Miracle-dz/UniFAR-FTUs huggingface dataset:
Biosensors Based on Bivalent and Multivalent Recognition by Nucleic Acid Scaffolds

Several biological macromolecules adopt bivalent or multivalent interactions to perform various cellular processes. In this regard, the development of molecular constructs presenting multiple ligands in a specific manner is becoming crucial for the understanding of multivalent interactions and for the detection of target macromolecules. Nucleic acids are attractive molecules to achieve this goal because they are capable of forming various, structurally well-defined 2D or 3D nanostructures and can bear multiple ligands on their structures with precisely controlled ligand–ligand distances. Thanks to the features of nucleic acids, researchers have proposed a wide range of bivalent and multivalent binding agents that strongly bind to target biomolecules;consequently, these findings have uncovered new biosensing strategies for biomolecule detection. To date, various bivalent and multivalent interactions of nucleic acid architectures have been applied to the design of biosensors with enhanced sensitivity and target accuracy. In this review, we describe not only basic biosensor designs but also recently designed biosensors operating through the bivalent and multivalent recognition of nucleic acid scaffolds. Based on these designs, strategies to transduce bi- or multivalent interaction signals into readable signals are discussed in detail, and the future prospects and challenges of the field of multivalence-based biosensors are explored.
Global Biogeochemical Cycles Finding forced trends in oceanic oxygen

Anthropogenically forced trends in oceanic dissolved oxygen are evaluated in Earth system models in the context of natural variability. A large ensemble of a single Earth system model is used to clearly identify the forced component of change in interior oxygen distributions and to evaluate the magnitude of this signal relative to noise generated by internal climate variability. The time of emergence of forced trends is quantiﬁed on the basis of anomalies in oxygen concentrations and trends. We ﬁnd that the forced signal should already be evident in the southern Indian Ocean and parts of the eastern tropical Paciﬁc and Atlantic basins; widespread detection of forced deoxygenation is possible by 2030–2040. In addition to considering spatially discrete metrics of detection, we evaluate the similarity of the spatial structures associated with natural variability and the forced trend. Outside of the subtropics, these patterns are not wholly distinct on the isopycnal surfaces considered, and therefore, this approach does not provide signiﬁcantly advanced detection. Our results clearly demonstrate the strong impact of natural climate variability on interior oxygen distributions, providing an important context for interpreting observations.
THREE-DIMENSIONAL RECOVERY OF BUILDINGS ENVIRONMENT UNDER MANHATTAN-WORLD CONSTRAINT

This paper proposes a 3-D recovery method of an environment containing buildings. The difficulties of buildings recovery include little texture regions and a large scale nature, resulting in the accumulation of recovery errors. The proposed method introduces the Manhattan-world constraint in the algorithm of structure from motion (SfM) which is employed for the shape recovery from a set of sparse feature points. Experimental results show that the proposed method achieves higher accuracy in the recovery compared to the existent methods based only on the SfM algorithm.
The role of evaporites in the formation of gems during metamorphism of carbonate platforms: a review

: The mineral and fluid inclusions trapped by gemstones during the metamorphism of rocks in carbonate platform successions are precious markers for the understanding of the gem genesis. The nature and chemical composition of inclusions highlight the major contribution of evaporites through dissolution or fusion, depending on the temperature of formation from the greenschist to the granulite facies. The fluids are highly saline NaCl-brines circulating either in an open system in the greenschist facies (Colombian and Afghan emeralds) and with huge fluid-rock metasomatic interactions, or sulphurous fluids (ruby, garnet tsavorite, zoisite tanzanite and lapis-lazuli) or molten salts formed in a closed system with a low fluid mobility (ruby in marble) in the conditions of the amphibolite to granulite facies. These chloride-fluoride-sulphate ± carbonate-rich fluids scavenged the metals essential for the gem formation. At high temperature, anions SO42-, NO3-, BO3- and F- which are powerful fluxes lowered the temperature of chlorine and fluoride ionic liquids. Abstract The mineral and fluid inclusions trapped by gemstones during the metamorphism of 37 rocks in carbonate platform successions are precious markers for the understanding of the 38 gem genesis. The nature and chemical composition of inclusions highlight the major 39 contribution of evaporites through dissolution or fusion, depending on the temperature of 40 formation from the greenschist to the granulite facies. The fluids are highly saline NaCl- 41 brines circulating either in an open system in the greenschist facies (Colombian and Afghan 42 emeralds) and with huge fluid-rock metasomatic interactions, or sulphurous fluids (ruby, 43 garnet tsavorite, zoisite tanzanite and lapis-lazuli) or molten salts formed in a closed system 44 with a low fluid mobility (ruby in marble) in the conditions of the amphibolite to granulite 45 facies. These chloride-fluoride-sulphate ± carbonate-rich fluids scavenged the metals essential 46 for the gem formation. At high temperature, anions SO 42- , NO 3- , BO 3- and F - which are 47 powerful fluxes lowered the temperature of chlorine and fluoride ionic liquids. They provided 48 transport over a very short distance of aluminium, and/or silica and transition metals which 49 are necessary for gem growth. So, the genetic models proposed for these high-value and 50 ornamental gems underline the importance of the metamorphism of evaporites formed on 51 carbonate continental shelves, and emphasises the chemical power accompanying the 52 metamorphism at moderate to high temperatures of these particular evaporite-rich and organic 53 matter-rich protoliths to form gem minerals. 54 55 56 57 58 59 61 62 63 gems, emerald, ruby, garnet, zoisite, lapis-lazuli, metamorphism , carbonate platform, evaporites, brines, fingerprints, salinity, molten salts, thermal reduction of sulphates
Eddy covariance ