intussusception and thus mimicking a cecal polyp, there are no reports in the literature describing invasion of the appendix through the rectal wall and thus mimicking a rectal polyp. The patient is a 75-year-old female who presented with spontaneous hematochezia and, on colonoscopy, was noted to have a rectal polyp that appeared to be located within a diverticulum. When endoscopic mucosal resection was not successful, she was referred to colorectal surgery for a low anterior resection. Preoperative imaging was notable for an enlarged appendix adjacent to the rectum. Intraoperatively, the appendix was found to be densely adherent to the right lateral rectal wall. An en bloc resection of the distal sigmoid colon, proximal rectum and appendix was performed, with pathology demonstrating appendiceal adenocarcinoma that invaded through the rectal wall. The prognosis in this type of malignancy weighs heavily on whether or not perforation and spread throughout the peritoneal cavity have occurred. In this unusual presentation, an en bloc resection is required for a complete resection and to minimize the risk of peritoneal spread. Unusual appearing polyps do not always originate from the bowel wall. Abnormal radiographic findings adjacent to an area of gastrointestinal pathology may signify locally advanced disease from a surrounding organ that secondarily involves the gastrointestinal tract. These findings warrant further investigation prior to any intervention to ensure appropriate treatment.
Topology Identification and Learning over Graphs: Accounting for Nonlinearities and Dynamics (2018)

Identifying graph topologies as well as processes evolving over graphs emerge in various applications involving gene-regulatory, brain, power, and social networks, to name a few. Key graph-aware learning tasks include regression, classification, subspace clustering, anomaly identification, interpolation, extrapolation, and dimensionality reduction. Scalable approaches to deal with such high-dimensional tasks experience a paradigm shift to address the unique modeling and computational challenges associated with data-driven sciences. Albeit simple and tractable, linear time-invariant models are limited since they are incapable of handling generally evolving topologies, as well as nonlinear and dynamic dependencies between nodal processes. To this end, the main goal of this paper is to outline overarching advances, and develop a principled framework to capture nonlinearities through kernels, which are judiciously chosen from a preselected dictionary to optimally fit the data. The framework encompasses and leverages (non) linear counterparts of partial correlation and partial Granger causality, as well as (non)linear structural equations and vector autoregressions, along with attributes such as low rank, sparsity, and smoothness to capture even directional dependencies with abrupt change points, as well as time-evolving processes over possibly time-evolving topologies. The overarching approach inherits the versatility and generality of kernel-based methods, and lends itself to batch and computationally affordable online learning algorithms, which include novel Kalman filters over graphs. Real data experiments highlight the impact of the nonlinear and dynamic models on consumer and financial networks, as well as gene-regulatory and functional connectivity brain networks, where connectivity patterns revealed exhibit discernible differences relative to existing approaches.
Convenient One-PotSynthesis of 4-(Dialkylaminobenzyl)triphenylphosphoniumSalts - Application to the Synthesis of a Fluorescent Probefor Multiphotonic Imaging of Biological Membranes (2003)

An efficient one-pot preparation of (dialkylaminobenzyl)triphenylphosphonium salts directly from dialkylbenzenamine is described. The one-pot procedure proceeds quickly in high yields and allows the synthesis of useful reagents for Wittig reaction. Their potential is illustrated by the synthesis of a bolaamphiphilic fluorophore of interest for biological membrane imaging.
The groESL operon of Agrobacterium tumefaciens: evidence for heat shock-dependent mRNA cleavage (1995)

The heat shock response of the groESL operon of Agrobacterium tumefaciens was studied at the RNA level. The operon was found to be activated under heat shock conditions and transcribed as a polycistronic mRNA that contains the groES and groEL genes. After activation, the polycistronic mRNA appeared to be cleaved between the groES and groEL genes and formed two monocistronic mRNAs. The groES cleavage product appeared to be unstable and subjected to degradation, while the groEL cleavage product appeared to be stable and became the major mRNA representing the groESL operon after long periods of growth at a high temperature. The polycistronic mRNA containing the groES and groEL genes was the major mRNA representing the groESL operon at a low temperature, and it reappeared when the cells were returned to the lower growth temperature after heat shock induction. These findings indicate that the cleavage event is part of the heat shock regulation of the groESL operon in A. tumefaciens.
The Cytoplasmic Tail Domain of Influenza B Virus Hemagglutinin Is Important for Its Incorporation into Virions but Is Not Essential for Virus Replication in Cell Culture in the Presence of Compensatory Mutations (2012)

