gebhart/patrepeval huggingface dataset:
Post-translational Modifications of the Protein Termini (2021)

Post-translational modifications (PTM) involve enzyme-mediated covalent addition of functional groups to proteins during or after synthesis. These modifications greatly increase biological complexity and are responsible for orders of magnitude change between the variety of proteins encoded in the genome and the variety of their biological functions. Many of these modifications occur at the protein termini, which contain reactive amino- and carboxy-groups of the polypeptide chain and often are pre-primed through the actions of cellular machinery to expose highly reactive residues. Such modifications have been known for decades, but only a few of them have been functionally characterized. The vast majority of eukaryotic proteins are N- and C-terminally modified by acetylation, arginylation, tyrosination, lipidation, and many others. Post-translational modifications of the protein termini have been linked to different normal and disease-related processes and constitute a rapidly emerging area of biological regulation. Here we highlight recent progress in our understanding of post-translational modifications of the protein termini and outline the role that these modifications play <i>in vivo</i>.
(Invited) Epitaxial Growth of Low Defect SiGe Buffer Layers for Integration of New Materials on 300 mm Silicon Wafers (2013)

We report on the structural characterization of state-of-the-art SiGe graded buffers on Si(001) substrates with a diameter of 300 mm with and without a backside stressor. The main beneficial effect of the backside stressor is a clear improvement in surface morphology in terms of reduced surface roughness and substantially decreased density of threading dislocation pile-ups all across the wafer. X-ray diffraction furthermore proves that the relaxation of the various layers in the SiGe buffer is triggered by the misfit stress of the subsequently deposited layer. In addition, spatially resolved micro-Raman studies demonstrate that the formed cross hatch pattern surface morphology is clearly correlated with strain field and not with Ge concentration fluctuations.
Perioperative fluid management in kidney transplantation: a black box (2018)

The incidence of delayed graft function in patients undergoing kidney transplantation remains significant. Optimal fluid therapy has been shown to decrease delayed graft function after renal transplantation. Traditionally, the perioperative volume infusion regimen in this patient population has been guided by central venous pressure as an estimation of the patient’s volume status and mean arterial pressure, but this is based on sparse evidence from mostly retrospective observational studies. Excessive volume infusion to the point of no further fluid responsiveness can damage the endothelial glycocalyx and is no longer considered to be the best approach. However, achievement of adequate flow to maintain sufficient tissue perfusion without maximization of cardiac filling remains a challenge. Novel minimally invasive technologies seem to reliably assess volume responsiveness, heart function and perfusion adequacy. Prospective comparative clinical studies are required to better understand the use of dynamic analyses of flow parameters for adequate fluid management in kidney transplant recipients. We review perioperative fluid assessment techniques and discuss conventional and novel monitoring strategies in the kidney transplant recipient.
A Synthetic Heparin‐like Compound which still Activates Antithrombin III although It Contains an Open Chain Fragment instead of α‐L‐Idopyranuronate (1988)

Control of the protecting group keyboard was necessary in order to prepare the activated (R)-glyceric acid derivative 1 from serine. 1 is the decisive precursor for the synthesis of 2, a partially opened analogue of the antithrombin III binding region of heparin. 2 likewise catalyzes the antithrombin-III-mediated deactivation of the coagulation factor Xa (R = CH3, R2 = SO).
Development of Thin-Film Bending Technique Induced by Ion-Beam Irradiation (2009)

We propose a thin-film bending technique induced by ion-beam irradiation, which allows for the fabrication of three-dimensional device structures and arrays, such as micro-electro mechanical systems (MEMS) devices. It can be applied to a wide range of materials deposited by non-specialized sputtering methods under a variety of conditions. It was found that the bending angle could be controlled by the depth of ion implantation, irrespective of the ion species or the film material. Using this technique, micron-sized regions of vertically standing thin film tens of nanometers thick could be produced.
The changes of band 3 protein and membrane fluidity in pathologic condition (2000)

