gebhart/patrepeval huggingface dataset:
Five-year overall survival from the anti-PD1 brain collaboration (ABC Study): Randomized phase 2 study of nivolumab (nivo) or nivo+ipilimumab (ipi) in patients (pts) with melanoma brain metastases (mets). (2021)

9508 Background: Preliminary data from the ABC (76 pts) and CheckMate 204 (94 pts) trials showed that nivo and nivo+ipi have activity in active melanoma brain metastases, with durable responses in a subset of pts. Here, we report updated 5-yr data from all pts enrolled on the ABC trial (NCT02374242). Methods: This open-label ph2 trial enrolled 3 cohorts of pts with active melanoma brain mets naïve to anti-PD1/PDL1/PDL2/CTLA4 from Nov 2014-Apr 2017. Pts with asymptomatic brain mets with no prior local brain therapy were randomised to cohort A (nivo 1mg/kg + ipi 3mg/kg, Q3Wx4, then nivo 3mg/kg Q2W) or cohort B (nivo 3mg/kg Q2W). Cohort C (nivo 3mg/kg Q2W) had brain mets i) that failed local therapy, ii) with neuro symptoms and/or iii) with leptomeningeal disease. Prior BRAF inhibitor (BRAFi) was allowed. The primary endpoint was best intracranial response (ICR) ≥wk12. Key secondary endpoints were IC PFS, overall PFS, OS, &amp; safety. Results: A total of 76 pts (med f/u 54 mo) were enrolled; median age 59y, 78% male. For cohorts A, B and C: elevated LDH 51%, 58% and 19%; V600BRAF 54%, 56% and 81%; prior BRAFi 23%, 24%, 75%. Efficacy and toxicity are shown in the table. There were no treatment-related deaths. 1/17 deaths in cohort A &amp; 4/16 in cohort B were due to IC progression only. Conclusions: Nivo monotherapy and ipi+nivo are active in melanoma brain mets, with durable responses in the majority of patients who received ipi+nivo upfront. A study of upfront ipi+nivo+/-SRS is underway (NCT03340129). Clinical trial information: NCT02374242. [Table: see text]
Intergenerational CAG repeat expansion at ERDA1 in a family with childhood‐onset depression, schizoaffective disorder, and recurrent major depression (1999)

Reported evidence of anticipation for schizophrenia and bipolar disorder has recently precipitated a search for unstable trinucleotide repeats for these diseases. Several initial studies suggested an increase in the frequency of large CAG/CTG repeats in the genomes of schizophrenic and bipolar individuals. Published reports do not demonstrate expansion per se, and may be suggestive of allelic association with the disease rather than actual dynamic DNA mutations. This report documents evidence of a significant expansion of CAG/CTG repeats from one generation to the next in a family demonstrating evidence of anticipation for psychiatric disorders. Using the repeat expansion detection (RED) technique, we observed that a proband with multiple psychiatric diagnoses, including childhood-onset depression, inherited a larger CAG/CTG repeat than either parent. Analysis of the ERDA1 locus on 17q21.3 revealed that the proband inherited a very large allele from the father which increased in repeat number through transmission. The mother was diagnosed with schizoaffective disorder and the father with depression. While this DNA mutation may be a stochastic event unconnected with the disease, it could represent DNA instability as an etiologic factor in psychiatric diseases. Am. J. Med. Genet. (Neuropsychiatr. Genet.) 88:79–82, 1999. © 1999 Wiley-Liss, Inc.
A Divergent Member of the Transforming Growth Factor β Receptor Family from Schistosoma mansoni Is Expressed on the Parasite Surface Membrane (1998)