Influenza B virus hemagglutinin (BHA) contains a predicted cytoplasmic tail of 10 amino acids that are highly conserved among influenza B viruses. To understand the role of this cytoplasmic tail in infectious virus production, we used reverse genetics to generate a recombinant influenza B virus lacking the BHA cytoplasmic tail domain. The resulting virus, designated BHATail(-), had a titer approximately 5 log units lower than that of wild-type virus but grew normally when BHA was supplemented in trans by BHA-expressing cells. Although the levels of BHA cell surface expression were indistinguishable between truncated and wild-type BHA, the BHATail(-) virus produced particles containing dramatically less BHA. Moreover, removal of the cytoplasmic tail abrogated the association of BHA with Triton X-100-insoluble lipid rafts. Interestingly, long-term culture of a virus lacking the BHA cytoplasmic tail in Madin-Darby canine kidney (MDCK) cells yielded a mutant with infectivities somewhat similar to that of wild-type virus. Sequencing revealed that the mutant virus retained the original cytoplasmic tail deletion but acquired additional mutations in its BHA, neuraminidase (NA), and M1 proteins. Viral growth kinetic analysis showed that replication of BHA cytoplasmic tailless viruses could be improved by compensatory mutations in the NA and M1 proteins. These findings indicate that the cytoplasmic tail domain of BHA is important for efficient incorporation of BHA into virions and tight lipid raft association. They also demonstrate that the domain is not absolutely required for virus viability in cell culture in the presence of compensatory mutations.
Improved DNS Server Selection for Multi-Homed Nodes (2011)

A multi-homed node can be connected to multiple networks that may
utilize different DNS namespaces. The node often receives DNS server
configuration information from all connected networks. Some of the DNS
servers may have information about namespaces other servers do not
have. When the multi-homed node needs to utilize DNS, it has to choose
which of the servers to contact to. This document describes a policy
based method for selecting DNS server for both forward and reverse DNS
lookup procedures with help of DNS suffix and IPv6 prefix information
received via DHCPv6.
Effects of osteogenic protein‐1 (OP‐1, BMP‐7) on gene expression in cultured medial collateral ligament cells (2003)

Osteogenic protein-1 (OP-1, also called BMP-7), a member of the BMP family and the TGF-beta superfamily, induces formation of new bone and cartilage, but also regulates a wide array of processes. In the present study, the expression of several characteristic biochemical markers of ligaments, such as Six1, Scleraxis, aggrecan, and type I collagen in primary cultures of adult rat medial collateral ligament (MCL) cells was determined. The effects of OP-1 on cell proliferation and on gene expression were subsequently examined. OP-1 stimulated cell proliferation, alkaline phosphatase (AP) activity, and the steady-state mRNA levels of the transcription factor Runx2/Cbfa1 in a dose- and time-dependent manner. The mRNA levels of type I collagen only increased slightly, but the activity of the cloned collagen promoter increased by 2-fold in transiently transfected MCL cells. OP-1 also stimulated aggrecan mRNA expression. The mRNA levels of Six1 and Scleraxis were not detectably altered by OP-1. In control cultures, the steady-state mRNA levels of ActR-I, BMPR-IA, BMPR-IB, and BMPR-II increased as a function of time in culture. The mRNA levels of BMP-1 and -4 increased significantly after 12 days, but those of BMP-2 and -6 did not change. The GDF-1, -3, -5, -6, and -8 mRNA levels in the control cultures also increased as a function of time. OP-1 treatment stimulated mRNA expression of BMPR-IA and BMPR-II, but had little effect on ActR-I and BMPR-IB mRNA expression. OP-1 lowered the BMP-1, -2, and -6 mRNA levels without changing the BMP-4 mRNA level. OP-1 treatment also reduced the mRNA levels of GDFs detected. In summary, the present study demonstrated that OP-1 stimulated cell proliferation and mRNA expression of several biochemical markers in this ligament cell culture model and established the spatial and temporal appearance of several members of the TGF-beta superfamily.
Renal allograft histology and correlation with function in children on triple therapy (1995)

Histopathological findings of 13 LRD and 17 CAD renal allografts of paediatric recipients were prospectively semiquantitatively scored and correlated with clinical and functional parameters 18 and 36 months after transplantation. The most common findings at 18 months were diffuse interstitial fibrosis (incidence 57%), glomerular mesangial matrix increase (91%), arteriolar intimal proliferation (70%), and tubular atrophy (83%). Most changes were mild and most biopsies were scored normal or borderline (Banff classification). At 18 and at 36 months 30% of grafts showed mild chronic rejection (CR). Only two grafts showed grade II CR at 18 months and one graft grade III CR at 36 months. Progressive CR was not seen. Donor source or recipient age had no effect on graft histology. Vascular-interstitial cyclosporin (CsA) nephrotoxicity was not found. On the contrary, cumulative CsA dose (mg/kg/day) showed an inverse correlation with arteriolar intimal proliferation (P < 0.001). 51Cr-EDTA and lithium clearances showed inverse correlations with diffuse interstitial fibrosis and lymphocytosis. PAH clearance did not correlate with interstitial or vascular changes. The results indicate good prognosis in children on triple immunosuppression (with CsA administered in three doses/day to pre school children) regardless of donor source.
Noninvasive Metabolic Profiling Using Microfluidics for Analysis of Single Preimplantation Embryos (2008)

