gebhart/patrepeval huggingface dataset:
H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations (2012)

The accuracy of atomistic biomolecular modeling and simulation studies depend on the accuracy of the input structures. Preparing these structures for an atomistic modeling task, such as molecular dynamics (MD) simulation, can involve the use of a variety of different tools for: correcting errors, adding missing atoms, filling valences with hydrogens, predicting pK values for titratable amino acids, assigning predefined partial charges and radii to all atoms, and generating force field parameter/topology files for MD. Identifying, installing and effectively using the appropriate tools for each of these tasks can be difficult for novice and time-consuming for experienced users. H++ (http://biophysics.cs.vt.edu/) is a free open-source web server that automates the above key steps in the preparation of biomolecular structures for molecular modeling and simulations. H++ also performs extensive error and consistency checking, providing error/warning messages together with the suggested corrections. In addition to numerous minor improvements, the latest version of H++ includes several new capabilities and options: fix erroneous (flipped) side chain conformations for HIS, GLN and ASN, include a ligand in the input structure, process nucleic acid structures and generate a solvent box with specified number of common ions for explicit solvent MD.
Dynamics of Atom-Mediated Photon-Photon Scattering II: Experiment (2000)

Temporal and angular correlations in atom-mediated photon-photon scattering are measured. Good agreement is found with the theory presented in Part~I.
The measurement of diffusion and perfusion in biological systems using magnetic resonance imaging (2000)

The aim of this review is to describe two recent developments in the use of magnetic resonance imaging (MRI) in the study of biological systems: diffusion and perfusion MRI. Diffusion MRI measures the molecular mobility of water in tissue, while perfusion MRI measures the rate at which blood is delivered to tissue. Therefore, both these techniques measure quantities which have direct physiological relevance. It is shown that diffusion in biological systems is a complex phenomenon, influenced directly by tissue microstructure, and that its measurement can provide a large amount of information about the organization of this structure in normal and diseased tissue. Perfusion reflects the delivery of essential nutrients to tissue, and so is directly related to its status. The concepts behind the techniques are explained, and the theoretical models that are used to convert MRI data to quantitative physical parameters are outlined. Examples of current applications of diffusion and perfusion MRI are given. In particular, the use of the techniques to study the pathophysiology of cerebral ischaemia/stroke is described. It is hoped that the biophysical insights provided by this approach will help to define the mechanisms of cell damage and allow evaluation of therapies aimed at reducing this damage.
Flying Ad Hoc Networks: A New Domain for Network Communications (2018)

The advent of flying ad hoc networks (FANETs) has opened an opportunity to create new added-value services. Even though it is clear that these networks share common features with its predecessors, e.g., with mobile ad hoc networks and with vehicular ad hoc networks, there are several unique characteristics that make FANETs different. These distinctive features impose a series of guidelines to be considered for its successful deployment. Particularly, the use of FANETs for telecommunication services presents demanding challenges in terms of quality of service, energy efficiency, scalability, and adaptability. The proper use of models in research activities will undoubtedly assist to solve those challenges. Therefore, in this paper, we review mobility, positioning, and propagation models proposed for FANETs in the related scientific literature. A common limitation that affects these three topics is the lack of studies evaluating the influence that the unmanned aerial vehicles (UAV) may have in the on-board/embedded communication devices, usually just assuming isotropic or omnidirectional radiation patterns. For this reason, we also investigate in this work the radiation pattern of an 802.11 n/ac (WiFi) device embedded in a UAV working on both the 2.4 and 5 GHz bands. Our findings show that the impact of the UAV is not negligible, representing up to a 10 dB drop for some angles of the communication links.
Multi-dimensional data regularization for modern acquisition (2007)

Data regularization is critical for the suppression of Kirchhoff migration noise and the production of a clean migration image. Techniques that perform data regularization simultaneously along two axes provide a solution where multiple passes of a 1D approach fail. We introduce a versatile two-dimensional Fourier reconstruction algorithm that regularizes the input data as well as filling gaps in the coverage. We validate the algorithm on a synthetic cross-spread gather example as well as demonstrating the technology on a real offset volume dataset. The results show an improved continuity of the data and preservation of the data character even where we observe conflicting dips. Our one-pass approach can handle empty and overfold bins thus making use of all recorded traces and simplify the pre-stack processing flow.
Towards Dynamic Control of Wettability by Using Functionalized Altitudinal Molecular Motors on Solid Surfaces (2013)

