Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemical approaches for nanoscale patterning based on particle lithography with proteins and organic thin films

Abstract Nanopatterning methods based on particle lithography offer generic capabilities for high-throughput fabrication with thin film materials, such as organothiol and organosilane self-assembled monolayers (SAMs), polymer films, biological samples, and nanoparticles. Combining scanning probe microscopy with sample preparation based on approaches with particle lithography produces robust test platforms for ultrasensitive surface measurements. For example, nanopatterns of octadecyltrichlorosilane (OTS) can be prepared on surfaces of Si(111) using designed protocols of particle lithography combined with steps of either vapor deposition, immersion, or contact printing. Changing the physical approaches for applying molecules to masked surfaces produces nanostructures with designed shapes and thickness. Billions of nanostructures can be prepared using strategies for particle lithography, requiring only basic steps of mixing, heating, centrifuging, and drying. Arrays of exquisitely small and regular nanopatterns can be prepared with few defects and high reproducibility. For nanopatterns prepared with SAMs, the endgroups can be designed to spatially define the interfacial selectivity for adsorption of proteins, nanoparticles, or electrolessly deposited metals. Particle lithography has become a mature technique, with broad applicability for thin film materials. Images and measurements acquired with scanning probe microscopy will be described for samples prepared using particle lithography-based approaches.
Estimating Erosion in Oil and Gas Pipe Line Due to Sand Presence

Transporting solid particles in oil and gas flow cause erosion damage to the pipeline and fittings. The aim of this thesis is to study the effect of impact velocity on the erosion damage in 90 degree long elbow by using two different erosion models namely, Oka model and E/CRC model. Those correlation applied at air-borne sand eroding, methane-borne sand eroding, mixed gas-borne sand eroding, and multiphase (gas- oil) borne sand eroding Inconel 625. The commercial computational fluid dynamics (CFD) code STAR-CCM+ is used to obtain the average and maximum erosion rate by using the above mentioned models and compared them with the previous results.
Fabrication of arrays of sub-wavelength nano-apertures in an optically thick gold layer on glass slides for optical studies

We report on the fabrication of two-dimensional arrays of nano-optical apertures in gold layers by electron beam lithography (EBL) on a transparent glass substrate. 30 × 30 µm2 large arrays of high aspect ratio sub-wavelength cylinders (400 nm diameter with period of 1.81 µm) and annular apertures (diameters 250/330 nm and 310/330 nm inner/outer with period of 600 nm) were patterned in a 750 nm thick resist layer using a high contrast negative tone resist. The resist structures show sharp and vertical edges after development. The 150 nm thick deposited gold layer ensures optical transmission of less than 1.1 × 10−4 at 633 nm wavelength. White light based optical characterizations agreed with theory predictions and prove the good quality of the structures.
Modified embedded-atom method interatomic potential for the Fe–Pt alloy system

A semi-empirical interatomic potential formalism, the modified embedded atom method (MEAM), has been applied to obtain an interatomic potential for the Fe–Pt alloy system, based on the previously developed potentials for pure Fe and Pt. The potential can describe basic physical properties of the alloys (lattice parameter, bulk modulus, stability of individual phases, and order/disorder transformations), in good agreement with experimental information. The procedure for the determination of potential parameter values and comparisons between the present calculation and experimental data or high level calculation are presented. The applicability of the potential to atomistic studies to investigate structural evolution of Fe_50Pt_50 alloy thin films during post-annealing is also discussed.
Slowly progressive LGI1 encephalitis with isolated late‐onset cognitive dysfunction: a treatable mimic of Alzheimer's disease

