gebhart/patrepeval huggingface dataset:
Glycans on the SARS-CoV-2 Spike Control the Receptor Binding Domain Conformation (2020)

The glycan shield of the beta-coronavirus (β-CoV) Spike (S) glycoprotein provides protection from host immune responses, acting as a steric block to potentially neutralizing antibody responses. The conformationally dynamic S-protein is the primary immunogenic target of vaccine design owing to its role in host-cell fusion, displaying multiple receptor binding domain (RBD) 'up' and 'down' state configurations. Here, we investigated the potential for RBD adjacent, N-terminal domain (NTD) glycans to influence the conformational equilibrium of these RBD states. Using a combination of antigenic screens and high-resolution cryo-EM structure determination, we show that an N-glycan deletion at position 234 results in a dramatically reduced population of the 'up' state RBD position. Conversely, glycan deletion at position N165 results in a discernable increase in 'up' state RBDs. This indicates the glycan shield acts not only as a passive hinderance to antibody meditated immunity but also as a conformational control element. Together, our results demonstrate this highly dynamic conformational machine is responsive to glycan modification with implications in viral escape and vaccine design.
Index guiding photonic liquid crystal fibers for application in fiber optic sensing setups (2011)

Photonic liquid crystal fibers (PLCFs) can be categorized in two principal groups: index guiding PLCFs and photonic bandgap PLCFs. In this paper we focus on index guiding PLCFs in which effective refractive index of the micro-structured cladding filled with liquid crystal is lower than refractive index of the fiber core. In such fibers broadband propagation of light is observed and also effective tuning of guiding properties is possible (i.e. birefringence, polarization dependent losses or attenuation tuning). Such fibers could be used for dynamic control of light in various fiber optics systems, including optical fiber sensing setups.
Photostimulated luminescence properties of Eu2+‐doped barium aluminate phosphor (2014)

An intense green photostimulated luminescence in BaAl2 O4 :Eu(2+) phosphor was prepared. The thermoluminescence results indicate that there are at least three types of traps (T1 , T2 , T3 ) with different trap depths in BaAl2 O4 :Eu(2+) phosphor according to the bands located at 327, 361 and 555 K, respectively, which are closely associated with the phosphor's long persistent luminescence and photostimulated luminescence properties. In addition, as a novel optical read-out form, a photostimulated persistent luminescence signal can be repeatedly obtained in BaAl2 O4 :Eu(2+) phosphor. This shows that re-trapping of the electron released from a deep trap plays an important role in photostimulated persistent luminescence.
Large Aperture, Scanning, L-Band SAR (2011)

We have developed the first L-band membrane-based active phased array. The antenna is a 16x16 element patch array with dimensions of 2.3mx2.6m. The array uses membrane-compatible Transmit/Receive (T/R) modules for electronic beam steering. We will discuss the antenna design, the fabrication of this large array, the T/R module development, the signal distribution approach and the measured results of the array
Oil & Gas (O&G) Industry Profile (2019)

We examine the role that 10 different industries can play in the circular economy and how they can realize significant value through large-scale adoption of circular principles. These are: metals and mining; oil and gas; chemicals; electricity; machinery and industrial equipment; information and communications technology (ICT); personal mobility; household; fashion and fast-moving consumer goods (FMCG). We also look at e-commerce’s cross-cutting industry role. Companies in every industry can generate circular value in three ways: value addition through cost reduction, revenue migration, and value addition through revenue generation. Although circular value opportunities are spread unevenly across the different industries, all present powerful ways to unlock true circularity at scale.
ChemInform Abstract: Generation of Chiral Phosphonium Dialkyl Phosphite as a Highly Reactive P‐Nucleophile: Application to Asymmetric Hydrophosphonylation of Aldehydes. (2009)

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 of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Electronic Band Shapes Calculated with Optimally Tuned Range-Separated Hybrid Functionals (2014)

Using a set of 20 organic molecules, we assess the accuracy of both the absorption and emission band shapes obtained by two optimally tuned range-separated hybrid functionals possessing 0% (LC-PBE*) and 25% (LC-PBE0*) of short-range exact exchange as well as by four other hybrid functionals including or not dispersion and long-range corrections (APF-D, PBE0-1/3, SOGGA11-X, and ωB97X-D). The band topologies are compared to experimental data and to previous time-dependent density functional theory calculations. It turns out that both optimally tuned functionals vastly improve the vibronic band shapes obtained with the non-tuned LC-PBE approach but, statistically, do not yield more accurate topologies than standard hybrid functionals. In other words, optimal tuning allows to obtain more accurate excited-state energies without degrading the description of band shapes. In addition, the LC-PBE0* 0-0 energies have been determined for a set of 40 compounds, and it is shown that the results are, on average, less accurate than those obtained by LC-PBE* for the same panel of molecules. The correlation between the optimal range-separation parameters determined for LC-PBE* and LC-PBE0* is discussed as well.
The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction (2013)

Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targets in the CASP competition. FindCore (Snyder and Montelione, Proteins 2005;59:673-686) is a superimposition independent method for identifying a core atom set and partitioning that set into domains. However, as FindCore optimizes superimposition by sensitively excluding not-well-defined atoms, the FindCore core may not comprise all atoms suitable for use in certain applications of NMR structures, including the CASP assessment process. Adapting the FindCore approach to assess predicted models against experimental NMR structures in CASP10 required modification of the FindCore method. This paper describes conventions and a standard protocol to calculate an "Expanded FindCore" atom set suitable for validation and application in biological and biophysical contexts. A key application of the Expanded FindCore method is to identify a core set of atoms in the experimental NMR structure for which it makes sense to validate predicted protein structure models. We demonstrate the application of this Expanded FindCore method in characterizing well-defined regions of 18 NMR-derived CASP10 target structures. The Expanded FindCore protocol defines "expanded core atom sets" that match an expert's intuition of which parts of the structure are sufficiently well defined to use in assessing CASP model predictions. We also illustrate the impact of this analysis on the CASP GDT assessment scores.
Corrigendum to “Erbium-Based Perfusion Contrast Agent for Small-Animal Microvessel Imaging” (2018)

[This corrects the article DOI: 10.1155/2017/7368384.].
Aortic invovement in fibromuscular dysplasia. 3-dimensional CT, case-control study. THE ARCADIA-POL BIS study (2020)

Abstract Background Fibromuscular dysplasia (FMD) is a non-atherosclerotic arterial disease that manifests as the presence of beaded or focal lesions in medium or small-sized arteries and may also include arterial dissection, aneurysm, and tortuosity. FMD could be revealed in various manifestations, however limited data on the involvement of the thoracic aorta is reported. Purpose To measure and evaluate involvement of thoracic aorta in patients with FMD. Methods We analysed aortas of 144 consecutive patients (mean age 50.2±14.0, 116 women) with confirmed FMD in at least one vascular bed. The control group consisted of 144 (mean age 50.5±14.0, 116 women) age and sex matched individuals. All patients underwent detailed clinical evaluation including angio-CT scan including aortic valve, thoracic aorta and coronary arteries. We measured the aortic valve annulus, sinus of valsalva, sinotubular junction, the diameters of ascending and descending aorta, aortic unfolding, the height of ostium of RCA and LCA and diameter of right and left coronary artery ostia in patients with fibromuscular dysplasia and compared them to matched controls. Results The FMD group had significantly smaller dimensions of aortic valve annulus and sinus of Valsalva than control group (2.3 [2.1–2.6] vs 2.9 [2.7–3.1] p&amp;lt;0,0001; 2.9 [2.7–3.2] vs 3.1 [2.8–3.3] p=0,0011 respectively). In addition the FMD group had a significantly greater mean diameter of the ascending and the descending aorta than the control group (3.1 [2.7–3.3] vs 3 [2.9–3] p=0,0436; 2.4 [2.2–2.7] vs 2.3 [1.8–2.5] p&amp;lt;0,0001 respectively). The height of the ostium of the left and of the right coronary artery was smaller in FMD than in the control group (1.2 [1.1–1.4] vs 1.3 [1.2–1.4] p=0,0001; 1.1 [1–1.3] vs 1.3 [1.1–1.4] p&amp;lt;0,0001 respectively). There was no difference in the diameter of sinotubular junction and the right and the left coronary artery ostias between the FMD and control groups (2.7 [2.5–2.9] vs 2.7 [2.5–2.9]; 0.3 [0.2–0.3] vs 0.3 [0.2–0.3]; 0.3 [0.3–0.3] vs 0.3 [0.3–0.4] respectively). Conclusions Patients with fibromuscular dysplasia display smaller dimensions of aortic valve and larger diameter of ascending and descending aorta as compared to control subjects. Despite the predominant clinical significance of focal pathologies in FMD patients, the disease may display a specific, pan-vascular phenotype. Funding Acknowledgement Type of funding source: None
Impact of inhibitor epitope profile on the neutralizing effect against plasma‐derived and recombinant factor VIII concentrates in vitro (2003)