To optimize reproductive success under the limitations determined by conditions within an individual host, parasitic helminths have evolved mechanisms that allow them to detect and respond to host factors such as species, age, sex, reproductive condition, and immune status. Using the model helminth Schistosoma mansoni, we have explored the possibility that parasitic helminths express signal-transducing receptor molecules on their surfaces. Here, we present the identification of a schistosome member of the transforming growth factor beta receptor family of cell-surface receptors, the first member of this family to be identified in a platyhelminth. The putative protein kinase domain of the schistosome receptor displays up to 58% amino acid identity to kinase domains of other type I receptor serine-threonine kinases, and contains a potential "GS domain," suggesting it is a divergent member of the type I receptor subfamily. This receptor is expressed on the surface of the parasite's syncytial tegument and expression of receptor messenger RNA and protein is up-regulated following infection of the mammalian host. The receptor protein can be isolated in a phosphorylated form from adult parasites, which together with its surface location, suggests that it functions in transducing signals across the parasite surface membrane.
Detection of Listeria monocytogenes in cheese with the magnetic immuno-polymerase chain reaction assay (1993)

A new detection system, the magnetic immuno-polymerase chain reaction (PCR) assay (MIPA) has been developed to detect Listeria monocytogenes in food. This method separates Listeria cells from PCR-inhibitory factors present in enrichment broths containing food samples by using magnetic beads coated with specific monoclonal antibodies (MAbs). The separated bacteria were lysed, and the supernatant containing the bacterial DNA was subjected to the PCR. Detection of L. monocytogenes in three naturally contaminated cheese samples with two different MAbs and PCR primers specific for the gene encoding the delayed-hypersensitivity factor showed that with MAb 55 all three samples were positive whereas with MAb A two samples were positive. A further improvement of the method was obtained by using a PCR step based on the listeriolysin O gene. A MIPA employing MAb 55 and the listeriolysin O gene primer set detected L. monocytogenes after 24 h of culture in Listeria Enrichment Broth samples from Port Salut artificially contaminated with 40 CFU/25 g. We could detect 1 CFU of L. monocytogenes per g of cheese after a second enrichment for 24 h in Fraser broth. The analysis time including both enrichments is approximately 55 h.
Cilostazol Could Ameliorate Platelet Responsiveness to Clopidogrel in Patients Undergoing Primary Percutaneous Coronary Intervention (2007)

The addition of cilostazol to the combination of aspirin plus clopidogrel significantly increases the inhibition of ADP-induced platelet aggregation. However, there was no additive effect on aspirin-induced antiplatelet activity or lowering of sCD40L.
A novel method of identifying motor primitives using wavelet decomposition (2018)

This study reports a new technique for extracting muscle synergies using continuous wavelet transform. The method allows to quantify coincident activation of muscle groups caused by the physiological processes of fixed duration, thus enabling the extraction of wavelet modules of arbitrary groups of muscles. Hierarchical clustering and identification of the repeating wavelet modules across subjects and across movements, was used to identify consistent muscle synergies. Results indicate that the most frequently repeated wavelet modules comprised combinations of two muscles that are not traditional agonists and span different joints. We have also found that these wavelet modules were flexibly combined across different movement directions in a pattern resembling directional tuning. This method is extendable to multiple frequency domains and signal modalities.
Saturation scanning of ubiquitin variants reveals a common hot spot for binding to USP2 and USP21 (2016)

A detailed understanding of the molecular mechanisms whereby ubiquitin (Ub) recognizes enzymes in the Ub proteasome system is crucial for understanding the biological function of Ub. Many structures of Ub complexes have been solved and, in most cases, reveal a large structural epitope on a common face of the Ub molecule. However, owing to the generally weak nature of these interactions, it has been difficult to map in detail the functional contributions of individual Ub side chains to affinity and specificity. Here we took advantage of Ub variants (Ubvs) that bind tightly to particular Ub-specific proteases (USPs) and used phage display and saturation scanning mutagenesis to comprehensively map functional epitopes within the structural epitopes. We found that Ubvs that bind to USP2 or USP21 contain a remarkably similar core functional epitope, or "hot spot," consisting mainly of positions that are conserved as the wild type sequence, but also some positions that prefer mutant sequences. The Ubv core functional epitope contacts residues that are conserved in the human USP family, and thus it is likely important for the interactions of Ub across many family members.
Piecewise Regression Using Cubic Splines (1973)