Noninvasive analysis of metabolism at the single cell level will have many applications in evaluating cellular physiology. One clinically relevant application would be to determine the metabolic activities of embryos produced through assisted reproduction. There is increasing evidence that embryos with greater developmental capacity have distinct metabolic profiles. One of the standard techniques for evaluating embryonic metabolism has been to evaluate consumption and production of several key energetic substrates (glucose, pyruvate, and lactate) using microfluorometric enzymatic assays. These assays are performed manually using constriction pipets, which greatly limits the utility of this system. Through multilayer soft-lithography, we have designed a microfluidic device that can perform these assays in an automated fashion. Following manual loading of samples and enzyme cocktail reagents, this system performs sample and enzyme cocktail aliquotting, mixing of reagents, data acquisition, and data analysis without operator intervention. Optimization of design and operating regimens has resulted in the ability to perform serial measurements of glucose, pyruvate, and lactate in triplicate with submicroliter sample volumes within 5 min. The current architecture allows for automated analysis of 10 samples and intermittent calibration over a 3 h period. Standard curves generated for each metabolite have correlation coefficients that routinely exceed 0.99. With the use of a standard epifluorescent microscope and CCD camera, linearity is obtained with metabolite concentrations in the low micromolar range (low femtomoles of total analyte). This system is inherently flexible, being easily adapted for any NAD(P)H-based assay and scaled up in terms of sample ports. Open source JAVA-based software allows for simple alterations in routine algorithms. Furthermore, this device can be used as a standalone device in which media samples are loaded or be integrated into microfluidic culture systems for in line, real time metabolic evaluation. With the improved throughput and flexibility of this system, many barriers to evaluating metabolism of embryos and single cells are eliminated. As a proof of principle, metabolic activities of single murine embryos were evaluated using this device.
Low Power PVT-Aware Transistor Sizing and Approximate Design Generation for Standard Cells Using Swarm Intelligence (2021)

This paper proposes low power optimization using a modified swarm intelligence algorithm for the scenarios-transistor sizing based static power reduction and low power standard cell generation for approximate computing. In these scenarios, we explore a lower abstraction level and see how standard cells can be tuned to a power-delay-quality optimal point. For transistor sizing, the algorithm considers fabrication process parameter variations (for ±3σ design) in addition to a wide range of temperature (-55°C to 125°C) and supply voltage (±10%) variations to yield PVT aware robust sizing solutions. The approach has been applied on numerous single and multistage circuits (including ISCAS benchmarks) while proposing a dual sizing solution for non-critical and critical path cells. For approximate systems, we present algorithm-generated full adder designs for speech processing systems. The designs vary in terms of accuracy and power. Results show leakage reductions up to 58.2% for conventional and 66.8% with approximation designs for 22nm metal gate high-K (MGK) technology cells.
Tachykinin Receptor Antagonists (2017)

Tachykinins (TKs) are a family of peptides that share the common C-terminal sequence Phe-Xaa-Gly-Leu-Met-NH2 where Xaa is an aromatic or a branched aliphatic amino acid. The three TK receptors have been isolated and cloned from various species. They all belong to the superfamily of rhodopsin-like G-protein-coupled receptors with seven hydrophobic transmembrane-spanning segments, which form the ligand recognition site; phosphoinositide generation is the main second-messenger system linked to their activation. The common C-terminal sequence of TK is essential for their interaction with neurokinin-1 (NK-1), NK-2, and NK-3 receptors, while some effects of substance P, not shared by other TKs, are mediated by its N-terminal region. A few studies have described the possible existence of differences between central and peripheral NK-1 receptors in both rat and guinea pig species. The pharmacological heterogeneity of the NK-2 receptors may be entirely species-related: however, examples of intraspecies heterogeneity have been described as well, suggesting the existence of true receptor subtypes.
Preclinical Evaluation of the Novel BTK Inhibitor Acalabrutinib in Canine Models of B-Cell Non-Hodgkin Lymphoma (2016)

