gebhart/patrepeval huggingface dataset:
The evolutionary background and functional consequences of the rs2071307 polymorphism in human tropoelastin (2020)

Elastin is a major polymeric protein of the extracellular matrix, providing critical properties of extensibility and elastic recoil. The rs2071307 genomic polymorphism, resulting in the substitution of a serine for a glycine residue in a VPG motif in tropoelastin, has an unusually high minor allele frequency in humans. A consequence of such allelic heterozygosity would be the presence of a heterogeneous elastin polymer in up to 50% of the population, a situation which appears to be unique to Homo sapiens. VPG motifs are extremely common in hydrophobic domains of tropoelastins and are the sites of transient β-turns that are essential for maintaining the conformational flexibility required for its function as an entropic elastomer. Earlier data demonstrated that single amino acid substitutions in tropoelastin can have functional consequences for polymeric elastin, particularly when present in mixed polymers. Here, using NMR and molecular dynamics approaches, we show the rs2071307 polymorphism reduces local propensity for β-turn formation, with a consequent increase in polypeptide hydration and an expansion of the conformational ensemble manifested as an increased hydrodynamic radius, radius of gyration and asphericity. Furthermore, this substitution affects functional properties of polymeric elastin, particularly in heterogeneous polymers mimicking allelic heterozygosity. We discuss whether such effects, together with the unusually high minor allele frequency of the polymorphism, could imply some some evolutionary advantage for the heterozygous state.
Vector Sequences Are Not Detected in Tumor Tissue from Research Subjects with Ornithine Transcarbamylase Deficiency Who Previously Received Adenovirus Gene Transfer (2013)

A 66-year-old woman heterozygous for a mutation in the ornithine transcarbamylase gene (Otc) participated in a phase I gene therapy trial for OTC deficiency. She received an adenovirus (Ad) vector expressing the functional OTC gene by intraportal perfusion. Fourteen years later she developed and subsequently died of hepatocellular carcinoma. A second subject, a 45-year-old woman, enrolled in the same trial presented with colon cancer 15 years later. We sought to investigate a possible association between the development of a tumor and prior adenoviral gene transfer in these two subjects. We developed and validated a sensitive nested polymerase chain reaction assay for recovering recombinant Ad sequences from host tissues. Using this method, we could not detect any Ad vector DNA in either tumor or normal tissue from the two patients. Our results are informative in ruling out the possibility that the adenoviral vector might have contributed to the development of cancer in those two subjects.
Towards Automated Monomer Synthesis: A Streamlined Approach for the Synthesis of Cyclic Carbonates (2020)

Accessing cyclic carbonate monomers on large scales is critical for development of any new carbonate-based material platform. This is particularly important in the context of using automated experimental systems for materials synthesis, which can often require large inputs of starting materials. However, the synthesis of carbonate monomers can be a challenging and tedious endeavor, requiring multiple synthetic steps and purifications. To address this, we report a drastically improved and scalable process for the synthesis of carbonate monomers via a two-step route that avoids the use of hazardous phosgene or chloroformate reagents. The cyclic carbonate monomers can be obtained in high yields and with minimal need for chromatographic purification. This process enables rapid access to a broad array of functional groups on the carbonate monomer and monomers generated from procedure can readily be polymerized via ring-opening polymerization.&lt;br&gt;
Abstract 9779: Abdominal Aortic Aneurysm Formation was Suppressed by an Agonist for α7 Nicotinic Acetylcholine Receptor via NF-kB Inactivation (2015)

Background: Previously we reported that activation of vagal nerve by acetylcholinesterase inhibitors attenuated atherogenesis via suppression of inflammatory responses. α7 nicotinic acetylcholine receptor (nAchR) plays an important role in vagal nerve activation. We sought to determine whether AR-R17779, a selective agonist of α7 nAchR, affects the development of abdominal aortic aneurysm (AAA). Methods and Results: AAA was induced by topical application of calcium chloride (CaCl2) to abdominal aorta (AAA group). NaCl (0.9%) was substituted for CaCl2 as a sham operation (SHAM group). AR-R17779 was administered in drinking water (AAA/AR-R group). One and 6 weeks after the operation, aortic tissue was excised for histological and molecular analyses. Aortic diameter and macrophage infiltration into the aortic adventitia were increased in AAA group compared with SHAM group at 6 weeks. Treatment with AR-R17779 reduced the diameter of the aorta (0.73±0.10 mm vs. 1.07±0.15 mm in AAA, p&lt;0.01) and macrophage infiltration compared with AAA group. Wavy morphology of the elastic lamellae was lost in AAA group while it was preserved in AAA/AR-R group. Expression of inflammatory cytokines (IL-1β, IL-6, MCP-1) and matrix metalloproteinase (MMP)-2 and 9 activities were enhanced in AAA group, which was suppressed in AAA/AR-R group. AR-R17779 treatment suppressed CaCl2-induced expression of cytokines, activities of MMPs and NF-κB activation (p65 phosphorylation) at 1 week when aortic dilatation had not been developed. Conclusion: Treatment with AR-R17779 prevented the enlargement of abdominal aorta induced by CaCl2 in association with reduced inflammation and extracellular matrix disruption via NF-kB inactivation. These findings suggest a therapeutic potential of α7nAchR activation for prevention of AAA development.
PHYSICAL LAYER ABSTRACTION FOR PERFORMANCE EVALUATION OF LEO SATELLITE SYSTEMS FOR IOT USING TIME-FREQUENCY ALOHA SCHEME (2018)

One of the main issues in using a Low Earth Orbit (LEO) satellite constellation to extend a Low-Powered Wide Area Network is the frequency synchronization. Using a link based on random access solves this concern, but also prevents delivery guarantees, and implies less predictable performance. This paper concerns the estimation of Bit Error Rate (BER) and Packet Error Rate (PER) using physical layer abstractions under a time and frequency random scheme, namely Time and Frequency Aloha. We first derive a BER calculation for noncoded QPSK transmission with one collision. Then, we use the 3GPP LTE NB-IoT coding scheme. We analyze the interference that could be induced by repetition coding scheme and propose an efficient summation to improve the decoder performance. Finally, to estimate a PER for any collided scenario, we propose a physical layer abstraction, which relies on an equivalent Signal-to-Noise Ratio (SNR) calculation based on Mutual Information.
Personal Visualization and Personal Visual Analytics [Guest editors' introduction] (2015)

The articles in this theme issue focus on the unique challenges of designing visualization and visual analytic tools for use in a personal context. From a total of 17 submissions, we selected six representative articles that range from predesign studies to deployed prototypes. The articles focus on a range of applications, including quantified self presentations, personal note-taking, home energy consumption, and sports data collection.
A prospective comparison of enteroclysis and capsule endoscopy in the diagnosis of obscure gastrointestinal bleeding (2003)

Purpose: Enteroclysis is considered the gold standard for evaluation of small bowel diseases. Small bowel series is preferred because of its simplicity and lack of patient (pt) discomfort. Recently, capsule endoscopy (CE) was shown to be superior to small bowel radiography for evaluation of small bowel diseases. (Gastroenterol 2002; 123; 999–1005) This study was undertaken to prospectively study the diagnostic yield of enteroclysis compared with CE in pts with obscure gastrointestinal bleeding.
The epoxidation of unsaturated macrolides. Stereocontrolled routes to ionophore subunits (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe epoxidation of unsaturated macrolides. Stereocontrolled routes to ionophore subunitsStuart L. Schreiber, Tarek. Sammakia, Bernard. Hulin, and Gayle. SchulteCite this: J. Am. Chem. Soc. 1986, 108, 8, 2106–2108Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/ja00268a070https://doi.org/10.1021/ja00268a070research-articleACS PublicationsRequest reuse permissionsArticle Views693Altmetric-Citations93LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Spatio-temporal regulation of ADAR editing during development in porcine neural tissues (2012)

Editing by ADAR enzymes is essential for mammalian life. Still, knowledge of the spatio-temporal editing patterns in mammals is limited. By use of 454 amplicon sequencing we examined the editing status of 12 regionally extracted mRNAs from porcine developing brain encompassing a total of 64 putative ADAR editing sites. In total 24 brain tissues, dissected from up to five regions from embryonic gestation day 23, 42, 60, 80, 100 and 115, were examined for editing. Generally, editing increased during embryonic development concomitantly with an increase in ADAR2 mRNA level. Notably, the Gria2 (GluR-B) Q/R site, reported to be ~100% edited in previous studies, is only 54% edited at embryonic day 23. Transcripts with multiple editing sites in close proximity to each other exhibit coupled editing and an extraordinary incidence of long-range coupling of editing events more than 32 kb apart is observed for the kainate glutamate receptor 2 transcript, Grik2. Our study reveals complex spatio-temporal ADAR editing patterns of coordinated editing events that may play important roles in the development of the mammalian brain.
Nested Nemo Tree Discovery (2009)

This paper describes a simple distance vector protocol that exposes
only a default route towards the infrastructure in a nested NEMO
configuration. The draft extends the Neighbor Discovery Protocol
[RFC4861] in order to carry information and metrics which will help a
Mobile Router select its Attachment Router(s) in an autonomous fashion
and provides generic rules which guarantee that the interaction of
different selection processes will not create loops.
A case for ending monolithic apps for connected devices (2015)

Connected sensing devices, such as cameras, thermostats, in-home motion, door-window, energy, water sensors [1], collectively dubbed as the Internet of Things (IoT), are rapidly permeating our living environments [2], with an estimated 50 billion such devices in use by 2020 [8]. They enable a wide variety of applications spanning security, efficiency, healthcare, and others. Typically, these applications collect data using sensing devices to draw inferences about the environment or the user, and use the inferences to perform certain actions. For example, Nest [10] uses motion sensor data to infer home occupancy and adjusts the thermostat.
The Influence of Engine Lubricating Oil on Diesel Nanoparticle Emissions and Kinetics of Oxidation (2003)

&lt;div class="htmlview paragraph"&gt;Earlier work [&lt;span class="xref"&gt;1&lt;/span&gt;] shows that kinetics of Diesel soot oxidation is different from that of ethylene diffusion flame soot oxidation [&lt;span class="xref"&gt;2&lt;/span&gt;], possibly due to metals from lube oil. This study investigates the influence of metals on soot oxidation and the exhaust particle emissions using lube oil dosed fuel (2 % by volume). This method does not simulate normal lube oil consumption, but is used as a means of adding metals to particles for oxidation studies. This study also provides insight into the effect of systems that mix lube oil with fuel to minimize oil change service.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;The HTO-TDMA (High Temperature Oxidation-Tandem Differential Mobility Analyzer) technique [&lt;span class="xref"&gt;1&lt;/span&gt;] was used to measure the surface specific oxidation rate of Diesel particles over the temperature range 500-750 °C. Diesel particles sampled from the exhaust stream of a Diesel engine were size segregated by differential mobility and oxidized in situ in air in a heated flow tube of known residence time and temperature profile. The change in particle diameter after oxidation took place was measured and converted into the surface specific oxidation rate. The pre-exponential factors increased by about a factor of two, whereas the activation energy determined for the lubrication oil dosed Diesel particles was very close to that of undosed Diesel particles (108 kJ mol&lt;sup&gt;-1&lt;/sup&gt;, [&lt;span class="xref"&gt;1&lt;/span&gt;]). This suggests that the increase of active sites by the presence of Ca (and possibly by other metals included in the additive package of the lube oil) results in the faster oxidation rate.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Particle size measurements show that particle volume emissions, which are roughly proportional to particle mass, decreased by about a factor of two, but that particle number emissions increased by an order of magnitude with lube oil dosed fuel.&lt;/div&gt;
Chemoimmunotherapy reinduction with epratuzumab in children with ALL with marrow relapse: A Children's Oncology Group (COG) pilot study (ADVL04P2) (2007)