J. Marquetand, M. van Lessen, B. Bender, M. Reimold, G. Elsen, W. Stoecker and M. Synofzik Department of Epileptology, HertieInstitute for Clinical Brain Research, T€ubingen, Section of Neuropsychology, Department of Cognitive Neurology, Hertie-Institute for Clinical Brain Research, T€ubingen, Department of Neuroradiology, University of T€ubingen, T€ubingen, Department of Nuclear Medicine, University of T€ubingen, T€ubingen, Euroimmun Medizinische Labordiagnostika AG, L€ubeck, Department of Neurodegenerative Diseases, Hertie-Institute for Clinical Brain Research, T€ubingen, and German Research Center for Neurodegenerative Diseases (DZNE), T€ ubingen, Germany
Heterogeneous client-server architecture for a virtual meeting environment

Magic Lounge is a shared virtual meeting environment which has been designed to support meetings between physically remote people who would like to interact with each other using any one of a number of heterogeneous communication devices. This paper describes the heterogeneous client-server architecture of the Magic Lounge which supports communication between PCs, PDAs, palmtops, and mobile telephones. This architecture combines a number of different technologies, including CORBA and MBone, to provide the necessary means of audio and textual communication between the users of different devices. This paper also discusses the various requirements of this type of meeting environment, as well as describing some of the Magic Lounge software tools and components which have been developed to provide intelligent communication services to its users.
Non-Deterministic Modelling of Food-Web Dynamics

A novel approach to model food-web dynamics, based on a combination of chance (randomness) and necessity (system constraints), was presented by Mullon et al. in 2009. Based on simulations for the Benguela ecosystem, they concluded that observed patterns of ecosystem variability may simply result from basic structural constraints within which the ecosystem functions. To date, and despite the importance of these conclusions, this work has received little attention. The objective of the present paper is to replicate this original model and evaluate the conclusions that were derived from its simulations. For this purpose, we revisit the equations and input parameters that form the structure of the original model and implement a comparable simulation model. We restate the model principles and provide a detailed account of the model structure, equations, and parameters. Our model can reproduce several ecosystem dynamic patterns: pseudo-cycles, variation and volatility, diet, stock-recruitment relationships, and correlations between species biomass series. The original conclusions are supported to a large extent by the current replication of the model. Model parameterisation and computational aspects remain difficult and these need to be investigated further. Hopefully, the present contribution will make this approach available to a larger research community and will promote the use of non-deterministic-network-dynamics models as ‘null models of food-webs’ as originally advocated.
Analysis of CMOS hot carrier light sources using back-end-of-line light directing structures for improved light extraction efficiency

Light emission from silicon is possible in CMOS through hot carrier electroluminescence. Low conversion and low extraction efficiency remains a challenge. By using existing back-end-of-line interconnect structures it is possible to improve the extraction efficiency. Such light directing structures were analysed with the use of a focused ion beam and scanning electron microscope. It was found that it is possible to improve light extraction efficiency and directionality of the light sources through a combination of back-end-of-line structures and field oxide manipulation resulting in an improved optical path for emitted photon radiation. However, further analysis indicates that total internal reflections, scattering and electromagnetic absorption from the via plugs and metal interconnects in the back-end-of-line stack are some of the key contributors to the inefficient light extraction efficiency.
Diagnosis and Management of the Metabolic Syndrome: An American Heart Association/National Heart, Lung, and Blood Institute Scientific Statement