The inhibitory capacity of plasma samples from 24 patients with severe haemophilia A and high-responding inhibitors were evaluated in a concentrate-based assay using two plasma-derived (Haemate and Monoclate-P) and three recombinant (Helixate, Recombinate and ReFacto) factor VIII concentrates and correlated with the corresponding epitope profile. In most, but not all, inhibitor plasmas with a relatively low reactivity against the von Willebrand-containing product Haemate, the main epitopes were located in the FVIII light chain. The reactivities within the group of recombinant products varied in that the reactivity against the B-domain deleted ReFacto was in general higher than that against Recombinate and Helixate. This difference did not correlate with any particular epitope profile and indicates that the B-domain, type of formulation and/or purification procedures may have an impact on the inhibitor reactivity in vitro. The ratio between the inhibitor titres in the concentrate-based assay and the Bethesda assay was dependent on the inhibitor plasma and concentrate used. Taken together, our results show that the reactivity of inhibitor plasmas varies considerably between different FVIII concentrates and that it does not fully correlate with the epitope profile. Potential clinical implications of the observed differences in inhibitor reactivity are discussed.
Evaluation of Primary Brain Tumor with Magnetic Resonance Imaging (2019)

The present study was a prospective study which was conducted among 30 patients with suspected brain tumor which were selected for undergoing MRI brain with IV contrast in Chettinad Hospital and Research Institute, Kelambakkam. All these patients were imaged on GE sigma 1.5 Tesla scanner, with the gradient strength 33mT/m at aslew rate of 120 mT/m/ms, an 8 channel head coil is used for signal receiver. Results: In this study, 30 patients were examined with the symptoms of brain tumor. Out of which, 23 patients were diagnosed with primary brain tumor. Many MRI sequences were done to rule out brain tumor. T2, T2 FLAIR, T1 FAT saturation pre contrast and post contrast were found to be best sequences to rule out primary brain tumor. Conclusion: MR is ideal imaging technique for evaluation of intracranial lesions because of excellent anatomic details as well as delineate pathological lesions discreetly. The diagnostic accuracy of MRI in the evaluation of brain tumors and tumors like lesions increases when combined with DWI and MRS with conventional MR imaging.
Data from Glypican-3–Specific CAR T Cells Coexpressing IL15 and IL21 Have Superior Expansion and Antitumor Activity against Hepatocellular Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer-related death in the world, and curative systemic therapies are lacking. Chimeric antigen receptor (CAR)–expressing T cells induce robust antitumor responses in patients with hematologic malignancies but have limited efficacy in patients with solid tumors, including HCC. IL15 and IL21 promote T-cell expansion, survival, and function and can improve the antitumor properties of T cells. We explored whether transgenic expression of IL15 and/or IL21 enhanced glypican-3-CAR (GPC3-CAR) T cells' antitumor properties against HCC. We previously optimized the costimulation in GPC3-CARs and selected a second-generation GPC3-CAR incorporating a 4-1BB costimulatory endodomain (GBBz) for development. Here, we generated constructs encoding IL15, IL21, or both with GBBz (15.GBBz, 21.GBBz, and 21.15.GBBz, respectively) and examined the ability of transduced T cells to kill, produce effector cytokines, and expand in an antigen-dependent manner. We performed gene-expression and phenotypic analyses of GPC3-CAR T cells and CRISPR-Cas9 knockout of the &lt;i&gt;TCF7&lt;/i&gt; gene. Finally, we measured GPC3-CAR T-cell antitumor activity in murine xenograft models of GPC3&lt;sup&gt;+&lt;/sup&gt; tumors. The increased proliferation of 21.15.GBBz T cells was at least in part dependent on the upregulation and maintenance of TCF-1 (encoded by &lt;i&gt;TCF7&lt;/i&gt;) and associated with a higher percentage of stem cell memory and central memory populations after manufacturing. T cells expressing 21.15.GBBz had superior &lt;i&gt;in vitro&lt;/i&gt; and &lt;i&gt;in vivo&lt;/i&gt; expansion and persistence, and the most robust antitumor activity &lt;i&gt;in vivo&lt;/i&gt;. These results provided preclinical evidence to support the clinical evaluation of 21.15.GPC3-CAR T cells in patients with HCC.&lt;/p&gt;&lt;/div&gt;
Synthesis and Characterization of UV‐Curable Resins from the Glycolysis of PET: Vinyl Ether/Maleate UV‐Curing System (2007)