9513 Background: CD22, a 135kd protein restricted to B-cells, is expressed in &gt; 90% of childhood B-precursor acute lymphoblastic leukemia (ALL). We conducted a feasibility/phase 2 study of epratuzumab, a humanized monoclonal antibody against CD22, with reinduction chemotherapy in children with relapsed CD22+ ALL. Methods: The feasibility portion (n=12) of the study is reported here. Patients with first or later ALL marrow relapse at any time following diagnosis, ± extramedullary disease, with = 25% blasts expressing CD22 and a presenting white blood cell count (WBC) of = 50,000/μl, were eligible. Therapy consisted of a 14-day single agent phase (epratuzumab 360 mg/m 2 /dose IV twice weekly × 4 doses), followed by 4 weekly doses of epratuzumab in combination with standard reinduction chemotherapy (vincristine, prednisone, PEG-asparaginase, doxorubicin). Remission induction rates and minimal residual disease (MRD) by flow cytometry were determined at the end of this 6-week period. PK studies were performed by ELISA based immunoassay (prior + 30 minutes after infusions). Results: 12 evaluable patients, median age 10 years (range 3 - 18), were accrued. 9 pts were in 1st (n=5 early; n=4 late), and 3 pts in 2nd or later marrow relapse. The mean (±SD) trough epratuzumab concentration increased from 69±23 to 232±74 μg/ml during the initial 14 days. Surface CD22 was not detected by flow cytometry on peripheral blood leukemic blasts within 24 hours of drug administration in all but one patient, indicating effective targeting of leukemic cells by epratuzumab. The most frequent toxicities were grade 1–2 infusion reactions (n=9). Two dose limiting toxicities occurred: one patient had a Grade 4 seizure of unclear etiology and one patient had asymptomatic Grade 3 ALT elevation. 9 patients achieved a complete remission following chemoimmunotherapy, of whom 7 were MRD-negative. Conclusions: Treatment with epratuzumab plus standard reinduction chemotherapy is feasible and well tolerated in children with relapsed ALL, producing favorable early responses in the majority of patients. The phase II portion of the study is ongoing. [Table: see text]
Nanocapsules Synthesized by Miniemulsion Technique for Application as New Contrast Agent Materials (2007)

Abstract Nanocapsules containing the hydrophilic contrast agents Magnevist® and Gadovist® are synthesized in an inverse miniemulsion process. First, nanodroplets of 100 to 550 nm are formed which are subsequently encapsulated by an interfacial polyaddition in polymeric shells of polyurethane, polyurea and crosslinked dextran. The shell thickness can be adjusted by the monomer concentration. Due to the porosity of the polymeric shell, exchange of water molecules through the capsule wall can be ensured and no significant compromises in the T 1 relaxitivity of the contrast compound is observed for magnetic resonance imaging (MRI). This clearly indicates the potential use of the contrast agent filled nanocapsules as new MRI contrast agents. magnified image
Adjuvant therapy for intracoronary stents. Investigations in atherosclerotic swine. (1990)

Early thrombosis has complicated human stent implantation in several trials. To determine the best anticoagulation/antiplatelet therapy to maintain stent patency after percutaneous transluminal coronary angioplasty, we implanted the flexible balloon-expandable coil stent into the left anterior descending coronary artery of 28 atherosclerotic 8-month-old Hanford miniature swine. Animals were randomly assigned to one of three treatment groups: group A, aspirin (1 mg/kg/day) and dipyridamole (1 mg/kg three times a day); group B, aspirin and dipyridamole (same doses) plus Coumadin (dose required to prolong prothrombin time 1.3-1.5-fold that of normal); and group C, control. Adjuvant therapy was begun 3 days before stenting. Two pigs (one from group A and one from group B) died during implantation, both without thrombosis. Twenty-six animals survived until follow-up angiography and sacrifice at 1 month. No occlusive thrombosis of the stent occurred in survivors. Reduction of the stent lumen diameter was observed in every case at follow-up. Percent lumen reduction was 19% in group A, 26% in group B, and 24% in group C. Marked smooth muscle cell hyperplasia was seen by light and transmission electron microscopy at stent struts. Scanning electron microscopy of the luminal surface showed a variable morphology consisting of normal endothelium, adherent leukocytes, stellate periluminal cells, and occasional fibrin strands and red blood cells. Luminal narrowing was not affected by anticoagulation therapy, antiplatelet drugs, cholesterol level, or stent sizing. We conclude that occlusive thrombosis does not complicate stent implantation in this model but that substantial luminal narrowing due in part to smooth muscle hyperplasia does occur. The significance of luminal narrowing at the stent site requires further study.
Supplementary Figures from E7386, a Selective Inhibitor of the Interaction between β-Catenin and CBP, Exerts Antitumor Activity in Tumor Models with Activated Canonical Wnt Signaling (2023)

