gebhart/patrepeval huggingface dataset:
Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations (2014)

Free energy calculation has long been an important goal for molecular dynamics simulation and force field development, but historically it has been challenged by limited performance, accuracy, and creation of topologies for arbitrary small molecules. This has made it difficult to systematically compare different sets of parameters to improve existing force fields, but in the past few years several authors have developed increasingly automated procedures to generate parameters for force fields such as Amber, CHARMM, and OPLS. Here, we present a new framework that enables fully automated generation of GROMACS topologies for any of these force fields and an automated setup for parallel adaptive optimization of high-throughput free energy calculation by adjusting lambda point placement on the fly. As a small example of this automated pipeline, we have calculated solvation free energies of 50 different small molecules using the GAFF, OPLS-AA, and CGenFF force fields and four different water models, and by including the often neglected polarization costs, we show that the common charge models are somewhat underpolarized.
Optimized relative Lempel-Ziv compression of genomes (2011)

High-throughput sequencing technologies make it possible to rapidly acquire large numbers of individual genomes, which, for a given organism, vary only slightly from one to another. Such repetitive and large sequence collections are a unique challange for compression. In previous work we described the RLZ algorithm, which greedily parses each genome into factors, represented as position and length pairs, which identify the corresponding material in a reference genome. RLZ provides effective compression in a single pass over the collection, and the final compressed representation allows rapid random access to arbitrary substrings. In this paper we explore several improvements to the RLZ algorithm. We find that simple non-greedy parsings can significantly improve compression performance and discover a strong correlation between the starting positions of long factors and their positions in the reference. This property is computationally inexpensive to detect and can be exploited to improve compression by nearly 50% compared to the original RLZ encoding, while simultaneously providing faster decompression.
Condition Monitoring and Fault Diagnosis of Electrical Motors—A Review (2005)

Recently, research has picked up a fervent pace in the area of fault diagnosis of electrical machines. The manufacturers and users of these drives are now keen to include diagnostic features in the software to improve salability and reliability. Apart from locating specific harmonic components in the line current (popularly known as motor current signature analysis), other signals, such as speed, torque, noise, vibration etc., are also explored for their frequency contents. Sometimes, altogether different techniques, such as thermal measurements, chemical analysis, etc., are also employed to find out the nature and the degree of the fault. In addition, human involvement in the actual fault detection decision making is slowly being replaced by automated tools, such as expert systems, neural networks, fuzzy-logic-based systems; to name a few. It is indeed evident that this area is vast in scope. Hence, keeping in mind the need for future research, a review paper describing different types of faults and the signatures they generate and their diagnostics' schemes will not be entirely out of place. In particular, such a review helps to avoid repetition of past work and gives a bird's eye view to a new researcher in this area.
Prognostic value of apoptosis in breast cancer (pT1-pT2). A TUNEL, p53, bcl-2, bag-1 and Bax immunohistochemical study. (2004)

Apoptosis or programmed cell death produces cells breaking into several fragments of nuclei, cytoplasm or both nuclei and cytoplasm, known as apoptotic bodies which can be visualized in haematoxylin-eosin staining. Some genes (promoters and suppressors) control this process and certain mutations may induce the expression of abnormal proteins, which can be detected by immunohistochemical staining. Apoptosis can be detected by the TUNEL method either identifying apoptotic bodies or cells at the initial stages of the fragmentation process. We have studied 186 cases of infiltrating ductal breast carcinoma, stages pT1-pT2, and analysed the prognostic significance of tumour recurrence and overall survival of apoptotic index (AI) through univariate and multivariate analysis. We have also studied the immunohistochemical protein expression of apoptosis promoter and suppressors gene (p53, nuclear expression; bcl-2 and Bax, cytoplasm expression; BAG-1, nuclear and cytoplasm expression). The results indicate prognostic significance of p53 and bcl-2 related to patient death and bcl-2 and tumour size to tumour recurrence, bcl-2 acting as a protector factor (apoptotic suppressor) in both situations. On the other hand, we have not found useful prognostic information of AI either to tumour recurrence or overall survival in univariate or multivariate studies. In this study, Bax expression does not provide a new prognostic role in breast carcinoma, although it contrasts to the bcl-2 action and accelerates death.
Clustering without a metric (1991)