Abstract Spline theory and piecewise regression theory are integrated to provide a framework in which structural change is viewed as occurring in a smooth fashion. Specifically, structural change occurs at given points through jump discontinuities in the third derivative of a continuous piecewise cubic estimating function. Testing procedures are developed for detecting structural change as well as linear or quadratic segments. Finally, the techniques developed are illustrated empirically in a learning-by-doing model.
Tumor Necrosis Factor-Related Apoptosis-Inducing Ligand (2004)

Mycobacterium bovis Bacillus Calmette-Guérin (BCG) use in the treatment of bladder cancer was first reported in 1976, but the mechanism of the induced antitumor activity has still not been fully explained. BCG is a potent immunostimulant, normally producing a Th1 cytokine response, including IFN. Recent studies have shown CpG oligodeoxynucleotide induce tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) expression via IFN production. Given that Mycobacterial DNA contains high amounts of CpG motifs, we hypothesized that BCG's antitumor properties are akin to CpG oligodeoxynucleotide, where the cytokine response to BCG induces TRAIL up-regulation. Using ELISA, urine IFN-gamma, and TRAIL levels were initially undetectable in BCG therapy patients but were high after later induction treatments. More importantly, patients that responded to BCG therapy had significantly higher urine TRAIL levels, which killed bladder tumor cells in vitro versus nonresponders. Flow cytometry of fresh urine revealed TRAIL-expressing neutrophils. Given these data, we propose TRAIL plays a role in BCG-induced antitumor effects.
Metalloporphyrins as versatile catalysts for oxidation reactions and oxidative DNA cleavage (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetalloporphyrins as versatile catalysts for oxidation reactions and oxidative DNA cleavageBernard MeunierCite this: Chem. Rev. 1992, 92, 6, 1411–1456Publication Date (Print):September 1, 1992Publication History Published online1 May 2002Published inissue 1 September 1992https://pubs.acs.org/doi/10.1021/cr00014a008https://doi.org/10.1021/cr00014a008research-articleACS PublicationsRequest reuse permissionsArticle Views8444Altmetric-Citations1829LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Cellular program controlling the recovery of adipose tissue mass: An in vivo imaging approach (2008)

The cellular program responsible for the restoration of adipose tissue mass after weight loss is largely uncharacterized. Leptin mRNA levels are highly correlated with adipose tissue mass, and leptin expression can thus be used as a surrogate for changes in the amount of adipose tissue. To further study the responses of adipocytes to changes in weight, we created a transgenic mouse expressing the luciferase reporter gene under the control of leptin regulatory sequences, which allows noninvasive imaging of the leptin expression of mice in vivo. We used these animals to show that weight loss induced by fasting or leptin treatment results in the retention of lipid-depleted adipocytes in adipose depots. To further study the cellular response to weight regain after leptin treatment, a leptin withdrawal protocol was used to induce a state of acute leptin deficiency in wild type mice. Acute leptin deficiency led to the transient deposition of large amounts of glycogen within pre-existing, lipid-depleted adipocytes. This was followed by rapid reaccumulation of lipid. Transcriptional profiling revealed that this cellular response was associated with induction of mRNAs for the entire pathway of enzymes necessary to convert glucose into acetyl-CoA and glycerol, key substrates for the synthesis of triglycerides.
Improving sleep apnea treatment adherence after traumatic brain injury: A nonrandomized feasibility study. (2022)

These results inform ways in which procedures should be modified to enhance the success of a future clinical trial testing the efficacy of this adherence intervention. Inclusion criteria should be reconsidered, and recruitment sites expanded, to capture eligible persons and adequately power an efficacy study. (PsycInfo Database Record (c) 2022 APA, all rights reserved).
Universal pulse design of refocusing kT-point pulses using parallel transmission: application to three-dimensional T2-weighted sequences at 7T (2017)

T2-weigthed sequences are particularly sensitive to the RF field inhomogeneity problem due to the errors accumulated by the imperfections of the train of refocusing pulses. In this work we report a universal RF pulse design for 3D refocusing pulses utilizing parallel transmission (pTx) to mitigate the RF inhomogeneity problem at ultra-high field.In this work Average Hamiltonian Theory was used to synthetize with pTx a single non-selective refocusing pulse able to mitigate the RF field inhomogeneity problem at 7T while optimizing its scaling properties in the presence of static field offsets. The design was performed under explicit power and specific absorption rate constraints on a database of 10 subjects. Simulations were conducted to support the theory and in-vivo brain imaging experiments using the Nova 8Tx-32Rx coil were finally carried out on additional test subjects to validate the proposed design with variable flip angle three-dimensional T2-weighted sequences at 7T. The simulation and experimental data demonstrate great improvement with the proposed calibration-free universal pulses, reaching on average 8 % normalized root mean square rotation angle error over the test subjects, compared to the standard, non-pTx, circularly-polarized mode of excitation.This work completes further the spectrum of 3D universal pulses to mitigate the RF field inhomogeneity problem throughout all 3D MRI sequences and without any pTx calibration. The approach returns a single pulse which can be scaled to match the desired flip angle train, thereby increasing the modularity of the proposed plug and play approach.
C(2)-Carboxy and Carboxymethyl Cephems (1989)

Abstracl -A series of C(2)-substituted [methyl, carboxy and carboxymethyll cephems have been prepared.Test data show a significant reduction in antiblot~c activity.Penicillin binding protein (PBP) studies show a decreased affinity to essential PBP-3 in S , aureus X1.l and E toll K12.The effect is believed to be steric in nature.We recently reported the synthesis of N-Boc-cephems using Boc anhydride, DMAP 14-dimethylaminopyridinel on the cephem amides.'I1 to 21Although this reaction also works on the a or R sulfoxides, the corresponding p o r S sulfoxides failed to give the N-Boc derivatives, resulting instead in C-carboxylation to give the C(2)-t-Bu ester 5.
Role of RNase H1 in DNA repair: removal of single ribonucleotide misincorporated into DNA in collaboration with RNase H2 (2015)

Several RNases H1 cleave the RNA-DNA junction of Okazaki fragment-like RNA-DNA/DNA substrate. This activity, termed 3'-junction ribonuclease (3'-JRNase) activity, is different from the 5'-JRNase activity of RNase H2 that cleaves the 5'-side of the ribonucleotide of the RNA-DNA junction and is required to initiate the ribonucleotide excision repair pathway. To examine whether RNase H1 exhibits 3'-JRNase activity for dsDNA containing a single ribonucleotide and can remove this ribonucleotide in collaboration with RNase H2, cleavage of a DNA8-RNA1-DNA9/DNA18 substrate with E. coli RNase H1 and H2 was analyzed. This substrate was cleaved by E. coli RNase H1 at the (5')RNA-DNA(3') junction, regardless of whether it was cleaved by E. coli RNase H2 at the (5')DNA-RNA(3') junction in advance or not. Likewise, this substrate was cleaved by E. coli RNase H2 at the (5')DNA-RNA(3') junction, regardless of whether it was cleaved by E. coli RNase H1 at the (5')RNA-DNA(3') junction in advance or not. When this substrate was cleaved by a mixture of E. coli RNases H1 and H2, the ribonucleotide was removed from the substrate. We propose that RNase H1 is involved in the excision of single ribonucleotides misincorporated into DNA in collaboration with RNase H2.
Immunization Maneuvers to Circumvent the Limited Capacity of Peripheral Lymph Nodes for Exogenous DC and Enhance Immunologic Control of Tumors (2004)

s for the 19th Annual Scientific Meeting of the International Society for Biological Therapy of Cancer, San Francisco, California, November 4-7, 2004: Dendritic Cells and Vaccines
An efficient, high-power F2 laser near 157 nm (1978)