Objective To study the relationship between band 3 protein and membrane fluidity.Methods The relative content of human band 3 protein,the membrane fluidity of erythrocyte and the plasma MDA were measured in normal and patients with hypertension and hemotologic disease.Results The membrane fluidity and the relative content of band 3 protein of erythrocyte from patients reduced,while the MDA level increased.Conclusion In pathological conditions,the reduced membrane fluidity concern with band 3 protein.
Supplementary Figure 2 from Novel Functional Germline Variants in the VEGF Receptor 2 Gene and Their Effect on Gene Expression and Microvessel Density in Lung Cancer (2023)

&lt;p&gt;PDF file - .97MB, Select analysis for KDR SNPs within three ethnic groups (MAF&gt;5%, r2�0.8). The top colored panels shows the genotype of each individual from the different ethnic groups using the SNP ID labels from Table S4. Haplotype tagging SNPs (tSNPs) are denoted with an asterisk and haplotype blocks with the line above. The bottom panels show the pair-wise LD pattern with r2�0.8.&lt;/p&gt;
Microflora Disturbance during Progression of Glucose Intolerance and Effect of Sitagliptin: An Animal Study (2016)

Background . Emerging evidences have shown a close interplay between obesity, diabetes, and intestinal flora disturbance. Dipeptidyl peptidase-4 inhibitor, exemplified by sitagliptin, is highly efficacious in treating type 2 diabetes (T2DM), yet little is known if sitagliptin exerts beneficial effects on microbiota associated with obesity and T2DM. We evaluated changes of gut microbiota following the induction of obesity and T2DM in a streptozotocin treated high fat/high carbohydrate fed (HF/HC-STZ) rat model and explored the effect of sitagliptin on gut microbiota for HF/HC-STZ rats. Methods . Sitagliptin was administered via oral gavage to diabetic rats. Fecal DNA extraction and 454 pyrosequencing based on analysis of 16S rRNA genes was utilized to determine the overall structure of microbiota in fecal DNA samples. Results . Results showed that, at the level of phylum, there was higher abundance of Firmicutes and Tenericutes and less abundance of Bacteroidetes in obese rats compared to their lean counterparts. At the level of genus, short-chain fatty acid- (SCFA-) producing bacteria, Blautia , Roseburia , and Clostridium , and probiotics Lactobacillus , Bifidobacterium , and so forth were identified significantly different from each other among conditions. Conclusion . Marked shifts of the gut microbiota structure were observed in the rats during development of glucose intolerance. Intestinal flora changed in the process of glucose intolerance, and treatment of sitagliptin moderately corrected the dysbiosis of microbiota in T2DM.
All-Solution Thin-film Capacitors and Their Deposition in Trench and Through-Via Structures (2013)

Thin integrated passive devices (IPDs) will play a critical role in the miniaturization of future high-performance electronic and bioelectronic systems. Silicon-based capacitors are currently manufactured with expensive processes such as sputtering and atomic layer deposition. Solution-deposited electrodes and dielectrics in trench and through-via structures provide alternative low-cost routes. Two solution-deposition techniques, spin-coating and vacuum infiltration, are investigated in this paper. A representative all-solution-derived thin-film capacitor consisting of sol-gel lanthanum nickel oxide (LNO) as the electrode, and sol-gel lead zirconate titanate as the dielectric thin-film is demonstrated in the first part of this paper. The role of barriers in reducing leakage currents is studied using three electrode systems: LNO/Si, LNO/ZrO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si, and LNO/Pt/Ta/Si. Capacitors with LNO electrodes directly deposited on naturally oxidized silicon resulted in higher leakages, more defects and a lower yield. The results show that the zirconia barrier suppresses the leakage current in the dielectric. The second part of this paper describes sol-gel films deposited in the through-via and trench surfaces to demonstrate the sol-gel conformal coating technique. Scanning electron microscopy cross-section analysis shows that the vacuum infiltration conformally coated through-vias. These solution deposition techniques may have the potential to fabricate IPD capacitors at low cost.
Cephalic-phase insulin secretion in normal and pancreatic islet-transplanted rats (1980)

