gebhart/patrepeval huggingface dataset:
Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture (2023)

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.
Chain Polymerization (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.
Hydrogen Ion Metabolism (1977)

The renal and respiratory systems regulate acid base homeostasis by modifying the bicarbonate buffer pair HCO 3 - and CO 2 ; other buffer systems adjust to alterations in this pair. The pH change following addition of metabolic acid, or base, is modified initially by the body's buffers. Subsequent respiratory compensation, by retention or excretion of CO 2 , modifies further this change before renal corrective responses finally occur. A primary respiratory acid base change is modified initially by cellular buffers, with renal compensatory mechanisms adjusting slowly to this change. However correction of the respiratory pH disorder only occurs with correction of the primary disease process. The body's capacity, therefore, to adjust to a metabolic acid base defect, appears greater than that observed with a primary respiratory pH abnormality. Treatment in all acid base disorders focuses initially upon the primary diseases process; thereafter therapeutic manipulation of the HCO 3 - , CO 2 buffer pair, to aid the body's compensatory processes, can be considered.
Evaluation of long term survival in pretreated metastatic colorectal cancer patients undergoing GOLFIG chemoimmunotherapy regimen. (2019)

e15057 Background: In the last few years, there has been a renewed interest on the potential use of immunotherapy alone or combined to chemotherapy (CHT) for mCRC patients. GOLFIG regimen (biweekly Gemcitabine+FOLFOX and IL2 and GM-CSF) was designed to enhance immunomodulating effects of selected cytotoxic drugs by combining them with cytokines able to promote priming and effector phases of the immune-response. This regimen has been tested in two different phase II and III clinical trials in mCRC patients, whose successful results have been published. Here we present the results a retrospective analyses including all the patients treated in a period of 16 years. Methods: This is a multi-institutional retrospective study including 179 mCRC patients (106 men, 73 women). They received a median of 12 courses of GOLFIG regimen (treated between June 2002 and November 2018). K-RAS mutational status has also been evaluated in 74 pts (41 wild type and 33 mutated); as for sidedness 112 pts had a left disease and 67 pts right disease; 71 pts received only one previous CHT line and 100 more than two lines. PFS and OS were evaluated by Kaplan-Meier curves and Cox-regression analyses in different subgroups (RAS mutational status, sidedness, previous CHT lines) to estimate their effect on survival endpoints. Results: We recorded a mean PFS and OS of 15,28 [95%CI:10,36-20,20] and 24,61 [95%CI:19,07-30,14] months, respectively, with no difference in efficacy outcomes observed among the different subgroups (one vs. more than one previous CHT lines; left vs. right primary side; k-ras status mutated vs. wt). Finally, we recorded a 2, 5 and 10 year OS-rate, in 42, 17 and 14 percent of the patients, respectively. The occurrence of self-limiting autoimmunity was confirmed as highly predictive of longer survival. Conclusions: These results confirm that GOLFIG regimen has strong efficacy in mCRC pts and may represent a reliable option in pretreated setting without evident effect of known prognostic variants. Such data offer a strong basis for future clinical trials in mCRC patients, where GOLFIG may represent a scaffold for combinatory immunotherapy approaches with immune-checkpoint blocking drugs.
Regioselectivity in the intramolecular ene reaction of cyclopropene derivatives (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegioselectivity in the intramolecular ene reaction of cyclopropene derivativesAlbert Padwa and William F. RiekerCite this: J. Am. Chem. Soc. 1981, 103, 7, 1859–1860Publication Date (Print):April 1, 1981Publication History Published online1 May 2002Published inissue 1 April 1981https://pubs.acs.org/doi/10.1021/ja00397a056https://doi.org/10.1021/ja00397a056research-articleACS PublicationsRequest reuse permissionsArticle Views173Altmetric-Citations26LEARN 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
Effect of orthodontic adhesive thickness on force required by debonding pliers (2014)

This in vitro study evaluated the relationship between removal force and the thickness of three orthodontic adhesives, namely, light- and chemical-cured resin cements and a resin-modified glass ionomer cement. The thickness of each adhesive was 50, 100, 150, or 200 µm, and all adhesives were bonded on bovine incisors. Removal force was measured before (TC-0) and after 1,000 thermal cycles (TC-1000), and values were compared. At TC-0, the removal strengths for adhesive thicknesses of 50 and 100 µm were significantly lower than those for thicknesses of 150 and 200 µm (P < 0.05). At TC-1000, removal strengths for adhesive thicknesses of 50 and 100 µm were also significantly lower than those for 150 and 200 µm. Superbond Orthomite specimens showed a significant difference in removal strength between TC-0 and TC-1000 (P < 0.05) at all thicknesses. There was no significant difference in the distribution of adhesive remnant index scores at any thickness. These findings indicate that decreasing the thickness of applied orthodontic adhesive reduces the removal strength required.
Molded and laminated infrared imager (2003)

