Miracle-dz/UniFAR-FTUs huggingface dataset:
1 α-Secretase processing of the Alzheimer amyloid-β precursor protein and its homolog APLP 2

The E1 domain of APP and APLP2 determines α-secretase specificity Manuscript 6 Additional publications  Jacobsen KT and Iverfeldt K Amyloid precursor protein and its homologues: a family of proteolysis-dependent receptors Exposure to the saturated free fatty acid palmitate alters BV-2 microglia inflammatory response Abstract The amyloid-β precursor protein (APP) has been widely studied due to its role in Alzheimer´s disease (AD). When APP is sequentially cleaved by β-and γ-secretase, amyloid-β (Aβ) is formed. Aβ is prone to aggregate and is toxic to neurons. However, the main processing pathway for APP involves initial cleavage at the α-site, within the Aβ region, instead generating a neu-roprotective soluble fragment, sAPPα. APP is a member of a protein family, also including the proteins APLP1 and APLP2, which are processed in a similar way as APP. In addition, knockout studies in mice have shown that the three proteins have overlapping functions where APLP2 play a key physiological role. The aim of this thesis was to study mechanisms regulating the α-secretase processing of APP and APLP2. We have used the human neuro-blastoma cell line SH-SY5Y as a model system and have stimulated α-secretase processing with insulin-like growth factor-1 (IGF-1) or retinoic acid (RA). Our results show that the stimulated α-site cleavage of APP and APLP2 is regulated by different signaling pathways and that the cleavage is mediated by different enzymes. APP was shown to be cleaved by ADAM10 in a PI3K-dependent manner, whereas APLP2 was cleaved by TACE in a PKC-dependent manner. We further show that protein levels and maturation of ADAM10 and TACE is increased in response to RA, mediated by a PI3K-or PKC-dependent signaling pathway, respectively. Another focus of our research has been O-GlcNAcylation, a dynamic post-translational modification regulated by the enzymes O-GlcNAc transferase and O-GlcNAcase (OGA). We show that decreased OGA activity stimulates sAPPα secretion, without affecting APLP2 processing. We further show that ADAM10 is O-GlcNAcylated. Lastly, we show that APP can be manipulated to be cleaved in a similar way as APLP2 during IGF-1 stimulation by substituting the E1 domain in APP with the E1 domain from APLP2. Together our results show distinct α-site processing mechanisms of APP and APLP2.
Spatial–Spectral Similarity Based on Adaptive Region for Landslide Inventory Mapping With Remote-Sensed Images

Landslide is one of the most serious geological disasters around the world, and acquiring landslide inventory mapping (LIM) with remote-sensed images (RSIs) plays an important role in disaster relief. However, various external imaging conditions of bitemporal RSIs usually cause pseudo-changes and challenges for achieving satisfied LIMs. In this article, a pioneering change magnitude measured distance named Spectral–Spatial Similarity based on Adaptive Region (S3AR) is proposed for achieving LIMs with bitemporal RSIs. First, an adaptive region is proposed to utilize the spatial-contextual information around each pixel, because the shapes and size of a landslide site are usually irregular and unpredictable. Then, a shape description algorithm is proposed for constructing a shape description vector, which aims at measuring the spatial difference of adaptive regions. Finally, to improve the separability between the landslide area and the background, brightness is suggested to couple with the shape description vector of an adaptive region to generate spatial–spectral similarity to measure the change magnitude between pairwise adaptive regions from the bitemporal RSIs. When the entire bitemporal RSIs are scanned and calculated via these steps, a change magnitude image between bitemporal RSIs can be generated, and then binary LIMs are obtained by a binary threshold. Experiments based on comparing eight state-of-the-art approaches demonstrated the feasibility and superiorities of the proposed S3AR for achieving LIMs with bitemporal RSIs. For example, the improvements on the four datasets are 5.81%, 14.06%, 6.03%, and 20.51% in terms of total error.
Present and Future of Intelligent Robots

Some fundamental characteristics of past, present and future robots are reviewed. In particular, the humanoid robot HERMES, an experimental robotic assistant of anthropomorphic size and shape, and the key technologies developed for it, are introduced. HERMES interacts dependably with people and their common living environment. It understands spoken natural language (English, French and German) speaker-independently, and can, therefore, be commanded by untrained humans. HERMES can see, hear, speak, and feel, as well as move about, localize itself, build maps of its environment and manipulate various objects. In its dialogues and other interactions with humans it appears intelligent, cooperative and friendly. In a long-term test (6 months) at a museum it chatted with visitors in natural language in German, English and French, answered questions and performed services as requested by them.
Long‐Range Distance Determination in a DNA Model System inside Xenopus laevis Oocytes by In‐Cell Spin‐Label EPR