A methodology for clustering data in which a distance metric or similarity function is not used is described. Instead, clusterings are optimized based on their intended function: the accurate prediction of properties of the data. The resulting clustering methodology is applicable, without further ad hoc assumptions or transformations of the data, (1) when features are heterogeneous (both discrete and continuous) and not combinable, (2) where some data points have missing feature values, and (3) where some features are irrelevant, i.e. have large variance but little correlation with other features. Further, it provides an integral measure of the quality of the resulting clustering. A clustering program, RIFFLE, has been implemented in line with this approach, and experiments with synthetic and real data show that the clustering is, in many respects, superior to traditional methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Adeno-associated virus vector mediated transduction of primary normal human breast epithelial cells. (1998)

Cultured human breast epithelial cells from reduction mammoplasty specimens were transduced using an adeno-associated virus vector encoding the marker gene E. coli -galactosidase. Subconfluent, growing, breast epithelial cells were more easily transduced than confluent, quiescent, cells. Transduction of non-dividing confluent cells could be greatly increased by ultraviolet light-induced DNA damage or by prior exposure to the DNA synthesis inhibitor hydroxyurea. The effects of ultraviolet light and hydroxyurea on transduction were additive when these agents were applied together.
MR multispectral analysis of multiple sclerosis lesions (1997)

Although quantification of the lesion burden from serial MR examinations of patients with multiple sclerosis (MS) is a common technique to assess disease activity in clinical trials, pathologic change may occur within a lesion without a corresponding change in volume. Therefore, measures of lesion volume and composition may improve the sensitivity of detecting disease activity. A new technique has been developed that provides information about the intensity composition of MS lesions in standard spin-echo MR examinations. The new technique is based on the multispectral "feature space" intensity distributions of the lesions and normal tissues. Analysis of MR examinations of materials with known T1 and T2 times showed that feature space position from spin-echo examinations is largely determined from proton density (rho), T2, and the interecho delay. Information about intensity composition was obtained by reducing the multidimensional intensity distribution to one dimension while minimizing the loss of information. This technique was used to analyze eight lesions in standard spin-echo MR examinations of three patients with MS. Lesion distributions were compared between examinations by first calibrating the examinations based on the intensity distributions of cerebrospinal fluid (CSF), an internal reference tissue. Many of the lesion distributions had a distinctive peak at low intensity, corresponding to normal-appearing white matter (WM). Within the lesion distributions, increases in high intensity peaks generally were accompanied by reductions in the WM peak. Serial analysis of the lesion distributions revealed some dramatic fluctuations, even when lesion volume remained constant.
Clinical and Genetic Characteristics of Chinese Patients with Occult Macular Dystrophy (2020)

To the best of our knowledge, this is the largest study in a cohort of Chinese OMD patients with RP1L1 mutations. Our findings revealed that the two recurrent RP1L1 variants are related to OMD in the Chinese population. Furthermore, multimodal imaging combined with genetic testing is valuable for diagnosing and monitoring OMD progression.
Potential for molecularly targeted therapy against epidermal growth factor receptor ligands. (2009)

Monoclonal antibodies and tyrosine kinase inhibitors against ErbB receptors have been developed and have progressed to clinical applications following several decades of research in cancer cell biology. Inhibition of epidermal growth factor receptor (EGFR) signaling represents a particularly promising arena for the application of molecularly targeted cancer therapies. In EGFR signaling inhibition, EGFR itself has been recognized as a target in epithelial malignancies, though clinical studies using EGFR antagonists have not always resulted in favorable clinical outcomes. The aberrant enhancement of EGFR ligand expression is speculated to be one of several different molecular mechanisms accounting for the acquired resistance to EGFR antagonists. Recently, emerging evidence has indicated that EGFR ligands deserve considerable attention as potential targets for cancer therapy. In this review, we discuss the EGFR signaling inhibition strategies directed at EGFR ligands such as HB-EGF and amphiregulin.
Application of flat panel OLED display technology for the point-of-care detection of circulating cancer biomarkers (2016)