We report the synthesis of altitudinal molecular motors that contain functional groups in their rotor part. In an approach to achieve dynamic control over the properties of solid surfaces, a hydrophobic perfluorobutyl chain and a relatively hydrophilic cyano group were introduced to the rotor part of the motors. Molecular motors were attached to quartz surfaces by using interfacial 1,3-dipolar cycloadditions. To test the effect of the functional groups on the rotary motion, photochemical and thermal isomerization studies of the motors were performed both in solution and when attached to the surface. We found that the substituents have no significant effect on the thermal and photochemical processes, and the functionalized motors preserved their rotary function both in solution and on a quartz surface. Preliminary results on the influence of the functional groups on surface wettability are also described.
Pathway Analysis of Gene Expression of E14 Versus E18 Fetal Fibroblasts (2017)

<b>Objective:</b> Fetuses early in gestation heal skin wounds without forming scars. The biological mechanisms behind this process are largely unknown. Fibroblasts, however, are cells known to be intimately involved in wound healing and scar formation. We examined fibroblasts in different stages of development to characterize differences in gene expression that may result in the switch from regenerative wound repair to repair with scarring. <b>Approach:</b> Fibroblasts were isolated and cultured from the back skin of BALB/c wild-type mouse fetuses at embryonic day (E)14 and E18 (<i>n</i> = 10). The fibroblast total RNA was extracted, and microarray analysis was conducted using chips containing 42,000 genes. Significance analysis of microarrays was performed to identify genes with greater than twofold expression difference and a false discovery rate of less than two. Identified genes subsequently underwent enrichment analysis to detect differentially expressed pathways. <b>Results:</b> Two hundred seventy-five genes were differentially expressed between E14 and E18 in fetal fibroblasts. Thirty genes were significantly downregulated and 245 genes were significantly upregulated at E18 compared with E14. Ingenuity pathway analysis identified the top 20 signaling pathways differentially activated in fetal fibroblasts between the E18 and E14 time points. <b>Innovation:</b> To our knowledge, this work represents the first instance where differentially expressed genes and signaling pathways between fetal fibroblasts at E14 and E18 have been studied. <b>Conclusion:</b> The genes and pathways identified here potentially underlie the mechanism behind the transition from fetal wound healing via regeneration to wound healing by repair, and may prove to be key targets for future therapeutics.
Concentration of Substance P, Neurokinin A, Calcitonin Gene-related Peptide, Neuropeptide Y and Vasoactive Intestinal Polypeptide in Synovial Fluid from Knee Joints in Patients Suffering from Rheumatoid Arthritis (1991)

We have studied the presence of five neuropeptides in knee joint synovial fluid from either patients suffering from rheumatoid arthritis and pain (n = 18) or being subjected to arthroscopy due to meniscal/cruciate ligament injuries (n = 13). Radioimmunoassay technique was used for peptide analysis using antisera SP2 against substance P (SP), K12 against neurokinin A (NKA), CGRPR8 against calcitonin gene-related peptide (CGRP), NPY1 against neuropeptide Y (NPY) and VIP2 against vasoactive intestinal polypeptide (VIP). No SP could be detected, and lower levels of NKA was found in arthritic joints vs controls. CGRP and NPY was found in higher concentrations in arthritic patients vs controls. VIP was found sporadically in both arthritis and control patients. Our data show some quantitative differences between patients suffering rheumatoid arthritis and pain, and patients with non-inflamed joints without pain; indicating an involvement of peptidergic fibers in arthritis in humans.
[Serum superoxide dismutase (SOD) activity in patients with renal disease by a spintrap method using electron spin resonance (ESR)]. (1993)