Acalabrutinib (ACP-196) is a second-generation inhibitor of Bruton agammaglobulinemia tyrosine kinase (BTK) with increased target selectivity and potency compared to ibrutinib. In this study, we evaluated acalabrutinib in spontaneously occurring canine lymphoma, a model of B-cell malignancy similar to human diffuse large B-cell lymphoma (DLBCL). First, we demonstrated that acalabrutinib potently inhibited BTK activity and downstream effectors in CLBL1, a canine B-cell lymphoma cell line, and primary canine lymphoma cells. Acalabrutinib also inhibited proliferation in CLBL1 cells. Twenty dogs were enrolled in the clinical trial and treated with acalabrutinib at dosages of 2.5 to 20mg/kg every 12 or 24 hours. Acalabrutinib was generally well tolerated, with adverse events consisting primarily of grade 1 or 2 anorexia, weight loss, vomiting, diarrhea and lethargy. Overall response rate (ORR) was 25% (5/20) with a median progression free survival (PFS) of 22.5 days. Clinical benefit was observed in 30% (6/20) of dogs. These findings suggest that acalabrutinib is safe and exhibits activity in canine B-cell lymphoma patients and support the use of canine lymphoma as a relevant model for human non-Hodgkin lymphoma (NHL).
Mobile Device Identification via Sensor Fingerprinting (2014)

We demonstrate how the multitude of sensors on a smartphone can be used to construct a reliable hardware fingerprint of the phone. Such a fingerprint can be used to de-anonymize mobile devices as they connect to web sites, and as a second factor in identifying legitimate users to a remote server. We present two implementations: one based on analyzing the frequency response of the speakerphone-microphone system, and another based on analyzing device-specific accelerometer calibration errors. Our accelerometer-based fingerprint is especially interesting because the accelerometer is accessible via JavaScript running in a mobile web browser without requesting any permissions or notifying the user. We present the results of the most extensive sensor fingerprinting experiment done to date, which measured sensor properties from over 10,000 mobile devices. We show that the entropy from sensor fingerprinting is sufficient to uniquely identify a device among thousands of devices, with low probability of collision.
Copper‐Catalyzed Trifluoromethylation of Unactivated Olefins (2011)

Activating the inactive: A copper-catalyzed allylic trifluoromethylation of unactivated terminal olefins proceeds under mild conditions to produce linear allylic trifluoromethylated products with high E/Z selectivity (see scheme). The reaction can be applied to a range of substrates bearing numerous functional groups. Furthermore, the reaction is scalable and amenable to a benchtop setup. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Theoretical Determination of Size Effects in Zeolite-Catalyzed Alcohol Dehydration (2019)

In the upgrading of biomass pyrolysis vapors to hydrocarbons, dehydration accomplishes a primary objective of removing oxygen and acidic zeolites represent promising catalysts for dehydration reaction. Here, we utilize density functional theory calculations to estimate adsorption energetics and intrinsic kinetics of alcohol dehydration over H-ZSM-5, H-BEA, and H-AEL zeolites. ONIOM calculations of adsorption energies were observed to be inconsistent when benchmarked against QM/Hartree-Fock and periodic boundary condition calculations. However, reaction coordinate calculations of adsorbed species and transition states were consistent across all levels considered. Comparison of ethanol, iso-propanol (IPA), and tert-amyl alcohol (TAA) over these three zeolites allowed for a detailed examination of how confinement impacts reaction mechanisms and kinetics. TAA, seen to proceed via a carbocationic mechanism, was found to have the lowest activation barrier, followed by IPA and then ethanol, both of which dehydrate via a concerted mechanism. Barriers in H-BEA were consistently found to be lower than in H-ZSM-5 and H-AEL, attributed to late transition states and either elevated strain or inaccurately estimating long-range electrostatic interactions in H-AEL, respectively. Molecular dynamics simulations revealed that the diffusivity of these three alcohols in H-ZSM-5 are significantly overestimated by Knudsen diffusion, which will complicate experimental efforts to develop a kinetic model for catalytic fast pyrolysis.
Radioimmunotherapy of non-Hodgkin’s lymphoma: a critical appraisal (2005)

Radioimmunotherapy is a unique form of radiation therapy that uses antibodies to specifically target radionuclides for systemic cancer treatment. While chemotherapy remains the frontline treatment for non-Hodgkin's lymphoma, two radioimmunotherapy agents are approved for use in certain follicular and transformed forms of recurrent non-Hodgkin's lymphoma as a second- or third-line treatment option. However, there are number of clinical trials underway that will likely lead to a more expanded use of this treatment modality in the future. New agents and approaches for radioimmunotherapy are also being developed that could offer an even greater potential for this new form of therapy.
Radical Reactions in Organic Synthesis (1995)

La synthse du sesbanimide (S3) requier;t la prparat;ion d''un glutarimide subst~tu~ en ppsition 4, 1~que1 est pr~par~.
Al‐Catalyzed Enantioselective Alkylation of α‐Ketoesters by Dialkylzinc Reagents. Enhancement of Enantioselectivity and Reactivity by an Achiral Lewis Base Additive. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.