Point-of-care molecular diagnostics can provide efficient and cost-effective medical care, and they have the potential to fundamentally change our approach to global health. However, most existing approaches are not scalable to include multiple biomarkers. As a solution, we have combined commercial flat panel OLED display technology with protein microarray technology to enable high-density fluorescent, programmable, multiplexed biorecognition in a compact and disposable configuration with clinical-level sensitivity. Our approach leverages advances in commercial display technology to reduce pre-functionalized biosensor substrate costs to pennies per cm(2). Here, we demonstrate quantitative detection of IgG antibodies to multiple viral antigens in patient serum samples with detection limits for human IgG in the 10 pg/mL range. We also demonstrate multiplexed detection of antibodies to the HPV16 proteins E2, E6, and E7, which are circulating biomarkers for cervical as well as head and neck cancers.
Microstrip-A New Transmission Technique for the Klilomegacycle Range (1952)

A novel approach to microwave transmission and components is described. In place of the more familiar waveguide or coaxial structures, this technique utilizes a single conductor supported above a ground plane. Such a configuration is equivalent to a parallel-wire system for the image of the conductor in the ground plane produces the required symmetry. Losses in this system are approximately equal to those of coaxial structures. The extent of the field spread about the conductor is small, thus making possible compact configuration. Printed-circuit techniques are particularly applicable to the construction of compact, rugged, inexpensive, and noncritical microwave components. A general description, background theory, and laboratory experiments are given in this and other papers.
High beam-coupling gain and deep- and shallow-trap effects in cobalt-doped barium titanate, BaTiO_3:Co (1992)

A series of cobalt-doped barium titanate (BaTiO3) crystals were grown; these crystals have the highest beam-coupling gain reported to date, 7.9 cm−1, measured by using the smallest electro-optic coefficient of BaTiO3. The intensity dependence of the absorption and the gain indicate that there are at least two active photorefractive species. These samples show light-induced absorption and negative absorptive coupling, which is indicative of crystals with deep and shallow traps. However, doping with cobalt diminishes the intensity dependence of the electro-optic gain and increases the electro-optic and absorptive coupling, which indicates that cobalt is a deep-level photorefractive dopant. The higher gain is attributed to an increase of the total effective trap density and to an increase in the deep- and shallow-trap intensity-dependent factor η(I), with higher cobalt doping.
Nanocrystalline Diamond Nanoelectrode Arrays and Ensembles (2011)

In this report, the fabrication of all-nanocrystalline diamond (NCD) nanoelectrode arrays (NEAs) by e-beam lithography as well as of all-diamond nanoelectrode ensembles (NEEs) using nanosphere lithography is presented. In this way, nanostructuring techniques are combined with the excellent properties of diamond that are desirable for electrochemical sensor devices. Arrays and ensembles of recessed disk electrodes with radii ranging from 150 to 250 nm and a spacing of 10 μm have been fabricated. Electrochemical impedance spectroscopy as well as cyclic voltammetry was conducted to characterize arrays and ensembles with respect to different diffusion regimes. One outstanding advantage of diamond as an electrode material is the stability of specific surface terminations influencing the electron transfer kinetics. On changing the termination from hydrogen- to oxygen-terminated diamond electrode surface, we observe a dependence of the electron transfer rate constant on the charge of the analyte molecule. Ru(NH(3))(6)(+2/+3) shows faster electron transfer on oxygen than on hydrogen-terminated surfaces, while the anion IrCl(6)(-2/-3) exhibits faster electron transfer on hydrogen-terminated surfaces correlating with the surface dipole layer. This effect cannot be observed on macroscopic planar diamond electrodes and emphasizes the sensitivity of the all-diamond NEAs and NEEs. Thus, the NEAs and NEEs in combination with the efficiency and suitability of the selective electrochemical surface termination offer a new versatile system for electrochemical sensing.
Modelling and control of photovoltaic panels utilising the incremental conductance method for maximum power point tracking (2012)

