Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of antigenic determinants and secondary structures of the K88 and CFA1 fimbrial proteins from enteropathogenic Escherichia coli

Recently the amino acid sequences of the K88ab and the CFA1 fimbrial proteins from enteropathogenic Escherichia coli have become available. To elucidate the immunological interrelationships among the K88 family of antigenic variants, and to estimate the nature and position of the antigenic determinants in the K88 and CFA1 proteins, the positions of these features in the amino acid sequences have been predicted. This has been done by computerized algorithms, incorporating such factors as hydrophilicity and secondary structural potential. Some of the predicted determinants of K88 show good correlation with the known sequence differences between the antigenic variants of this protein. The presented results point to a possible use of synthetic vaccines against fimbriated pathogenic E. coli strains.
Solution Structure of the Focal Adhesion Adaptor PINCH LIM1 Domain and Characterization of Its Interaction with the Integrin-linked Kinase Ankyrin Repeat Domain*

PINCH is a recently identified adaptor protein that comprises an array of five LIM domains. PINCH functions through LIM-mediated protein-protein interactions that are involved in cell adhesion, growth, and differentiation. The LIM1 domain of PINCH interacts with integrin-linked kinase (ILK), thereby mediating focal adhesions via a specific integrin/ILK signaling pathway. We have solved the NMR structure of the PINCH LIM1 domain and characterized its binding to ILK. LIM1 contains two contiguous zinc fingers of the CCHC and CCCH types and adopts a global fold similar to that of functionally distinct LIM domains from cysteine-rich protein and cysteine-rich intestinal protein families with CCHC and CCCC zinc finger types. Gel-filtration and NMR experiments demonstrated a 1:1 complex between PINCH LIM1 and the ankyrin repeat domain of ILK. A chemical shift mapping experiment identified regions in PINCH LIM1 that are important for interaction with ILK. Comparison of surface features between PINCH LIM1 and other functionally different LIM domains indicated that the LIM motif might have a highly variable mode in recognizing various target proteins.
Latitudinal gradients in the phenetic diversity of New World bat communities

Although the examination of latitudinal gradients of species richness is common, little attention has been devoted to other components of biodiversity such as phenetic diversity. Because the phenotype reflects aspects of an organism's environment, ecological relationships and evolutionary history, measures of phenetic diversity likely provide complimentary information to that of species richness, and may provide unique insights for understanding the mechanistic basis to patterns of biodiversity. Herein, we evaluate latitudinal gradients in the phenetic diversity of 32 New World bat communities. Seven morphological characters were used to estimate phenotypic variation among bat species within local communities. Principal components analysis decomposed this variation into axes of size and shape. Three measures of phenetic diversity were calculated separately for size and for shape axes. The range of species scores on a particular axis described the amount of phenetic variation encompassed by species in a community. The standard deviation of minimum spanning-tree segment lengths described uniformity of species. Average nearest-neighbor distances described local packing. We separately regressed these six measures on local species richness and latitude separately. Variation in species richness accounted for a significant amount of variation in each measure of phenetic diversity. Latitude also accounted for significant variation in phenetic diversity except for the standard deviation of minimum-spanning tree segment lengths and the average nearest-neighbor distance on the shape axis. More importantly, gradients in phenetic diversity were significantly different than would be expected as a consequence of latitudinal gradients in species richness. Nonetheless, when variation among communities regarding the richness and composition of their regional faunas was taken into consideration, differences between empirical and simulated gradients were nonsignificant. Thus, factors that determine the composition of regional faunas have a great impact on the phenetic diversity of communities and ultimately the latitudinal gradient in biodiversity.
Histochemical and ultrastructural analysis of pathology and cell responses in gills of channel catfish affected with proliferative gill disease.