The ability of saccharin, in comparison with glucose and tap water, to elicit glycemia-independent neurally mediated insulin secretion was investigated in chronically catheterized, freely moving rats. Plasma glucose and insulin concentrations were measured continuously from venous blood with a sampling resolution of one per minute. In normal rats, 1 ml of 0.15% saccharin caused a significant rapid rise in peripheral plasma insulin levels lasting up to 5 min, without significant changes in glycemia. Tap water alone also induced a transient elevation in insulinemia but was much smaller than the saccharin-induced response. In streptozotocin diabetic rats bearing intrahepatic, presumably denervated islet isografts, these rapid insulin responses to oral saccharin and tap water stimulation were completely abolished, whereas the early insulin response to intravenous glucose was decreased by only about 30%. These results are consistent with the concept of gustatory and other oral sensory signals acting as triggers for neurally mediated insulin release.
Adaptive Fault Tolerance in Real Time Cloud Computing (2011)

With the increasing demand and benefits of cloud computing infrastructure, real time computing can be performed on cloud infrastructure. A real time system can take advantage of intensive computing capabilities and scalable virtualized environment of cloud computing to execute real time tasks. In most of the real time cloud applications, processing is done on remote cloud computing nodes. So there are more chances of errors, due to the undetermined latency and loose control over computing node. On the other side, most of the real time systems are also safety critical and should be highly reliable. So there is an increased requirement for fault tolerance to achieve reliability for the real time computing on cloud infrastructure. In this paper, a fault tolerance model for real time cloud computing is proposed. In the proposed model, the system tolerates the faults and makes the decision on the basis of reliability of the processing nodes, i.e. virtual machines. The reliability of the virtual machines is adaptive, which changes after every computing cycle. If a virtual machine manages to produce a correct result within the time limit, its reliability increases. And if it fails to produce the result within time or correct result, its reliability decreases. A metric model is given for the reliability assessment. In the model, decrease in reliability is more than increase. If the node continues to fail, it is removed, and a new node is added. There is also a minimum reliability level. If any processing node does not achieve that level, the systems will perform backward recovery or safety measures. The proposed technique is based on the execution of design diverse variants on multiple virtual machines, and assigning reliability to the results produced by variants. The virtual machine instances can be of same type or of different types. The system provides both the forward and backward recovery mechanism, but main focus is on forward recovery. The main essence of the proposed technique is the adaptive behavior of the reliability weights assigned to each processing node and adding and removing of nodes on the basis of reliability.
Understanding interobserver agreement: the kappa statistic. (2005)

Items such as physical exam findings, radiographic interpretations, or other diagnostic tests often rely on some degree of subjective interpretation by observers. Studies that measure the agreement between two or more observers should include a statistic that takes into account the fact that observers will sometimes agree or disagree simply by chance. The kappa statistic (or kappa coefficient) is the most commonly used statistic for this purpose. A kappa of 1 indicates perfect agreement, whereas a kappa of 0 indicates agreement equivalent to chance. A limitation of kappa is that it is affected by the prevalence of the finding under observation. Methods to overcome this limitation have been described.
Wide-field radiofrequency ablation (RFA) of anal high-grade dysplasia (HSIL) decreases recurrence over targeted ablation (2018)