In previous work, laminated midwave infrare imagers were designed and manufactured. These systems used the technique of laminating a piece of plastic on to a silicon substrate lens and then single-point diamond turning an aspheric/diffractive surface on the plastic. These lenses had a focal length of 50 mm and f/# of 2.6. This paper updates the progress of the developing prototype to show initial results of compression molding the aspheric/diffractive surface onto the plastic laminated surface. The results of the previous built imagers will be compared to the ones that have been molded.
A method for the prediction of GPCRs coupling specificity to G-proteins using refined profile Hidden Markov Models (2005)

Our method demonstrates high correct classification rate. Unlike previously published methods performing the same task, it does not require any transmembrane topology prediction in a preceding step. A web-server for the prediction of GPCRs coupling specificity to G-proteins available for non-commercial users is located at http://bioinformatics.biol.uoa.gr/PRED-COUPLE.
Sensor-based Autonomous Path-Planner for Sea-Bottom Exploration and Mosaicking∗∗This work has been carried out at the Centre for Autonomous Marine Operations and Systems (AMOS). The Norwegian Research Council is acknowledged as the main sponsor of AMOS through the Centres of Excellence funding scheme, Project number 223254. (2015)

A typical mission for an underwater vehicle is to research and map OOIs (Objects Of Interest). Objects Of Interest are specified in connection with the mission purposes, relevant examples span from biological species (e.g. seagrass or coral colonies) to artifacts (e.g. ship wrecks). For their research and mapping the deployment of Autonomous and Remotely Operated Vehicles is becoming the state-of-art, due to their ease of performing difficult operations in a safe way. Moreover, photo-mosaicking tools can be used to provide a complete map of the explored area. In order to achieve this aim, the navigation usually relies on simple lawn-mower or zig-zag patterns, where an area is scanned extensively to collect the pictures, that would be analyzed, processed and stitched after the mission. This paper aims to increase the autonomy of underwater vehicles that are equipped with a still-picture camera by using a deliberative, sensor-driven planning strategy. By sensing the environment extracting its information from the pictures, the path can be defined on-the-fly, in order to increase the collected data.
Hydrophilic vs hydrophobic: which is the better option? (2008)

Dr Christophe Chassain believes blue-blocking square-edged hydrophilic lenses are just as safe as their hydrophobic counterparts
ChemInform Abstract: COPPER(II) SIMPLE AND MIXED COMPLEXES CONTAINING TRIDENTATE LIGANDS WITH OXYGEN, SULFUR OR SELENIUM DONOR ATOMS IN AQUEOUS SOLUTION. SPECTROSCOPIC INVESTIGATIONS AND THERMODYNAMIC CONSIDERATIONS (1981)

Abstract Anhand EPR‐ und elektronenspektroskopischer Untersuchungen wird die Komplexbildung von Cu(II) mit 0xy‐, Thio‐ und Se1enodiacetat sowie 2,2′‐Bipyridy1 und 2,2′,2"‐Terpyridyl in Lösung betrachtet.
Competitive ABPP unveiling palmostatin B targets among the serine hydrolases in mouse brain membrane proteome. (2015)

&lt;p&gt;Membranes (100 µg) were pretreated for 1 h with DMSO or the indicated concentrations of the serine hydrolase inhibitors, after which TAMRA-FP labelling was conducted for 1 hour at RT. The reaction was stopped, 10 µg protein (10 µl) was loaded per lane and the proteins were separated in SDS-electrophoresis gel (10%). TAMRA-FP labeling was visualized after in-gel fluorescence imaging as described in the Methods section. Molecular weight markers are indicated at left. Reference inhibitors JJKK-048, WWL70, THL and JZL195 were used at the indicated concentrations to identify the following serine hydrolases from the gel: fatty acid amide hydrolase (FAAH), inhibited by JZL195 &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Long2" target="_blank"&gt;[21]&lt;/a&gt;; MAGL doublet, inhibited by JJKK-048 &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Aaltonen1" target="_blank"&gt;[22]&lt;/a&gt; and JZL195 &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Long2" target="_blank"&gt;[21]&lt;/a&gt;; ABHD6, inhibited by WWL70 &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Li1" target="_blank"&gt;[23]&lt;/a&gt;–&lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Patel1" target="_blank"&gt;[24]&lt;/a&gt;, THL &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Parkkari1" target="_blank"&gt;[18]&lt;/a&gt;, and also by JZL195 at the used concentration; BAT5, inhibited by THL &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Hoover1" target="_blank"&gt;[4]&lt;/a&gt;, &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Parkkari1" target="_blank"&gt;[18]&lt;/a&gt;. Note that palmostatin B dose-dependently inhibits probe labeling of BAT5, ABHD12 and LYPLA1/2, two closely-related proteins migrating at ∼25 kDa &lt;a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109869#pone.0109869-Adibekian1" target="_blank"&gt;[25]&lt;/a&gt;. At the highest concentration, probe labeling of MAGL and ABHD6 is also inhibited. Note the absence of additional visible targets for palmostatin B at the tested concentrations. Data are representative from three ABPP experiments with similar outcome.&lt;/p&gt;
Tools for integrating multidomain technologies into microelectronic circuit design curricula (2003)