The metabolic syndrome has received increased attention in the past few years. This statement from the American Heart Association (AHA) and the National Heart, Lung, and Blood Institute (NHLBI) is intended to provide up-to-date guidance for professionals on the diagnosis and management of the metabolic syndrome in adults. The metabolic syndrome is a constellation of interrelated risk factors of metabolic origin—metabolic risk factors—that appear to directly promote the development of atherosclerotic cardiovascular disease (ASCVD). 1 Patients with the metabolic syndrome also are at increased risk for developing type 2 diabetes mellitus. Another set of conditions, the underlying risk factors, give rise to the metabolic risk factors. In the past few years, several expert groups have attempted to set forth simple diagnostic criteria to be used in clinical practice to identify patients who manifest the multiple components of the metabolic syndrome. These criteria have varied somewhat in specific elements, but in general they include a combination of both underlying and metabolic risk factors. The most widely recognized of the metabolic risk factors are atherogenic dyslipidemia, elevated blood pressure, and elevated plasma glucose. Individuals with these characteristics commonly manifest a prothrombotic state and a proinflammatory state as well. Atherogenic dyslipidemia consists of an aggregation of lipoprotein abnormalities including elevated serum triglyceride and apolipoprotein B (apoB), increased small LDL particles, and a reduced level of HDL cholesterol (HDL-C). The metabolic syndrome is often referred to as if it were a discrete entity with a single cause. Available data suggest that it truly is a syndrome, ie, a grouping of ASCVD risk factors, but one that probably has more than one cause. Regardless of cause, the syndrome identifies individuals at an elevated risk for ASCVD. The magnitude of the increased risk can vary according to which components of the syndrome are present plus the other, non–metabolic syndrome risk factors in a particular person.
Cryo-electron microscopy of vitrified specimens

Cryo-electron microscopy of vitrified specimens was just emerging as a practical method when Richard Henderson proposed that we should teach an EMBO course on the new technique. The request seemed to come too early because at that moment the method looked more like a laboratory game than a useful tool. However, during the months which ellapsed before the start of the course, several of the major difficulties associated with electron microscopy of vitrified specimens found surprisingly elegant solutions or simply became non-existent. The course could therefore take place under favourable circumstances in the summer of 1983. It was repeated the following years and cryo-electron microscopy spread rapidly. Since that time, water, which was once the arch enemy of all electronmicroscopists, became what it always was in nature – an integral part of biological matter and a beautiful substance.
Asy1, a protein required for meiotic chromosome synapsis, localizes to axis-associated chromatin in Arabidopsis and Brassica

The Arabidopsis thaliana ASY1 gene is essential for homologous chromosome synapsis. Antibodies specific to Asy1 protein and its homologue BoAsy1 from the related crop species Brassica oleracea have been used to investigate the temporal expression and localization of the protein in both species. Asy1 is initially detected in pollen mother cells during meiotic interphase as numerous punctate foci distributed over the chromatin. As leptotene progresses the signal appears to be increasingly continuous and is closely associated with the axial elements but not to the extended chromatin loops associated with them. By the end of zygotene the signal extends almost the entire length of the synapsed homologues, although not to the telomeres. The protein begins to disappear as the homologues desynapse, until by late diplotene it is no longer associated with the chromosomes. Immunogold labelling in conjunction with electron microscopy established that Asy1 localizes to regions of chromatin that associate with the axial/lateral elements of meiotic chromosomes rather than being a component of the synaptonemal complex itself. These data together with the previously observed asynaptic phenotype of the asy1 mutant suggest that Asy1 is required for morphogenesis of the synaptonemal complex, possibly by defining regions of chromatin that associate with the developing synaptonemal complex structure.
Preclinical Evaluation of a Tailor-Made DOTA-Conjugated PSMA Inhibitor with Optimized Linker Moiety for Imaging and Endoradiotherapy of Prostate Cancer

Despite many advances in the past years, the treatment of metastatic prostate cancer still remains challenging. In recent years, prostate-specific membrane antigen (PSMA) inhibitors were intensively studied to develop low-molecular-weight ligands for imaging prostate cancer lesions by PET or SPECT. However, the endoradiotherapeutic use of these compounds requires optimization with regard to the radionuclide-chelating agent and the linker moiety between chelator and pharmacophore, which influence the overall pharmacokinetic properties of the resulting radioligand. In an effort to realize both detection and optimal treatment of prostate cancer, a tailor-made novel naphthyl-containing DOTA-conjugated PSMA inhibitor has been developed. Methods: The peptidomimetic structure was synthesized by solid-phase peptide chemistry and characterized using reversed-phase high-performance liquid chromatography and matrix-assisted laser desorption/ionization mass spectrometry. Subsequent 67/68Ga and 177Lu labeling resulted in radiochemical yields of greater than 97% or greater than 99%, respectively. Competitive binding and internalization experiments were performed using the PSMA-positive LNCaP cell line. The in vivo biodistribution and dynamic small-animal PET imaging studies were investigated in BALB/c nu/nu mice bearing LNCaP xenografts. Results: The chemically modified PSMA inhibitor PSMA-617 demonstrated high radiolytic stability for at least 72 h. A high inhibition potency (equilibrium dissociation constant [Ki] = 2.34 ± 2.94 nM on LNCaP; Ki = 0.37 ± 0.21 nM enzymatically determined) and highly efficient internalization into LNCaP cells were demonstrated. The small-animal PET measurements showed high tumor-to-background contrasts as early as 1 h after injection. Organ distribution revealed specific uptake in LNCaP tumors and in the kidneys 1 h after injection. With regard to therapeutic use, the compound exhibited a rapid clearance from the kidneys from 113.3 ± 24.4 at 1 h to 2.13 ± 1.36 percentage injected dose per gram at 24 h. The favorable pharmacokinetics of the molecule led to tumor-to-background ratios of 1,058 (tumor to blood) and 529 (tumor to muscle), respectively, 24 h after injection. Conclusion: The tailor-made DOTA-conjugated PSMA inhibitor PSMA-617 presented here is sustainably refined and advanced with respect to its tumor-targeting and pharmacokinetic properties by systematic chemical modification of the linker region. Therefore, this radiotracer is suitable for a first-in-human theranostic application and may help to improve the clinical management of prostate cancer in the future.
Indian family systems, collectivistic society and psychotherapy

Indian society is collectivistic and promotes social cohesion and interdependence. The traditional Indian joint family, which follows the same principles of collectivism, has proved itself to be an excellent resource for the care of the mentally ill. However, the society is changing with one of the most significant alterations being the disintegration of the joint family and the rise of nuclear and extended family system. Although even in today's changed scenario, the family forms a resource for mental health that the country cannot neglect, yet utilization of family in management of mental disorders is minimal. Family focused psychotherapeutic interventions might be the right tool for greater involvement of families in management of their mentally ill and it may pave the path for a deeper community focused treatment in mental disorders. This paper elaborates the features of Indian family systems in the light of the Asian collectivistic culture that are pertinent in psychotherapy. Authors evaluate the scope and effectiveness of family focused psychotherapy for mental disorders in India, and debate the issues and concerns faced in the practice of family therapy in India.
Using gene networks to drug target identification

Abstract The complete genome sequences have provided a plethora of potential drug targets. Gene network technique holds the promise of providing a conceptual framework for analysis of the profusion of biological data being generated on potential drug targets and providing insights to understand the biological regulatory mechanisms in diseases, which are playing an increasingly important role in searching for novel drug targets from the information contained in genomics. In this paper, we discuss some of the network-based approaches for identifying drug targets, with the emphasis on the gene network strategy. In addition, some of the relevant data resources and computational tools are given.
Assessment of strategies for male involvement in the prevention of mother-to-child transmission of HIV services in Blantyre, Malawi