&lt;p&gt;Supplementary Figures 1-9. Supplementary Fig. S1 Wnt/β-catenin-dependent reporter activity in ECC10 cells. Supplementary Fig. S2 Effect of E7386 on the interaction between β-catenin and p300 in ECC10 cells. Supplementary Fig. S3 Comparison of IC50 values among β-catenin/CBP inhibitors, as determined by HEK-293 TCF/LEF reporter assay. Supplementary Fig. S4 Upstream regulators of gene expression changes in whisker follicle tissues of ApcMin/+ mice treated with E7386. Supplementary Fig. S5 Inhibitory activity of E7386 against cell growth in ECC10 cells. Supplementary Fig. S6 Antitumor activity of E7386 and ICG-001 in a human ECC10 gastric tumor xenograft model. Supplementary Fig. S7 Gating strategy for the flow cytometry analysis of myeloid and T-cell populations. Supplementary Fig. S8 Flow cytometry analysis of the effect of E7386 on immune cell populations in the MMTV-Wnt1 model. Supplementary Fig. S9 Effect of PRI-724 on spontaneous intestinal polyp formation in ApcMin/+ mice.&lt;/p&gt;
Mutation analysis of the 5′ noncoding regulatory region of the BCL-6 gene in non-Hodgkin lymphoma: evidence for recurrent mutations and intraclonal heterogeneity (2000)

The BCL-6 proto-oncogene is involved in the genesis of non-Hodgkin lymphoma (NHL). Rearrangements due to chromosomal translocations and somatic mutations of the 5' noncoding regulatory region of the BCL-6 gene are potential mechanisms for altering its expression in NHL. To further elucidate the nature of the somatic mutations in the regulatory region of this gene, we have studied 10 healthy donors and 11 NHL biopsy samples by extensive molecular cloning and sequencing. In addition, we analyzed the BCL-6 genes of tumor and nontumor cells from 2 of the cases. The germ line sequence of this region was defined, which differs in 7 positions from that previously reported. In addition, 1 polymorphic variation at position 397(G or C) was identified. Deletions, insertions, and repeated substitution mutations were detected among the molecular isolates in 8 tumor specimens, with a mutational incidence ranging from 1.3 x 10(-3) to 1.3 x 10(-2)/bp (base pair). A total of 20 distinct substitution mutations, 1 insertion and 3 deletions were observed. One of these deletion mutations and 2 of the substitutions were observed in more than 1 tumor specimen from different individuals. In 3 tumor samples, identical mutations affecting both alleles were observed. These findings suggest the presence of mutational hot spots and hot specific events, a finding supported by our compilation of previously published data. In 6 samples, the nucleotide sequences showed evidence of intraclonal heterogeneity, consistent with a stepwise ongoing mutational process affecting the BCL-6 gene in the tumor cells. These mutations accumulating in the regulatory region of the BCL-6 gene could play a role in lymphoma progression and in the transformation of follicular lymphomas to more aggressive large cell lymphomas. (Blood. 2000;95:1400-1405)
Inhibition of Angiogenesis‐Relevant Receptor Tyrosine Kinases by Sulindac Analogues (2005)

It's in the blood. Analogues (see formula) of the non-steroidal inflammatory drug Sulindac are potent and selective inhibitors of the angiogenesis-related receptor tyrosine kinases VEGFR-2 and -3, IGF1R, FGF1R and Tie-2; this suggests a possible link between the antiangiogenic properties of Sulindac metabolites and kinase inhibition.