Recurrence post HSIL ablation is high primarily from development of metachronous HSIL. Trials of hemi-circumferential and circumferential RFA of anal HSIL demonstrated reduced HSIL in treated areas at one year. We now examine long-term treatment durability and safety. A retrospective analysis of long-term treatment results in participants returning for follow-up HRA after hemi-circumferential and circumferential RFA trials. Participants had to have an HRA >1 year post completion of initial RFA trials. A non-HSIL biopsy or no lesion on HRA without biopsy was considered no recurrence. Twenty-two participants underwent hemi-circumferential and 10 underwent circumferential RFA and 15 (68%) and 9 (90%), respectively returned for follow-up. Eighteen (75%) were white, 1 was female and 8 (33%) were HIV+ (all treated circumferentially). Median age was 52.5 (range 32–74) years with duration of follow-up post RFA a median 3.2 (range 1–4.5) years. During post-study follow-up median number of HRA's was 1 (range 1–4). No participants developed HSIL within the RFA treatment zone after completion of the initial trial. One participant treated with hemi-circumferential RFA developed metachronous HSIL in the non-ablated area at 3.8 years. Another developed recurrence at 12 months, was retreated with targeted cautery ablation, and post-trial remains disease free for 2.5 years. At last follow-up 14/23 (61%) individuals tested were high-risk HPV negative (6 HIV+). No long-term treatment related adverse events were identified. When compared to targeted ablation, wide-field RFA appears to reduce HSIL recurrence. No long-term adverse events related to treatment were identified. Further study is warranted.
Continuous Operation of a 10 kWth Chemical Looping Integrated Fluidized Bed Reactor for Gasifying Biomass Using an Iron-Based Oxygen Carrier (2014)

Chemical looping gasification (CLG) was investigated in a 10 kWth interconnected fluidized bed reactor with Fe2O3/Al2O3 as oxygen carriers (OC) and pine sawdust as fuel. The effects of the operation temperatures and sawdust feeding rate on the gas composition, cold gas efficiency, and carbon conversion rate of biomass were investigated. The fresh and used oxygen carrier particles were characterized by means of XRD, SEM, and BET. The results indicated that the sawdust was partially oxidized to syngas by lattice oxygen from the oxygen carrier. The syngas yield, cold gas efficiency, and carbon conversion increased with increasing operating temperature. Also, the concentrations of CO, H2, and CH4 in the syngas increased at the elevated temperature, while the CO2 fraction decreased. The feeding rate of biomass has a significant impact on the syngas composition and cold gas efficiency. There was an optimal value of feeding rate at 2.24 kg/h corresponding to the maximum cold gas efficiency in the tested reactor system. XRD analysis showed that the oxygen carrier particles were reduced to Fe3O4 from Fe2O3 in the course of the CLG reactions. BET results indicated the surface area, total pore volume, and average pore size of the oxygen carrier particles increased initially and then slightly decreased with the reaction proceeding, due to the interstice and thermal sintering. However, the OC samples were well regenerated and maintained a good crystalline state after 60 h of operation, which illustrated that the synthesized oxygen carrier had a stable reactivity and good resistance to agglomeration.
Data from Hypercholesterolemia Increases Colorectal Cancer Incidence by Reducing Production of NKT and γδ T Cells from Hematopoietic Stem Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Obesity will soon surpass smoking as the most preventable cause of cancer. Hypercholesterolemia, a common comorbidity of obesity, has been shown to increase cancer risk, especially colorectal cancer. However, the mechanism by which hypercholesterolemia or any metabolic disorder increases cancer risk remains unknown. In this study, we show that hypercholesterolemia increases the incidence and pathologic severity of colorectal neoplasia in two independent mouse models. Hypocholesterolemia induced an oxidant stress–dependent increase in miR101c, which downregulated Tet1 in hematopoietic stem cells (HSC), resulting in reduced expression of genes critical to natural killer T cell (NKT) and γδ T-cell differentiation. These effects reduced the number and function of terminally differentiated NKT and γδ T cells in the thymus, the colon submucosa, and during early tumorigenesis. These results suggest a novel mechanism by which a metabolic disorder induces epigenetic changes to reduce lineage priming of HSC toward immune cells, thereby compromising immunosurveillance against cancer. &lt;i&gt;Cancer Res; 77(9); 2351–62. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Titanium Dioxide Single-Crystal and Powder Surfaces in the Presence and Absence of Platinum (1985)

This study examined the changes in surface composition, as indicated by O/Ti and C/Ti ratios measured by AES, as temperatures were varied from 300 to 1075K and surfaces were exposed to H2, O2, and CO. ESD studies were also conducted by continuous exposure of one region to the Auger electron beam and comparison to another region outside the beam. On the single crystals without Pt, initial O/Ti ratios between 1.5 and 2.0 increased rapidly between 650K and 850K to values near or above 2.5. The addition of Pt eliminated the high O/Ti ratios at 900K. The high O/Ti ratios attained above 900K infer that the slow step in the reduction of TiO2 is the removal of oxygen from the surface, and either ESD or Pt enhances this step.
New resistance welding techniques for steel and aluminium (1993)