For photovoltaic panels, maximum power point tracking (MPPT) is a crucial process to ensure energy capture is maximised. Various tracking algorithms are available for this purpose. Of these, one of the more common presently implemented is the incremental conductance method. However, no linearised small signal model incorporating an incremental conductance-based MPPT process exists. As will be demonstrated, this is attributed to the formation of a degenerate model when conventional linearisation techniques are applied. In this study, a modelling approach is developed that overcomes this deficiency and permits linearisation of the incremental conductance MPPT algorithm. As a case study adopting this developed approach, a complete small signal dynamic model of the incremental conductance method utilising a boost converter is derived. The model is validated against simulations in PSCAD/EMTDC. This study also presents some applications of the model, such as controller design and stability testing. The results demonstrate that the system is highly robust to variations in the lighting condition.
VMn underlayer for CoCrPt Longitudinal Recording Media (2000)

In this study, the magnetic properties of CoCrPt films (for longditudinal recording) on a novel VMn underlayer were measured and compared with similar films on conventional Cr underlayers. It was found that the VMn film had (200) preferred orientation and the lattice constant was about 0.2967 ㎚, which is slightly larger than that of the Cr film, 0.2888 ㎚. The grain size of the VMn film was 9.8 ㎚ at 30 ㎚ thickness, about 39% smaller than that of a similarly deposited Cr. The CoCrPt/VMn films showed higher coercivity in comparison with the CoCrPt/Cr films. The coercivity increase is attributed to the increased Co (11.0) texture, improved lattice matching between Co (11.0) and VMn (200), and lower stacking fault density. V or Mn must have diffused into the CoCrPt magnetic layer uniformly rather than preferentially along grain boundaries. This reduced Ms at higher substrate temperature
<i>In Vitro</i> and <i>in Vivo</i> Studies of Benzisoquinoline Ligands for the Brain Synaptic Vesicle Monoamine Transporter (1996)

Tetrabenazine is a high-affinity inhibitor of the vesicular monoamine transporter in mammalian brain. As part of a program to develop in vivo imaging agents for these transporters in human brain, a series of 2-alkylated dihydrotetrabenazine ligands was synthesized and evaluated in vitro and in vivo for binding to the brain vesicular monoamine transporter. Additions of organometallic reagents to tetrabenazine produced 2-methyl, 2-ethyl, 2-n-propyl, 2-isopropyl, and 2-isobutyl derivatives of dihydrotetrabenazine. The stereochemistry and conformation of the addition products were thoroughly verified by two-dimensional NMR techniques. All of these alkyl derivatives displayed in vitro affinity for the vesicular monoamine transporter binding site in rat brain using competitive assays with the radioligand [3H]methoxytetrabenazine. Except for the isopropyl derivative, all compounds when tested at 10 mg/kg iv showed an ability to inhibit in vivo accumulation of the radioligand [11C]methoxytetrabenazine in the mouse brain striatum. Derivatives with small alkyl groups (methyl, ethyl) were more effective than those with large groups (propyl, isobutyl). These studies suggest that large groups in the 2-position of the benzisoquinoline structure will significantly diminish both in vitro and in vivo binding of these compounds to the vesicular monoamine transporter.
Perl and CGI for the World Wide Web: Visual QuickStart Guide (2001)