Elucidating the structure and dynamics of biomacromolecules, for example, proteins, RNA, or DNA, is crucial for understanding their physiological function. Beside widespread techniques, such as NMR spectroscopy or crystallography, sophisticated electron paramagnetic resonance spectroscopy (EPR) methods in combination with site-directed spin labelingll ) are receiving increasing attention for this purpose. Spin-label EPR (SL-EPR) offers access to structural information on a length scale between approximately 0.5 and 10 nm, and enables the study of dynamics in the picoto microsecond rangeY-B) To date, SLEPR has been carried out in defined buffer solutions. However, recently an in-cell SL-EPR experiment investigating the conformation of ubiquitin was reported;(9) this suggests that the technique can be applied to nucleic acids as well, which is of particular importance since non-canonical DNA conformations are involved in many processes, such as regulatory functions. The development of analytical tools for elucidating native structures inside cells is an ongoing challenge to be addressed by in-cell spectroscopy. (10) Here, we describe long-range distance measurements on a DNA model system in oocytes of Xenopus laevis utilizing in-cell EPR. Compared to in-cell NMR spectroscopy, in-cell EPR has two main advantages. Low concentrations can be used because EPR is much more sensitive per spin than NMR spectroscopy, and since EPR only detects unpaired electron spins no background from diamagnetic molecules is observed. The latter is of particular importance since in contrast to structural studies of isolated macromolecules, in-cell experiments are often hampered by many different cellular components and thereby provide for high background signals. On the other hand, in-cell studies are of greater significance since, in contrast to pure solution experiments, a natural environment is provided, which can be crucial for observing the biologically relevant conformation of biomacromolecules.lll. l2) Double electron-electron resonance (DEER or PELDOR) is a pulsed, two-frequency EPR technique for determining distance distributions (from 1.5 up to 8 nm) between two paramagnetic centers by measuring their dipoledipole interaction. I131S) Diamagnetic biomacromolecules can be site-directly labeled with nitroxides.ll )
Hormonal contraception and risk of sexually transmitted disease acquisition: results from a prospective study.

OBJECTIVES To examine the relationship between use of oral contraceptive pills or depot medroxyprogesterone acetate and sexually transmitted disease acquisition. STUDY DESIGN Prospective cohort included 948 Kenyan prostitutes. Multivariate Andersen-Gill proportional hazards models were constructed, adjusting for sexual behavioral and demographic variables. RESULTS When compared with women who were using no contraception, users of oral contraceptive pills were at increased risk for acquisition of chlamydia (hazard ratio, 1.8; 95% confidence interval, 1.1-2.9) and vaginal candidiasis (hazard ratio, 1.5; 95% confidence interval, 1.2-1.9) and at decreased risk for bacterial vaginosis (hazard ratio, 0.8; 95% confidence interval, 0.7-1.0). Women using depot medroxyprogesterone acetate had significantly increased risk of chlamydia infection (hazard ratio, 1.6; 95% confidence interval, 1.1-2.4) and significantly decreased risk of bacterial vaginosis (hazard ratio, 0.7; 95% confidence interval, 0.5-0.8), trichomoniasis (hazard ratio, 0.6; 95% confidence interval, 0.4-1.0), and pelvic inflammatory disease (hazard ratio, 0.4; 95% confidence interval, 0.2-0.7). Consistent condom use was associated with significantly decreased risk of gonorrhea, chlamydia, genital ulcer disease, bacterial vaginosis, and pelvic inflammatory disease. CONCLUSIONS The use of oral or injectable hormonal contraception altered susceptibility to sexually transmitted diseases, which may in turn influence transmission of human immunodeficiency virus type 1. Consistent condom use was protective with regards to sexually transmitted disease and should be encouraged for the prevention of sexually transmitted disease and human immunodeficiency virus type 1 among women who use hormonal contraception.
DIALIGN: finding local similarities by multiple sequence alignment

MOTIVATION DIALIGN is a new method for pairwise as well as multiple alignment of nucleic acid and protein sequences. While standard alignment programs rely on comparing single residues and imposing gap penalties, DIALIGN constructs alignments by comparing whole segments of the sequences. No gap penalty is employed. This point of view is especially adequate if sequences are not globally related, but share only local similarities, as is the case in genomic DNA sequences and in many protein families. RESULTS Using four different data sets, we show that DIALIGN is able correctly to align conserved motifs in protein sequences. Alignments produced by DIALIGN are compared systematically to the results of five other alignment programs. AVAILABILITY DIALIGN is available to the scientific community free of charge for non-commercial use. Executables for various UNIX platforms including LINUX can be downloaded at http://www.gsf.de/biodv/dialign.html CONTACT werner, morgenstern@gsf.de
Cascade controller design via controller synthesis for load frequency control of electrical power systems