Superoxide dismutase (SOD) activity in serum samples of patients with chronic glomerulonephritis (CGN) and chronic renal failure (CRF) was measured by a spin trap method using electron spin resonance (ESR). Twenty-three patients with CGN, 10 patients with CRF and 10 healthy adults were examined. Among 23 patients with CGN, there were 12 patients with IgA nephropathy and one patient with membranous nephropathy diagnosed by immunofluorescence of renal biopsy specimens. Other CGN patients were diagnosed by its clinical criteria. The serum activity of SOD in patients with CGN or CRF was significantly higher than those in healthy adults (p < 0.05). The serum SOD activity in patients with CRF was also higher than those in patients with CGN (p < 0.05). Marked high levels of serum SOD activity were observed histologically in the advanced stage of IgA nephropathy. These results suggest an increase in serum SOD activity may reflect renal injuries in patients with CGN and CRF.
A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus (2020)

The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. In parallel, we generated an RNA-sequencing dataset from human islets treated with brefeldin A (BFA), a known GA stress inducer. Overlapping the T1D and T2D groups with the BFA dataset, we identified 120 and 204 differentially expressed genes, respectively. In both the T1D and T2D models, pathway analyses revealed that the top pathways were associated with GA integrity, organization, and trafficking. Quantitative RT-PCR was used to validate a common signature of GA stress that included &lt;i&gt;ATF3&lt;/i&gt;, &lt;i&gt;ARF4&lt;/i&gt;, &lt;i&gt;CREB3&lt;/i&gt;, and &lt;i&gt;COG6&lt;/i&gt;. Taken together, these data indicate that GA-associated genes are dysregulated in diabetes and identify putative markers of β-cell GA stress.
Dual Effect of the Acidic Polysaccharose Ulvan on the Inhibition of Amyloid-β Protein Fibrillation and Disintegration of Mature Fibrils (2020)

The abnormal folding and aggregation of amyloid-β protein (Aβ) is the main reason for the occurrence and development of Alzheimer's disease (AD). The discovery of novel inhibitors against Aβ aggregation is still the current research focus. Herein, we report the inhibitory effect of ulvan, an acidic polysaccharide from green algae of the genus <i>Ulva</i>, against Aβ fibrillation using thioflavin T (ThT) fluorescence and atomic force microscopy (AFM) assays. It is shown that ulvan effectively inhibits Aβ fibrillogenesis in a concentration-dependent manner and actively inhibits the formation of A11-reactive Aβ oligomers, the most toxic Aβ species. The circular dichroism spectrum reveals that ulvan blocks the conformational transition of Aβ40 from the initial random coil to a β-sheet structure, but it only delays the conformational transition of Aβ42. It is also found that ulvan greatly reduces Aβ-induced cytotoxicity by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. In addition, ulvan effectively downregulates intracellular reactive oxygen species production and protects PC12 cells from the damage caused by Aβ fibrillation. Moreover, ulvan disaggregates preformed mature fibrils into off-pathway oligomers and greatly decreases their associated cytotoxicity, as revealed using ThT fluorescence, AFM, MTT, and dot-blotting assays. The above results not only fully describe the inhibitory effect of ulvan on Aβ fibrillation and its related cytotoxicity but also provide novel ideas for the development of functional food ingredients from seaweed to treat AD.
Metaproteomics as a Complementary Approach to Gut Microbiota in Health and Disease (2017)

Classic studies on phylotype profiling are limited to the identification of microbial constituents, where information is lacking about the molecular interaction of these bacterial communities with the host genome and the possible outcomes in host biology. A range of OMICs approaches have provided great progress linking the microbiota to health and disease. However, the investigation of this context through proteomic mass spectrometry-based tools is still being improved. Therefore, metaproteomics or community proteogenomics has emerged as a complementary approach to metagenomic data, as a field in proteomics aiming to perform large-scale characterization of proteins from environmental microbiota, such as the human gut. The advances in molecular separation methods coupled with mass spectrometry (e.g., LC-MS/MS) and proteome bioinformatics have been fundamental in these novel large-scale metaproteomic studies, which have further been performed in a wide range of samples including soil, plant and human environments. Metaproteomic studies will make major progress if a comprehensive database covering the genes and expresses proteins from all gut microbial species is developed. To this end, we here present some of the main limitations of metaproteomic studies in complex microbiota environments, such as the gut, also addressing the up-to-date pipelines in sample preparation prior to fractionation/separation and mass spectrometry analysis. In addition, a novel approach to the limitations of metagenomic databases is also discussed. Finally, prospects are addressed regarding the application of metaproteomic analysis using a unified host-microbiome gene database and other meta-OMICs platforms.
Virtual Reality Applications for Prevention, Disability Awareness, and Physical Therapy Rehabilitation in Neurology (2002)