Current advances in technology, along with application-specific demands in areas such as wireless communication and biomedical engineering, are driving the development of tools and techniques for producing miniaturized system elements from mechanical, magnetic, fluidic and many other nonelectrical domains. Each domain poses its own design and validation challenges. Moreover, integration of multidomain components with electrical components is a challenging task in itself. The authors discuss curriculum materials they are developing to prepare students to meet these design challenges.
Local activation of surface and hybrid acoustic waves in optical microwires (2018)

Elastic vibrations in subwavelength structures have gained importance recently in fundamental light-matter studies and various optoacoustic applications. Existing techniques have revealed the presence of distinct acoustic resonances inside silica microwires yet remain unable to individually localize them. Here, we locally activate distinct classes of acoustic resonances inside a tapered fiber using a phase-correlation distributed Brillouin method. Experimental results verify the presence of surface and hybrid acoustic waves at distinct fiber locations and demonstrate, to the best of our knowledge, the first distributed surface acoustic wave measurement. This technique is important for understanding properties of optoacoustic interactions and enabling designs of novel optomechanical devices.
Reliability of Tanner stage assessments in a multi‐center study (1990)

Tanner stage indices have been frequently used in research studies to characterize the level of sexual maturation among adolescents. The Cooperative Study of Sickle Cell Disease (CSSCD) is a large multi-center study in which the assessment of Tanner stage indices has been performed to describe delays in sexual maturation and correlates of delays. Rigorous training, however, in rating Tanner stages was not provided for the clinicians in the study. Data from the CSSCD were analyzed to characterize the reliability of the assessment of sexual maturation in this study, and demonstrate the potential for increasing the reliability by more careful training. In lieu of a gold standard, a maximum likelihood algorithm was employed to examine the longitudinal consistency of Tanner stage assessments. Based on the assumption that the underlying process of sexual maturation is progressive, models were developed that allowed one to estimate jointly the incidence distribution for the attainment of Tanner stages and the error rates of assessment. Estimated false-positive rates for assessing the attainment of Tanner stages from the CSSCD ranged from 2% to 19%. Estimated false-negative rates ranged from 1% to 18%. The occurrence of these errors was found not to vary markedly with the subject's age. Error rates of this magnitude can introduce considerable bias to the estimation of the distribution of Tanner stages and result in serious losses in relative efficiency. While the validity of Tanner stage indices can be demonstrated from study data, the loss in statistical efficiency and power associated with the study error rates was severe. This underscores the utility of careful training in pubertal rating for research studies.
The 6 O’Clock Anchor Increases Labral Repair Strength in a Biomechanical Shoulder Instability Model (2019)

Objectives: Despite a growing body of literature regarding optimal repair configurations, little is known about inferior suture anchor placement (6 o’clock position). Here, we determine the biomechanical strength of adding a 6’oclock anchor to a “standard” Bankart repair in a normal glenoid and a 13% anterior bone loss model. Methods: 12 cadaveric shoulders were tested on a six axis industrial robot to measure the peak resistance to translation force with anterior displacement (1 centimeter). The rotator cuff muscles were loaded during testing to simulate physiological conditions. Test conditions included intact shoulder, Bankart lesion, Bankart repair (3, 4, and 5 o’clock anchors), and Bankart repair with a 6 o’clock anchor. A 13% anterior bone defect was then created (based on pretest CT scan) and all conditions were repeated. Repeated measures ANOVA was used to test for significant differences among groups. Results: In the no bone loss group, the addition of a 6 o’clock anchor yielded the highest peak resistance force (52.8 N, SD: 4.5 N) and was significantly stronger than the standard Bankart repair by 15.8% (7.2 N, p = 0.003). With 13% bone loss from the anterior glenoid, both the standard Bankart repair (peak force 49.3 N, SD: 6.1 N, p = 0.02) and repair with the addition of the 6 o’clock anchor (peak force 52.6 N, SD: 6.1 N, p = 0.006) had a significantly higher peak resistance force compared to the bone loss with Bankart lesion group (35.2 N, SD: 5.8 N). While the 6 o’clock anchor did increase the strength of the standard repair by 6.7%, this was not statistically significant (p = 0.9) in the bone loss model. Conclusion: The addition of a 6 o’clock suture anchor to a ”standard” Bankart repair increases to the peak resistance to translation force (no bone loss), although this additional strength is lost with creation of a 13% anterior glenoid bone defect.
Genes Involved in Galactooligosaccharide Metabolism in Lactobacillus reuteri and Their Ecological Role in the Gastrointestinal Tract (2019)