Pond-reared channel catfish Ictalurus punctatus with proliferative gill disease (PGD), caused by the myxozoan parasite Henneguya spp. , were examined with light and transmission electron microscopy to better characterize the inflammatory response during infection. The early stages of disease are characterized by the destruction of collagen in the matrix of the gill filament cartilage causing weakness and breaks within the gill filaments. These early lesions lacked a notable inflammatory response around the disrupted cartilage, a chondrocyte response was not apparent, and the parasite was not present, suggesting that the cartilage breaks occur prior to inflammation and arrival of the parasite in the gill. In later lesions, a significant inflammatory response was generated in areas of disrupted cartilage, and the inflammatory infiltrate was composed of a mixed population of granulocytes including neutrophils and cells that resembled eosinophils. The majority of eosinophil-like cells demonstrated evidence of degranulation. Trophozoites of Henneguya spp. were surrounded by a uniform population of cells believed to be neutrophils. The granulocytes were infiltrated within the dense collagen layer of the gill filament cartilage and often appeared within chondrocyte lacunae in place of the chondrocyte. The gill lamellae adjacent to the lesions were fused and contained an inflammatory infiltrate containing granulocytes and cells with pericentriolar granules that resembled previous descriptions of Langerhans-like cells. These cells were abundant within damaged lamellar epithelium, but were only rarely found within the gill filament. Lesions that appeared to be recovering lacked the dense collagenous layer around the cartilage and contained hyperplastic and hypertrophic chondrocytes that formed a callus. Other chondrocytes in the lesions had ultrastructural features indicative of cell death.
Overview of Software Tools for Obtaining UML Class Diagrams and Sequence Diagrams from Source Code within TFM4MDA

Topological Functioning Modeling for Model Driven Architecture (TFM4MDA) is an approach for software development starting from formal domain models. We plan to enhance TFM4MDA with reverse engineering principles in order to decrease a number of errors during software migration to other platforms or integration with other systems. TFM4MDA foresees the preliminary analysis of the target software system's structure and behavior at the high-level of abstraction. Since we plan to work with legacy systems, the reverse engineering can be used for obtaining the structure and behavior of the software system from source code. For better integration with TFM4MDA the system structure and behavior should be represented by Unified Modeling Language (UML) class diagrams and sequence diagrams, correspondingly. This paper presents an overview of the selected tools that supports reverse engineering and the Eclipse platform. The goal is to check what elements of the UML sequence and class diagrams can be obtained by them. The tool owners' documentation and tool tests were used for getting and analyzing this information.
Non‐producer human cells induced by murine sarcoma virus

Non‐producer (NP) human cells were isolated from transformed foci induced by the Kirsten mouse sarcoma virus. These morphologically altered NP cells produced neither infectious virus nor complement‐fixing antigens of the murine sarcoma‐leukemia virus complex. However, the sarcoma virus genome could be rescued from these NF cells by co‐cultivation with cells carrying „helper”︁ Kirsten mouse leukemia virus or Woolly Monkey leukemia virus. The possible usefulness of these cells in efforts designed to detect covert or repressed RNA tumor viruses in various animal and human tissues is discussed.
Universal Dynamical Decoupling of a Single Solid-State Spin from a Spin Bath

Avoiding Loss in a Quantum System Single electron spins in solid-state environments have been explored as candidates for quantum information storage and computation; however, they often interact strongly with their surroundings and lose the stored information on the time scale of pico- to milliseconds. Dynamical decoupling schemes have been introduced to “undo” the effects of this interaction by applying a sequence of control pulses that reverse the undesirable evolution of the system. De Lange et al. (p. 60, published online 9 September) tested several decoupling schemes on a nitrogen vacancy center in diamond and found that a scheme with evenly spaced pulses with double-axis decoupling could prolong the coherence time of an arbitrary spin state up to 25-fold. The coherence time of single spins is extended by a sequence of microwave pulses. Controlling the interaction of a single quantum system with its environment is a fundamental challenge in quantum science and technology. We strongly suppressed the coupling of a single spin in diamond with the surrounding spin bath by using double-axis dynamical decoupling. The coherence was preserved for arbitrary quantum states, as verified by quantum process tomography. The resulting coherence time enhancement followed a general scaling with the number of decoupling pulses. No limit was observed for the decoupling action up to 136 pulses, for which the coherence time was enhanced more than 25 times compared to that obtained with spin echo. These results uncover a new regime for experimental quantum science and allow us to overcome a major hurdle for implementing quantum information protocols.
DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia

We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine‐site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32‐trnL, psbA‐trnH, trnL‐F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single‐locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32‐trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology.
Oxidative stress and antioxidant effects of herbs and spices in diabetes

Reactive oxygen and nitrogen species are produced during metabolism and immune activity, and are triggered by several environmental factors such as pollution, chemicals, smoke, and sunlight. Harmful effects of these reactive species include cellular damage to nucleic acids, proteins and lipids leading to several diseases. The quality of life and the lifespan of the patients with these diseases depend on their complications. Increased oxidative stress is a widely accepted participant in the development and progression of diabetes and its complications. This has accelerated the global effort to harness and harvest those herbs and spices that bear substantial amount of potential phytochemicals, showing multiple beneficial effects in combating diabetes and diabetes-related complications. Herbal products or plant products rich in phenolic compounds, flavonoids, terpenoids, coumarins, and other constituents show reduction in blood glucose levels. Therefore, to combat the ever-increasing oxidative stress-induced diseases, increased consumption of diet derived antioxidants may be particularly helpful as antioxidants, in diminishing cumulative oxidative damage.
Towards Better Understanding of Pea Seed Dormancy Using Laser Desorption/Ionization Mass Spectrometry

Seed coats of six pea genotypes contrasting in dormancy were studied by laser desorption/ionization mass spectrometry (LDI-MS). Multivariate statistical analysis discriminated dormant and non-dormant seeds in mature dry state. Separation between dormant and non-dormant types was observed despite important markers of particular dormant genotypes differ from each other. Normalized signals of long-chain hydroxylated fatty acids (HLFA) in dormant JI64 genotype seed coats were significantly higher than in other genotypes. These compounds seem to be important markers likely influencing JI64 seed imbibition and germination. HLFA importance was supported by study of recombinant inbred lines (JI64xJI92) contrasting in dormancy but similar in other seed properties. Furthemore HLFA distribution in seed coat was studied by mass spectrometry imaging. HLFA contents in strophiole and hilum are significantly lower compared to other parts indicating their role in water uptake. Results from LDI-MS experiments are useful in understanding (physical) dormancy (first phases of germination) mechanism and properties related to food processing technologies (e.g., seed treatment by cooking).
Effects of iron-core topology on inrush currents in three-phase multi-leg power transformers

This paper investigates the inrush currents of three-phase (a)symmetric multi-leg transformer cores considering magnetic core structure (e.g., three-leg vs. five-leg) and switching effects (e.g., recloser operating). The electromagnetic steady-state and transient behavior of three-phase transformers significantly differs from single-phase transformer operation mainly because of the unique flux coupling interactions in multi-leg and asymmetric core structures. A recently developed three-leg nonlinear transformer core model is applied to this study which considers the influence of magnetic hysteresis, flux couplings in the core-structure and nonsinusoidal operation in three-phase transformers. Simulations results for multi-leg (e.g., three-leg and five-leg) transformer cores demonstrating inrush current behavior based on the model are presented and discussed.
Maternal Thyroid Disease and Preterm Birth: Systematic Review and Meta-Analysis.