Virtual reality (VR) is a relatively new technology that may be useful for physical therapists working in neurology. In this paper our recent work related to the development and evaluation ofVR applications for demonstrating transfer of training, improvement of spatial memory, teaching disability awareness, prevention of pedestrian injuries, and improvement of balance is discussed. Our experiences as researchers in this area are discussed including collaboration with industry and the limitations and strengths of the technology. Our research and the research of others have shown that skills can be learned in VR, that these skills can transfer to similar tasks in the real world, that patient (consumer) involvement is essential in making VR environments meaningful, and that collaboration with industry requires special knowledge and skills. We conclude that VR has a future in neurologic physical therapy but that it may be some time before strong evidence for each possible application is available to clinicians. As this evidence becomes available, VR may provide physical therapists with interesting and innovative ways to extend evaluation and treatment in neurology.
Leitfaden Herzkatheter (2009)

Der "Leitfaden Herzkatheter" fasst den aktuellen und umfangreichen Wissenszuwachs in der Kardiologie für alle Belange der Herzkatheterdiagnostik und der besonders wichtigen invasiven Koronartherapie z
New Class of Hole-Blocking Amorphous Molecular Materials and Their Application in Blue-Violet-Emitting Fluorescent and Green-Emitting Phosphorescent Organic Electroluminescent Devices (2003)

A new class of hole-blocking amorphous molecular materials for use in organic electroluminescent (EL) devices have been developed, which include 1,3,5-tri(4-biphenylyl)benzene, 1,3,5-tris(4-fluorobiphenyl-4‘-yl)benzene (F-TBB), 1,3,5-tris(9,9-dimethylfluoren-2-yl)benzene, and 1,3,5-tris[4-(9,9-dimethylfluoren-2-yl)phenyl]benzene. They readily form stable amorphous glasses with well-defined glass-transition temperatures and are characterized by relatively high oxidation potentials and large HOMO−LUMO energy gaps. The use of these materials as hole blockers enabled blue-violet emission from several emitting amorphous molecular materials with hole-transporting properties in organic EL devices. A multilayer organic EL device using N,N-bis(9,9-dimethylfluoren-2-yl)aniline (F2PA) as a blue-violet emitter, F-TBB as a hole blocker, and 4,4‘,4‘ ‘-tris[3-methylphenyl(phenyl)amino]triphenylamine and tris(8-quinolinolato)aluminum as hole and electron transporters, respectively, exhibited blue-violet emission peaking at 405 nm with a high external quantum efficiency of 1.95%. This device also enabled the doping of a phosphorescent iridium complex, tris(2-phenylpyridine)iridium (Ir(ppy)3), tuning the emission color from blue violet to green by excitation energy transfer from F2PA to Ir(ppy)3.
Utilization of β‐Cyclodextrin for Improved Flavor Retention in Thermally Processed Foods (2004)

ABSTRACT: Four flavorants were complexed individually with β‐cyclodextrin, and the resulting inclusion complexes were used to flavor hard candy, fruit leathers, and angel food cake. Flavor retention during preparation using complexed and liquid flavor forms was assessed by instrumental analysis. Complexation of flavors in β‐cyclodextrin markedly improved heat stability in some cases; the more severe the heat treatment experienced by the food, the greater the observed benefit; for example, 86‐fold better retention of l‐menthol in a hard candy. However, results of sensory evaluation were mixed, indicating that the benefits of enhanced flavor retention achieved through the use of flavor/cyclodextrin complexation could be mitigated by poor release from inclusion complexes during consumption.
Control of the Shape and the Size of Copper Metallic Particles (1996)