Strains of <i>Lactobacillus reuteri</i> are commonly used as probiotics due to their demonstrated therapeutic properties. Many strains of <i>L. reuteri</i> also utilize the prebiotic galactooligosaccharide (GOS), providing a basis for formulating synergistic synbiotics that could enhance growth or persistence of this organism <i>in vivo</i> In this study, in-frame deletion mutants were constructed to characterize the molecular basis of GOS utilization in <i>L. reuteri</i> ATCC PTA-6475. Results suggested that GOS transport relies on a permease encoded by <i>lacS</i>, while a second unidentified protein may function as a galactoside transporter. Two β-galactosidases, encoded by <i>lacA</i> and <i>lacLM</i>, sequentially degrade GOS oligosaccharides and GOS disaccharides, respectively. Inactivation of <i>lacL</i> and <i>lacM</i> resulted in impaired growth in the presence of GOS and lactose. <i>In vitro</i> competition experiments between the wild-type and <i>ΔlacS ΔlacM</i> strains revealed that the GOS-utilizing genes conferred a selective advantage in media with GOS but not glucose. GOS also provided an advantage to the wild-type strain in experiments in gnotobiotic mice but only on a purified, no sucrose diet. Differences in cell numbers between GOS-fed mice and mice that did not receive GOS were small, suggesting that carbohydrates other than GOS were sufficient to support growth. On a complex diet, the <i>ΔlacS ΔlacM</i> strain was outcompeted by the wild-type strain in gnotobiotic mice, suggesting that <i>lacL</i> and <i>lacM</i> are involved in the utilization of alternative dietary carbohydrates. Indeed, the growth of the mutants was impaired in raffinose and stachyose, which are common in plants, demonstrating that α-galactosides may constitute alternate substrates of the GOS pathway.<b>IMPORTANCE</b> This study shows that <i>lac</i> genes in <i>Lactobacillus reuteri</i> encode hydrolases and transporters that are necessary for the metabolism of GOS, as well as α-galactoside substrates. Coculture experiments with the wild-type strain and a <i>gos</i> mutant clearly demonstrated that GOS utilization confers a growth advantage in medium containing GOS as the sole carbohydrate source. However, the wild-type strain also outcompeted the mutant in germfree mice, suggesting that GOS genes in <i>L. reuteri</i> also provide a basis for utilization of other carbohydrates, including α-galactosides, ordinarily present in the diets of humans and other animals. Collectively, our work provides information on the metabolism of <i>L. reuteri</i> in its natural niche in the gut and may provide a basis for the development of synbiotic strategies.
Threshold behavior in the collision broadening of microcavity polaritons (1998)

The problem of the density-dependent homogeneous broadening of microcavity polaritons due to exciton-exciton Coulomb interaction is addressed using the self-consistent Born approximation. The theoretical results predict that, for resonant pumping of the lower polariton, the dependence of its broadening on the density of excitations has a threshold behavior. Below the threshold density, scattering is strongly inhibited because it involves only the small region of $k$ space where the polariton effective mass is very light. Above threshold, the region of $k$ space with excitonlike dispersion becomes allowed, giving the dominant contribution to the collision broadening.
A mutation allowing an mRNA secondary structure diminishes translation of Saccharomyces cerevisiae iso-1-cytochrome c. (1985)

The CYC1-239-O mutation in the yeast Saccharomyces cerevisiae produces a -His-Leu- replacement of the normal -Ala-Gly- sequence at amino acid positions 5 and 6, which lie within a dispensable region of iso-1-cytochrome c; this mutation can accommodate the formation of a hairpin structure at the corresponding site in the mRNA. The amount of the altered protein was diminished to 20% of the wild-type level, whereas the amount of the mRNA remained normal. However, in contrast to the normal CYC1+ mRNA that is associated mainly with four to seven ribosomes, the bulk of the CYC1-239-O mRNA is associated with one to four ribosomes. These results suggest that the stable secondary structure within the translated region of the CYC1 mRNA diminishes translation by inhibiting elongation.