CONTEXT Thyroid disease in pregnancy is increasing with rising average maternal ages in developed countries. The evidence for an association between preterm birth and thyroid disease has been confounded by small studies with varying outcomes and methodology. OBJECTIVE The aim of this meta-analysis is to review the literature regarding thyroid disease including subclinical and overt hypothyroidism, hyperthyroidism, and isolated hypothyroxinemia and the specific outcome of preterm birth. DATA SOURCES A search of PubMed and Embase databases was performed in May 2015. A fixed-effects model was used to calculate the overall combined odds ratio (OR) with its corresponding 95% confidence interval (95% CI) to evaluate the relationship between thyroid disease and preterm delivery. STUDY SELECTION Studies were considered eligible if they met the following criteria: prospective cohort study or a case control study; the exposure of interest was maternal thyroid disease, including subclinical hypothyroidism, overt hypothyroidism, hyperthyroidism, or isolated hypothyroxinemia; the outcome of interest was preterm delivery; and data regarding numbers of preterm births in each cohort were reported. DATA EXTRACTION Data were recorded in a database evidence table including any incidence data for maternal thyroid disease and preterm birth compared to a reference group. DATA SYNTHESIS Fourteen cohort studies and one case control study involving 2 532 704 participants were included. The combined OR of preterm delivery for pregnant women with overt hypothyroidism compared with the reference group was 1.19 (95% CI, 1.12-1.26; P < .00001). There was also a significant risk of preterm birth in women with hyperthyroidism (OR, 1.24 [95%, CI 1.17-1.31]; P < .00001). Subclinical hypothyroidism and isolated hypothyroxinemia showed no significant increase in OR. Sensitivity analysis made no change to these results. CONCLUSION Both overt hypothyroidism and hyperthyroidism are associated with a small but statistically significant increase in OR for preterm birth not seen in subclinical hypothyroidism or isolated hypothyroxinemia.
Arnold: Swimming Against the Tide

Epigraph by B. A. Khesin and S. L. Tabachnikov By Arnold: Arnold in his own words by V. I. Arnold From Hilbert's superposition problem to dynamical systems by V. I. Arnold Recollections by J. Moser Polymathematics: Is mathematics a single science or a set of arts? by V. I. Arnold A mathematical trivium by V. I. Arnold Comments on A Mathematical Trivium by B. A. Khesin and S. L. Tabachnikov About Vladimir Abramovich Rokhlin by V. I. Arnold About Arnold: To whom it may concern by A. Givental Remembering Vladimir Arnold: Early years by Y. Sinai Vladimir I. Arnold by S. Smale Memories of Vladimir Arnold by M. Berry Dima Arnold in my life by D. Fuchs V. I. Arnold, as I have seen him by Y. Ilyashenko My encounters with Vladimir Igorevich Arnold by Y. Eliashberg On V. I. Arnold and hydrodynamics by B. A. Khesin Arnold's seminar, first years by A. Khovanskii and A. Varchenko Topology in Arnold's work by V. Vassiliev Arnold and symplectic geometry by H. Hofer Some recollections of Vladimir Igorevich by M. Sevryuk Remembering V. I. Arnold by L. Polterovich Several thoughts about Arnold by A. Vershik Vladimir Igorevich Arnold: A view from the rear bench by S. Yakovenko
The Ribosomal Database Project.

The Ribosomal Database Project (RDP) is a curated database that offers ribosome-related data, analysis services, and associated computer programs. The offerings include phylogenetically ordered alignments of ribosomal RNA (rRNA) sequences, derived phylogenetic trees, rRNA secondary structure diagrams, and various software for handling, analyzing and displaying alignments and trees. The data are available via anonymous ftp (rdp.life.uiuc.edu), electronic mail (server/rdp.life.uiuc.edu) and gopher (rdpgopher.life.uiuc.edu). The electronic mail server also provides ribosomal probe checking, approximate phylogenetic placement of user-submitted sequences, screening for chimeric nature of newly sequenced rRNAs, and automated alignment.
Differential expression pattern of the four mitochondrial adenine nucleotide transporter ant genes and their roles during the development of Caenorhabditis elegans