Abstract The synthesis and characterization of photopolymerizable unsaturated α , ω ‐bismaleate poly(ethylene terephthalate) oligomer resins based on glycolysis of PET waste using diethylene glycol and the study of their photopolymerization with divinyl ethers have been described in a previous article. The use of PET glycolysis by DEG can be problematic because this oligoester is partially crystalline. The objective of this paper is to develop the UV‐curing technology for a new kind of glycolysate that are completely amorphous. Glycolysates with different molecular weights have been synthesized and functionalized by a methyl hemiester of maleic acid. The photopolymerization of these new functionalized oligoesters with divinyl ether is studied and the materials obtained are characterized. The influence of the glycolysate structures on the properties of the crosslinked materials is highlighted. magnified image
Generalized HIV-associated kaposi's sarcoma with multiorgan lesion in a comorbid patient (2023)

An important role in a number of different clinical manifestations of HIV infection is played by the pathology of the skin and mucous membranes. Kaposi sarcoma (KS) is a multifocal malignant tumor of vascular origin with a predominant lesion of the skin and involvement of internal organs. Prior to the development of the HIV epidemic, KS was considered a rare tumor. Under conditions of increasing immunosuppression, HIV-associated KS tends to have a more severe course, generalization, and is accompanied by damage to visceral organs, leading to the death of patients. The authors demonstrate a clinical case of generalized KS with lesions of the skin, mucous membranes and internal organs (lungs) in a patient with HIV infection. The pulmonary form of KS is rare, but often leads to death.
Toponym matching through deep neural networks (2017)

Toponym matching, i.e. pairing strings that represent the same real-world location, is a fundamental problemfor several practical applications. The current state-of-the-art relies on string similarity metrics, either specifically developed for matching place names or integrated within methods that combine multiple metrics. However, these methods all rely on common sub-strings in order to establish similarity, and they do not effectively capture the character replacements involved in toponym changes due to transliterations or to changes in language and culture over time. In this article, we present a novel matching approach, leveraging a deep neural network to classify pairs of toponyms as either matching or nonmatching. The proposed network architecture uses recurrent nodes to build representations from the sequences of bytes that correspond to the strings that are to be matched. These representations are then combined and passed to feed-forward nodes, finally leading to a classification decision. We present the results of a wide-ranging evaluation on the performance of the proposed method, using a large dataset collected from the GeoNames gazetteer. These results show that the proposed method can significantly outperform individual similarity metrics from previous studies, as well as previous methods based on supervised machine learning for combining multiple metrics.
A Review of Hydration (2010)

THIS ARTICLE REVIEWS THE GUIDELINES AND CONSIDERATIONS OF HYDRATION APPLICABLE TO VARIOUS POPULATION GROUPS AND RESPECTIVE CONDITIONS. AN AREA OF INTEREST AND CONTROVERSY WITH HYDRATION IS THE IMPACT OF ADDING PROTEIN, AS COMPARED WITH CARBOHYDRATE OR THE COMBINATION OF THE TWO, ON OVERALL HYDRATION AND PERFORMANCE STATUS.
Directed Coherence of EEG on ICSS Rats with Methamphetamine‐induced Hyperactivity and Stereotyped Behavior (2000)