Colloidal copper particles were prepared in aqueous solution via the reduction of copper dodecyl sulfate, Cu(DS)2, by sodium borohydrate. Below the critical micellar concentration (cmc), it has been obtained isolated particles forming an interconnected network of either oxide or pure metallic copper aggregates. Syntheses performed above the cmc show the formation of elongated or spherical copper metallic particles. The size and shape of crystallites are controlled by surfactant concentration. The change in the shape of metallic copper particles from spheres to rods is followed by TEM and UV−visible spectroscopy. As it has been predicted by calculation, a red shift in the plasmon peak is observed when the elongation of the particles increases. It is demonstrated that the shape and the size of the particles are controlled by the formation and the number of micellar aggregates.
The effect of phacoemulsification on late bleb failure or intraocular pressure in patients with glaucoma: a systematic review (2012)

The purpose of our systematic review is to document the adverse events that follow phacoemulsification in eyes with trabeculectomy due to glaucoma and to determine whether phacoemulsification jeopardizes the survival of the trabeculectomy. Our research was based on English- and non-English-language articles obtained using the Medline, Embase, Web of Science and Scopus databases. Additional studies were identified by searching bibliographies in the British Library and abstracts presented at the Association for Research in Vision and Ophthalmology annual meetings. Search terms included randomized controlled trial, controlled clinical trial, random allocation, double-blind method, matched studies and trabeculectomy failure, glaucoma-filtering operation failure, bleb failure and cataract surgery or phacoemulsification. Only prospective or retrospective matched studies testing the survival of a trabeculectomy alone versus clear corneal phacoemulsification after a trabeculectomy in patients with glaucoma were included. Data were independently extracted by two authors using predefined data fields. PubMed yielded 152 results, Scopus 235, Embase 222, and Web of Science (science citation index) 216. We read the abstracts of all the trials, and after reading the full text of 31 studies, we decided that 13 studies should be comprehensively evaluated. Current evidence does not allow us to draw safe conclusions on the scientific question so far.
A Nonsense Mutation in Mycobacterium marinum That Is Suppressible by a Novel Mechanism (2016)

Mycobacterial pathogens use the ESAT-6 system 1 (Esx-1) exporter to promote virulence. Previously, we used gene disruption and complementation to conclude that the MMAR_0039 gene in Mycobacterium marinum is required to promote Esx-1 export. Here we applied molecular genetics, proteomics, and whole-genome sequencing to demonstrate that the MMAR_0039 gene is not required for Esx-1 secretion or virulence. These findings suggest that we initially observed an indirect mechanism of genetic complementation. We identified a spontaneous nonsense mutation in a known Esx-1-associated gene which causes a loss of Esx-1 activity. We show that the Esx-1 function was restored by nonsense suppression. Moreover, we identified a polar mutation in the ppsC gene which reduced cellular impermeability but did not impact cytotoxicity in macrophages. Our studies reveal insight into Esx-1 export, nonsense suppression, and cell envelope lipid biogenesis.
Antimicrobial Agents from Higher Plants. New Synthesis and Bioactivity of Tryptanthrin(Indolo-[2,1-b]quinazolin-6,12-dione) and Its Analogues (1981)

Rbstract -Base-catalyzed condensation of substituted isatins and substituted isatoic anhydrides provldes a convenient, one-step flexible synthesis of indolo-[2,1-&]-quinazo11n-6,12-diones, including the antifungal natural product tryptanthrin.Thls new
Deep feature-based face detection on mobile devices (2016)

We propose a deep feature-based face detector for mobile devices to detect user's face acquired by the front-facing camera. The proposed method is able to detect faces in images containing extreme pose and illumination variations as well as partial faces. The main challenge in developing deep feature-based algorithms for mobile devices is the constrained nature of the mobile platform and the non-availability of CUDA enabled GPUs on such devices. Our implementation takes into account the special nature of the images captured by the front-facing camera of mobile devices and exploits the GPUs present in mobile devices without CUDA-based frameworks, to meet these challenges.