The adenine nucleotide transporter (ANT) mediates exchange of cytosolic ADP and mitochondrial ATP. Although most species contain more than one ANT family member, it is not known whether their roles in developmental processes are redundant or specific. Here, we show that the Caenorhabditis elegans genome encodes four candidate ant genes (ant‐1.1, ant‐1.2, ant‐1.3, and ant‐1.4). We have investigated their spatiotemporal expression patterns and discovered that, whereas ANT‐1.1 is a ubiquitously expressed mitochondrial protein, the other three ANT proteins show a restricted range of cell type expression. Moreover, only the disruption of ant‐1.1 function, through RNA interference (RNAi), gives a mutant phenotype. Most of the ant‐1.1(RNAi) mutant embryos arrest before the morphogenesis stage. Furthermore, ant‐1.1 is also required postembryonically because RNAi mutants exhibit small size and life‐span extension. Our results suggest that ant‐1.1 is the only ant gene strictly required for embryonic and postembryonic development in C. elegans. Developmental Dynamics 237:1668–1681, 2008. © 2008 Wiley‐Liss, Inc.
FPGA-based high throughput XTS-AES encryption/decryption for storage area network

The key issue to improve the performance for secure large-scale Storage Area Network (SAN) applications lies in the speed of its encryption/decryption module. Software-based encryption/decryption cannot meet throughput requirements. To solve this problem, we propose a FPGA-based XTS-AES encryption/decryption to suit the needs for secure SAN applications with high throughput requirements. Besides throughput, area optimization is also considered in this proposed design. First, we reuse the same AES encryption to produce the tweak value and unify the operations of AES encryption/decryption in XTS-AES encryption/decryption. Second, we transfer the computations of AES encryption/decryption from GF(28) to GF(24)2, which enables us move the map and the inverse map functions outside the AES round. Third, we propose to support the SubBytes and the inverse SubBytes by the same hardware component. Finally, pipelined registers have been inserted into the proposed unrolled architecture for XTS-AES encryption/decryption. The experiments show that the proposed design achieves 36.2 Gbits/s throughput using 6784 slices on XC6VLX240T FPGA.
The Effect of Thalamic Hemorrhage on the Fornix

ABSTRACT Objectives: The fornix is indirectly connected to the anterior thalamus via the mamilothalamic tract. There has been no diffusion tensor tractography (DTT) study on the effect of thalamic hemorrhage on the fornix. Using DTT, we attempted to investigate the effect of thalamic hemorrhage on the fornix in patients with thalamic hemorrhage. Subjects and Methods: Twenty-one consecutive patients with thalamic hemorrhage and 21 age-matched normal healthy control subjects were recruited. DTT data were acquired at an average of 21 days after onset. We measured fractional anisotropy (FA) and apparent diffusion coefficient (ADC) of the three parts of the fornix (column, body, and crus) respectively. Results: FA values of the affected and unaffected hemispheres in the patient group were lower than those of the control group in all three parts of the fornix (p < .05). By contrast, compared with the control group, the ADC value was found to be increased only in the body (p < .05). Conclusions: According to our results, the FA value decrement with increased or normal ADC value in the patient group seems to indicate neuronal loss in the fornix, which appeared to be ascribed to secondary degeneration following thalamic hemorrhage.
Combined Central and Local Active and Reactive Power Control of PV Inverters

The increasing amount of photovoltaic (PV) generation results in a reverse power flow and a violation of the overvoltage limits in distribution networks. PV inverters can curtail active power or consume reactive power to avoid these excessive high voltages. Local controllers of active and reactive power that are based on measurements of the produced PV power have a fast response to the changing production levels of the PV installation. The performance of these local controllers depends on the tuning of the control parameters, which are grid and time dependent. In this paper, local control functions are defined as piecewise linear functions. The parameters of all the local control functions are regularly reoptimized. This results in an optimal use of reactive power and a minimum amount of curtailed active power, while respecting network limitations. The optimization of these parameters is formulated as a convex optimization problem, which can be solved sufficiently fast. The performance of the control is evaluated on an existing three-phase four-wire distribution grid and is compared with different local control methods.