Methamphetamine (MAP) can reinforce intracranial self-stimulation (ICSS) in rats, that is, reward-seeking behavior. However, the ICSS can be inhibited by the stereotyped behavior induced by MAP. This study was designed to observe the mutual information flow between prefrontal cortex (PFC) and ventral tegmental area (VTA) using directed coherence (DC) analysis during the hyperactivity and stereotyped behavior induced by administration of MAP (a derivative of amphetamine). The DC from PFC to VTA increased at 5-7 Hz in the hyperactivity as compared to the stereotypy. In contrast, enhanced information flow from VTA to PFC was observed in the stereotypy as compared to the hyperactivity. We found a reciprocal information flow between PFC and VTA corresponding to the hyperactivity and stereotyped behavior that was induced by administration of MAP.
Eliminating the Synthesis of Mature Lamin A Reduces Disease Phenotypes in Mice Carrying a Hutchinson-Gilford Progeria Syndrome Allele (2008)

Hutchinson-Gilford progeria syndrome is caused by the synthesis of a mutant form of prelamin A, which is generally called progerin. Progerin is targeted to the nuclear rim, where it interferes with the integrity of the nuclear lamina, causes misshapen cell nuclei, and leads to multiple aging-like disease phenotypes. We created a gene-targeted allele yielding exclusively progerin (Lmna HG ) and found that heterozygous mice (Lmna HG/ ) exhibit many phenotypes of progeria. In this study, we tested the hypothesis that the phenotypes elicited by the Lmna HG allele might be modulated by compositional changes in the nuclear lamina. To explore this hypothesis, we bred mice harboring one Lmna HG allele and one Lmna LCO allele (a mutant allele that produces lamin C but no lamin A). We then compared the phenotypes of Lmna HG/LCO mice (which produce progerin and lamin C) with littermate Lmna HG/ mice (which produce lamin A, lamin C, and progerin). Lmna HG/LCO mice exhibited improved body weight curves (p < 0.0001), reduced numbers of spontaneous rib fractures (p < 0.0001), and improved survival (p < 0.0001). In addition, Lmna HG/LCO fibroblasts had fewer misshapen nuclei than Lmna HG/ fibroblasts (p < 0.0001). A likely explanation for these differences was uncovered; the amount of progerin in Lmna HG/LCO fibroblasts and tissues was lower than in Lmna HG/ fibroblasts and tissues. These studies suggest that compositional changes in the nuclear lamina can influence both the steady-state levels of progerin and the severity of progerialike disease phenotypes.
Aprendiendo física con grafos (2021)

El objetivo de este trabajo es utilizar inteligencia artificial para aprender las leyes físicas que gobiernan un sistema arbitrario y predecir así su evolución en el tiempo. Para ello se utilizan varios sesgos inductivos, que aseguran la correcta estructura matemática del problema y mejoran su capacidad de generalización.
Deoxidation Study on V‐Ti‐Fe as Hydrogen Storage Alloy (2015)

This chapter contains sections titled: Introduction Experimental Results and Discussion Conclusions Acknowledgements
Thawing of fresh‐frozen plasma with a new microwave oven (1988)

In the Federal Republic of Germany fresh-frozen plasma (FFP) is still the most important therapeutic agent for acquired coagulation disorders. However, thawing by waterbath (WB) requires about 30 minutes, which is too slow in emergency situations and carries the risk of bacterial contamination of the FFP. There are conflicting data about the use of microwaves for thawing. Therefore, we examined a new microwave oven (MWO; 2450 +/- 50 MHz), which was developed with our cooperation and allows thawing of FFP in 5 minutes, heating FFP to a surface temperature of 21.5 degrees C. A shaking WB (30 min, 37 degrees C) was also used in parallel for comparison. We measured activated partial thromboplastin time (aPTT), nonactivated PTT (NaPTT), fibrinogen, factors VIII:C, X, and XI, fibrinopeptide A, beta-thromboglobulin (beta-TG), thrombin-AT III-complexes, factor VIII-related antigen, C3c, C4, and the plasticizer di(2-ethylhexyl)phthalate (DEHP) in 84 units of FFP as paired samples from 42 double aphereses. Immediately after thawing there was no significant difference in the coagulation test results of FFP with low-cell contamination, regardless of the thawing procedure. Two hours later, after storage at room temperature, FFP thawed by MWO showed even less change than that thawed by WB (NaPTT, p less than 0.01; FX, p less than 0.01). The differences became more evident in comparison with FFP with higher cell contamination and could be observed immediately after thawing (FVIII:C p less than 0.001; FXI, p less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)