We have demonstrated high powers (7 MW) and high efficieny (3.5%) in an e-beam excited, molecular F2 laser operating in mixtures of high pressure He and a few Torr of F2. The wavelengths of the three F2 laser lines observed are 156.71, 157.48, and 157.59 nm.
A network forensics tool for precise data packet capture and replay in cyber-physical systems (2016)

Network data packet capture and replay capabilities are basic requirements for forensic analysis of faults and securityrelated anomalies, as well as for testing and development. Cyber-physical networks, in which data packets are used to monitor and control physical devices, must operate within strict timing constraints, in order to match the hardware devices' characteristics. Standard network monitoring tools are unsuitable for such systems because they cannot guarantee to capture all data packets, may introduce their own traffic into the network, and cannot reliably reproduce the original timing of data packets. Here we present a high-speed network forensics tool specifically designed for capturing and replaying data traffic in Supervisory Control and Data Acquisition systems. Unlike general-purpose "packet capture" tools it does not affect the observed network's data traffic and guarantees that the original packet ordering is preserved. Most importantly, it allows replay of network traffic precisely matching its original timing. The tool was implemented by developing novel user interface and back-end software for a special-purpose network interface card. Experimental results show a clear improvement in data capture and replay capabilities over standard network monitoring methods and general-purpose forensics solutions.
Interrogation of the Active Sites of Protein Arginine Deiminases (PAD1, -2, and -4) Using Designer Probes (2013)

Protein arginine deiminases (PADs) are involved in a number of cellular pathways, and they catalyze the transformation of peptidyl arginine residue into a citrulline as part of post-translational modifications. To understand ligand preferences, a group of probe molecules were investigated against PAD1, PAD2, and PAD4. These probe molecules carried a well-known covalent modifier of the catalytic cysteine residue, 2-chloroacetamidine moiety, which was tethered to an α-amino acid via a carbon linker. The chain length for the linker varied from 0 to 4. Time-dependent assays indicated that 2-chloroacetamidine (2CA) with no linker inhibited all PAD enzymes with a similar trend in the second-order rate constants, although with poor affinity. Among the other three probe molecules, compound 3 with a three-carbon linker exhibited the best second-order rate constants for optimal ligand reactivity with the binding site. These analyses provide insights into the relative patterns of covalent inactivation of PAD isozymes and the design of novel inhibitors targeting PAD enzymes as potential therapeutic targets.
Optimisation of Conditions for the Affinity Chromatography of Human Enterokinase on Immobilised p-Aminobenzamidine. Improvement of the Preparative Procedure by Inclusion of Negative Affinity Chromatography with Glycylglycyl-aniline (1978)

The affinity chromatography of human enterokinase using p-aminobenzamidine as the ligand [Grant, D.A.W. & Hermon-Taylor, J. (1976) Biochem. J. 155, 243-254] has been reassessed and the optimal conditions for the synthesis and operation of the derivatised gel defined. Satisfactory adsorbants were only produced using high concentrations of both CNBr and spacer-arm in the initial coupling slurry. Under these conditions it seemed likely that the majority of the ligand in a sterically favourable position to bind enterokinase was on the external surface of the bead. Trypsin binding to the adsorbant was not so critically dependent on the synthetic conditions and correlated closely with the degree of substitution. Dilution of the adsorbant with unlabelled Sepharose 4B indicated that there was more than one binding site per enterokinase molecule. The highest affinity was presumably for the active site, with adsorption supported by secondary interactions with spacer-arm or gel matrix not necessarily on the same bead. Maximal resolution was obtained by prolonged washing of the gel after loading; two populations of intestinal aminopeptidase were identified. Substitution of aniline for p-aminobenzamidine abolished specific enterokinase adsorption and improved the purification procedure by further removal of onon-specifically adsorbed contaminants.