: The regulation of tie-line electricity flow and frequency of electrical power systems (EPS) is crucial for ensuring their robustness to parameter changes and eﬀicient management of disturbances. To this end, a novel cascade control design approach utilizing a serial Proportional-Integral-Derivative controller with a filter (PIDF) is proposed in this paper. The parameters of the controllers are derived analytically, and it is employed in both loops of the cascade control system to regulate the Load Frequency Control (LFC) of EPS. The implementation of PIDF controllers in both loops is utilized in the cascade control scheme for various power systems featuring different turbine topologies. This approach has been applied to single, and two-area power systems and has exhibited enhanced performance compared to other commonly referenced studies in the literature. To assess the effectiveness of the cascade control approach proposed performance metrics such as settling time, peak value (overshoot), and integral absolute error (IAE) value of frequency and tie-line power variations are utilized to gauge the system’s response to a load perturbation. Additionally, the suggested cascade control technique and design process have undergone robustness testing with ± 50% changes in system parameters to validate their reliability.
Weak extinction versus global exponential growth of total mass for superdiffusions

Consider a superdiffusion X on R d corresponding to the semi-linear operator A(u) = Lu + βu − ku 2 ,w hereL is a second order elliptic operator, β(·) is in the Kato class, and k(·) ≥ 0 is bounded on compact subsets of R d and is positive on a set
A performance comparison between the DR-net and a hierarchical RAID system

When the number of disks rises in disk array systems that contain multiple disk drives, system performance is limited by a bottleneck at a centralized controller and/or at a communication path that uses a bus. We evaluate, through simulation, a scalable architecture called DR-net, in which the controller functions are distributed to all disk drives and each disk has autonomy in processing its tasks. DR-net provided high throughput in proportion to the number of disks. In a conventional system, the influence of the bus setup time and concentration of the parity calculation load caused the throughput to saturate. We also show that DR-net can take advantage of disk autonomy when reconstructing data stored in failed disks. Our results indicate that the distribution of functions and the autonomy of disk drives enable better scalability and more effective utilization of system resources than with a hierarchical system.
Bursty research topic detection from scholarly data using dynamic Co-word networks: A preliminary investigation

Discovering emerging research topics from scholarly data is crucial to facilitate the understanding of trends and history of a target field. In a traditional science mapping approach, a co-word network, which shows the co-occurrence relationship between words, is depicted using a set of papers published in each of time periods. To identify bursty research topics in dynamic co-word networks, as a preliminary investigation, this paper proposes to introduce a scheme that identifies sudden increase in frequency of each word pair. Specifically, we first apply a burst detection model to a time-series of edge weights in the networks, and then reconstruct a network that consists of bursty word co-occurrences for each time period. To show the effectiveness of the proposed framework, we present a case study on conference papers in the fields of information retrieval, data mining, and WWW. The results of the experiments demonstrate that our method can reflect the research trend as compared with original co-word networks.
SCREENING AND CHARACTERIZATION OF PGPRs COLLECTED FROM RHIZOSPHERE SOILS OF SORGHUM CROP GROWN VERTISOLS

Different plant growth promoting rhizo bacteria were isolated from sorghum growing vertisols of different districts of Andhra Pradesh during the year 2018-19. Isolations were carried out in microbiology lab at Agricultural Research Station, ANGRAU, Amaravathi. A total of sixty isolates were obtained from 20 different rhizospheric soil samples.The PGP bacteria such as Azotobacter, Azospirillium, PSB, KRB, ZnSB and PGP isolates were isolated. The isolated PGPRs were screened for their morphological, physiological and biochemical characteristics. All the 60 isolates i.e. Azotobacter, Azospirillium, PSB, KRB, ZnSB and PGP isolate performed differently based on the strain specificity
SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes

ABSTRACT We report the development of SearchDOGS Bacteria, software to automatically detect missing genes in annotated bacterial genomes by combining BLAST searches with comparative genomics. Having successfully applied the approach to yeast genomes, we redeveloped SearchDOGS to function as a standalone, downloadable package, requiring only a set of GenBank annotation files as input. The software automatically generates a homology structure using reciprocal BLAST and a synteny-based method; this is followed by a scan of the entire genome of each species for unannotated genes. Results are provided in a HTML interface, providing coordinates, BLAST results, syntenic location, omega values (Ka/Ks, where Ks is the number of synonymous substitutions per synonymous site and Ka is the number of nonsynonymous substitutions per nonsynonymous site) for protein conservation estimates, and other information for each candidate gene. Using SearchDOGS Bacteria, we identified 155 gene candidates in the Shigella boydii sb227 genome, including 56 candidates of length < 60 codons. SearchDOGS Bacteria has two major advantages over currently available annotation software. First, it outperforms current methods in terms of sensitivity and is highly effective at identifying small or highly diverged genes. Second, as a freely downloadable package, it can be used with unpublished or confidential data.
On the Approximation of the Generalized-K PDF by a Gamma PDF Using the Moment Matching Method