(1993). New resistance welding techniques for steel and aluminium. Welding International: Vol. 7, No. 10, pp. 820-827.
Preparation of Enantiopure Butane‐2,3‐diacetals of Glycolic Acid and Alkylation Reactions Leading to α‐Hydroxyacid and Amide Derivatives. (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Investigation of Nonlinear Optical Properties of Quantum Dots Deposited onto a Sample Glass Using Time-Resolved Inline Digital Holography (2022)

We report on the application of time-resolved inline digital holography in the study of the nonlinear optical properties of quantum dots deposited onto sample glass. The Fresnel diffraction patterns of the probe pulse due to noncollinear degenerate phase modulation induced by a femtosecond pump pulse were extracted from the set of inline digital holograms and analyzed. The absolute values of the nonlinear refractive index of both the sample glass substrate and the deposited layer of quantum dots were evaluated using the proposed technique. To characterize the inhomogeneous distribution of the samples' nonlinear optical properties, we proposed plotting an optical nonlinearity map calculated as a local standard deviation of the diffraction pattern intensities induced by noncollinear degenerate phase modulation.
Modeling structures of cellular materials for application at various length-scales (2013)

The paper presents the spectrum of methods and results for design of structures, which are frequently applied in numerical simulations of properties and processes taking place in cellular materials. The methods described here are universal for many applications at various length-scales. They can be efficiently applied for complex cellular structures such as polycrystals or foams, where the elements (grains or pores) are distributed and shaped in a controlled way. The digital material representations created by these methods can be used for a number of numerical techniques such as: Molecular dynamics (MD), Monte Carlo (MC), Cellular Automaton (CA), Finite Element Method (FEM) or Finite Volume Method (FVM). The examples of structures consisting of atoms, fields or finite elements are presented in this paper. The applications of such structures are demonstrated by the properties and processes relevant to the specific length scales.
Negative-Pressure Wound Therapy I: The Paradox of Negative-Pressure Wound Therapy (2009)

Negative-pressure wound therapy increases tissue pressure proportionately to the amount of suction, although this becomes less pronounced over 48 hours. This suggests that negative-pressure wound therapy dressings should be used with caution on tissues with compromised perfusion, particularly when they are circumferential.
Abstracts of the 27th Annual Meeting of the Human Biology Association, Buffalo, New York April 12–14 2001 (2002)

The effect of famine on fetal loss has been well documented for a number of populations. In this paper we examine the effect of famine on fetal loss in rural Bangladesh, which experienced a severe famine during 1973 and 1974 following the 1971 war for independence. Using data from the Internal Centre for Diarrhoeal Disease Research, Bangladesh, the effect of famine on fetal loss is examined considering both maternal age (MA) and paternal age (PA). Observations include records of 65,590 pregnancies from 254,471 individuals followed from 1974 to 1982. Logistic regression was used to model the effects of MA, PA, and birth year on the probability of fetal loss. As expected, risk of fetal loss increased with MA. An unexpected but consistent finding was that the probability of fetal loss decreased with increasing PA (see figure). The probability of fetal loss declined from 1974 to 1976, but then increased through 1982. These results support previous studies indicating an increase in fetal loss with MA, but are inconsistent with previous research indicating an increase in fetal loss with PA. Given the marginal health conditions in rural Bangladesh during the study period, the decline in fetal loss with PA may reflect the effects of better nutritional status for the wives of older males.
Silver-catalyzed synthesis of amides from amines and aldehydes (2023)

The invention provides a method for producing amides via the reaction of aldehydes and amines with oxygen adsorbed on a metallic silver or silver alloy catalyst. An exemplary reaction is shown in Scheme 1: (I), (II), (III). ##STR00001##