From the Publisher:
Perl is by far the most popular programming language for creating scripts that add powerful interactive features to Web pages. Included on most UNIX platforms and available free of charge for Windows and Macintosh, Perl lets you place forms on your Web site that collect and process user input such as product orders and comments, enable visitors to conduct keyword searches for information on your site, and integrate a database into your site, among many other capabilities.Perl and CGI for the World Wide Web: Visual QuickStart Guide gets you to the heart of Perl scripting with CGI. Even first-time programmers will be able to create interactive Web pages and, more importantly, you'll be able to use your new-found familiarity with Perl to understand and customize the multitude of scripts that already exist on the Web. Following on the huge success of Liz Castro's top-selling HTML:Visual QuickStart Guide-the book to have to learn or reference HTML-Castro's Perl and CGI for the World Wide Web: Visual QuickStart Guide is soon to becomethe choice for learning Perl and CGI. Author of the acclaimed, best-selling HTML:Visual QuickStart Guide, with over 100,000 copies sold. Teaches you all you need to know to start creating CGI scripts in Perl. Shows how to make your Web pages stand out with interactive features such as guest books and forms. Assumes no prior programming experience.
BCL11A gene DNA methylation contributes to the risk of type 2 diabetes in males (2014)

<i>BCL11A</i> is a critical modulator involved in hemoglobin switching. Recent studies have established an association between <i>BCL11A</i> gene polymorphisms and a risk of type 2 diabetes (T2D). The aim of the present study was to assess the correlation between <i>BCL11A</i> DNA methylation and T2D. A total of 48 T2D cases and 48 age- and gender-matched controls were recruited to evaluate <i>BCL11A</i> methylation using bisulfite pyrosequencing technology. Although no significant association was observed in <i>BCL11A</i> methylation between T2D patients and healthy controls (P=0.322), breakdown analysis by gender identified a significant association between <i>BCL11A</i> methylation and T2D in males (P=0.018). Notably, there was also a significant female-specific association between the mean <i>BCL11A</i> DNA methylation and triglyceride (TG) concentration (r=-0.34; P=0.019). The results indicated that <i>BCL11A</i> methylation contributed to the risk of T2D in males. In addition, <i>BCL11A</i> methylation may have an effect on the development of T2D by influencing TG metabolism. Thus, gender difference may provide new information to aid the understanding of T2D pathogenesis.
Dietary omega-3 fatty acids and accumulation of docosahexaenoic acid in rod photoreceptor cells of the retina and at synapses. (1990)

Docosahexaenoic acid (DHA), the major biosynthetic product of the omega-3 family of fatty acids, is uniquely concentrated in the retina and synaptic membranes. In the perinatal period of life, when the bulk of synaptogenesis and photoreceptor biogenesis takes place, large requirements of DHA may be met first by the placenta and then by maternal milk. Linolenic acid (LLA), the precursor of DHA, is the most prevalent fatty acid of the omega-3 series in the stomach contents of newborn mice. In this study we have investigated the fate of radiolabeled LLA and DHA injected intraperitoneally in developing postnatal mouse. Our results show that radiolabeled LLA was taken up by the liver and DHA was synthesized; at 72 hrs post-injection about 90% of the label had been converted to DHA. Since there was a time-dependent buildup of radiolabeled DHA in blood plasma with negligible early uptake of LLA by the brain and retina, we hypothesize that the liver may secrete lipoproteins containing DHA and that this process is regulated by the nervous tissue.
Efficiency of traditional water wheels (2015)

For centuries mankind have used water wheels as a source of mechanical power for mills, weaving factories and machine workshops. By the time the theories and manufacturing methods of water wheels improved; the most developed technology took a significant leap into the turbines at the end of the Nineteenth century and water wheels development ceased. Thanks to a new sensibility to renewable energy and to local and smart electricity production, nowadays the traditional water wheels are regarded again as a clean and accessible way for micro electricity generation from water, especially in presence of very low heads, improving and conciliating the local economy with the local sustainable development. The present work illustrates some theoretical, experimental and numerical results related to a breastshot and an overshot water wheel. Overshot wheels are generally more efficient than breastshot ones and they are particularly suited for sites with small flow rates and high heads, while breastshot wheels are more suited for sites with abundant flow rates and low heads. The calibrated Computational Fluid Dynamic model of the wheels will also give us the possibility of maximizing their mechanical output power and efficiency, by testing different geometries, numbers of buckets and changes in water supply.