Using the Nakagami probability density function (PDF) to model multipath fading and the Gamma PDF to model shadowing, in a wireless channel, has led to a closed-form expression for the composite fading PDF, known as the generalized-K PDF (also called Gamma-Gamma PDF). However, further derivations have shown that the cumulative distribution function (CDF) and the characteristic function of the generalized-K PDF contain special functions that are involved to handle. In this paper, an approximation of the generalized-K PDF by the familiar Gamma PDF is introduced. The parameters of the approximating Gamma PDF are computed using the moment matching method. The accuracy of this approximation in the lower and upper tail regions is enhanced by adjusting the parameters of the approximating Gamma distribution in each region. The CDF and the complementary CDF plots show that this approximation is sufficiently accurate for both integer and non-integer practical values of the multipath fading and shadowing parameters. The region-wise approximation obtained by the adjusted moment matching method is used to well-approximate the PDF of the sum of identically and independent generalized-K random variables. Applications of the obtained results arise in distributed antenna systems (DASs), cooperative relay networks, radar, and sonar systems.
Latent classes of delinquent behaviour associated with criminal social identity among juvenile offenders in Pakistan

Purpose – The purpose of this paper is to examine the number and nature of latent classes of delinquency that exist among male juvenile offenders incarcerated in prisons in Pakistan. Design/methodology/approach – The sample consisted of 415 young male offenders incarcerated in prisons in Khyber Pakhtunkhwa (KPK) Pakistan. Latent class analysis was employed to determine the number and nature of delinquency latent classes. Multinomial logistic regression was used to estimate the associations between latent classes and the three factors of criminal social identity (cognitive centrality, in-group affect, and in-group ties) whilst controlling for criminal friends, period of confinement, addiction, age, and location. Findings – The best fitting latent class model was a three-class solution. The classes were labelled: “minor delinquents” (the baseline/normative class; Class 3), “major delinquents” (Class 1), and “moderate delinquents” (Class 2). Class membership was predicted by differing external variables. Spe.
QUANTUM TOPOLOGY CHANGE IN (2 + 1)d

The topology of orientable (2+1) space–times can be captured by certain lumps of nontrivial topology called topological geons. They are the topological analogs of conventional solitons. We give a description of topological geons where the degrees of freedom related to topology are separated from the complete theory that contain metric (dynamical) degrees of freedom. The formalism also allows us to investigate processes of quantum topology change. They correspond to creation and annihilation of quantum geons. Selection rules for such processes are derived.
Sweet Bones: The Pathogenesis of Bone Alteration in Diabetes

Diabetic patients have increased fracture risk. The pathogenesis underlying the status of bone alterations in diabetes mellitus is not completely understood but is multifactorial. The major deficits appear to be related to a deficit in mineralized surface area, a decrement in the rate of mineral apposition, deceased osteoid surface, depressed osteoblast activity, and decreased numbers of osteoclasts due to abnormal insulin signaling pathway. Other prominent features of diabetes mellitus are an increased urinary excretion of calcium and magnesium, accumulation of advanced glycation end products, and oxidative stress leading to sweet bones (altered bone's strength, metabolism, and structure). Every diabetic patient should be assessed for risk factors for fractures and osteoporosis. The pathogenesis of the bone alterations in diabetes mellitus as well as their molecular mechanisms needs further study.
Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma

Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A–T and G–C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating “proof of concept” experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
Pathogenesis of Chronic Chagas Heart Disease

Background— Chagas disease remains a significant public health issue and a major cause of morbidity and mortality in Latin America. Despite nearly 1 century of research, the pathogenesis of chronic Chagas cardiomyopathy is incompletely understood, the most intriguing challenge of which is the complex host-parasite interaction. Methods and Results— A systematic review of the literature found in MEDLINE, EMBASE, BIREME, LILACS, and SCIELO was performed to search for relevant references on pathogenesis and pathophysiology of Chagas disease. Evidence from studies in animal models and in anima nobile points to 4 main pathogenetic mechanisms to explain the development of chronic Chagas heart disease: autonomic nervous system derangements, microvascular disturbances, parasite-dependent myocardial aggression, and immune-mediated myocardial injury. Despite its prominent peculiarities, the role of autonomic derangements and microcirculatory disturbances is probably ancillary among causes of chronic myocardial damage. The pathogenesis of chronic Chagas heart disease is dependent on a low-grade but incessant systemic infection with documented immune-adverse reaction. Parasite persistence and immunological mechanisms are inextricably related in the myocardial aggression in the chronic phase of Chagas heart disease. Conclusions— Most clinical studies have been performed in very small number of patients. Future research should explore the clinical potential implications and therapeutic opportunities of these 2 fundamental underlying pathogenetic mechanisms.