Background Despite the documented benefits of prevention of mother-to-child transmission (PMTCT) of human immunodeficiency virus (HIV) services, the uptake remains low in sub-Saharan Africa. The lack of male involvement (MI) may be one of the reasons for this. However, there are limited data on strategies for MI in PMTCT. Objective The objective of this study was to identify strategies that may promote MI in PMTCT services in antenatal care (ANC) services in Blantyre, Malawi. Study design An exploratory qualitative study was conducted from December 2012 to January 2013 at South Lunzu Health Centre (SLHC) in Blantyre, Malawi. It consisted of six face-to-face key informant interviews (KIIs) with healthcare workers and four focus group discussions (FGDs) with 18 men and 17 pregnant women attending ANC at SLHC. The FGDs were divided according to sex and age. All FGDs and KIIs were digitally recorded and simultaneously transcribed and translated verbatim into English. Data were analyzed using thematic content analysis. Results Three major themes with several subcategories emerged. Theme 1 was a gatekeeping strategy with two subcategories: (1) healthcare workers refusing service provision to women accessing antenatal clinic without their partners and (2) women refusing ANC attention in the absence of a partner. Theme 2 comprised extending invitations and had six subcategories: (1) word of mouth, (2) card invites, (3) woman's health passport book invites, (4) telephonic invites, (5) use of influential people, and (6) home visits. Theme 3 was information education and communication, such as health education forums and advertisements. Of all the strategies, an invitation card addressed to the male partner was most preferred by study participants. Conclusions There are several strategies by which men may be involved in PMTCT. Healthcare workers should offer a pregnant woman all strategies available for MI for her to select the appropriate one. Further research and consultations with men should continue to achieve higher levels of MI.
Browsers to support awareness and social interaction

Information sharing and social interaction are the Web's main features that have enabled online communities to abound and flourish. However, the Web is lacking cues and browsing mechanisms for the online social spaces. The challenge of creating social browsing tools to access such social information and patterns is of interest as a visual analytic problem for two reasons. Browsers that combine social visualizations and tools let newcomers and visitors explore information and patterns. Here we present social browsers for two Web communities. In addition to the novel visualizations and representation of two facets of a group's identity, our work has three other notable contributions.
Strains of Synechocystis sp. PCC 6803 with Altered PsaC

Two [4Fe-4S] clusters, FA and FB, function as terminal electron carriers in Photosystem I (PS I), a thylakoid membrane-bound protein-pigment complex. To probe the function of these two clusters in photosynthetic electron transport, site-directed mutants were created in the transformable cyanobacterium Synechocystis sp. PCC 6803. Cysteine ligands in positions 14 or 51 to FB and FA, respectively, were replaced with aspartate, serine, or alanine, and the effect on the genetic, physiological, and biochemical characteristics of PS I complexes from the mutant strains were studied. All mutant strains were unable to grow photoautotrophically, and compared with wild type, mixotrophic growth was inhibited under normal light intensity. The mutant cells supported lower rates of whole-chain photosynthetic electron transport. Thylakoids isolated from the aspartate and serine mutants have lower levels of PS I subunits PsaC, PsaD, and PsaE and lower rates of PS I-mediated substrate photoreduction compared with the wild type. The alanine and double aspartate mutants have no detectable levels PsaC, PsaD, and PsaE. Electron transfer rates, measured by cytochrome c6-mediated NADP+ photoreduction, were lower in purified PS I complexes from the aspartate and serine mutants. By measuring the P700+ kinetics after a single turnover flash, a large percentage of the backreaction in the aspartate and serine mutants was found to be derived from A1 and FX, indicating an inefficiency at the FX → FA/FB electron transfer step. The alanine and double aspartate mutants failed to show any backreaction from [FA/FB]−. These results indicate that the various mutations of the cysteine 14 and 51 ligands to FB and FA affect biogenesis and electron transfer differently depending on the type of substitution, and that the effects of mutations on biogenesis and function can be biochemically separated and analyzed.
Document Image Binarization with Fully Convolutional Neural Networks

Binarization of degraded historical manuscript images is an important pre-processing step for many document processing tasks. We formulate binarization as a pixel classification learning task and apply a novel Fully Convolutional Network (FCN) architecture that operates at multiple image scales, including full resolution. The FCN is trained to optimize a continuous version of the Pseudo F-measure metric and an ensemble of FCNs outperform the competition winners on 4 of 7 DIBCO competitions. This same binarization technique can also be applied to different domains such as Palm Leaf Manuscripts with good performance. We analyze the performance of the proposed model w.r. t. the architectural hyperparameters, size and diversity of training data, and the input features chosen.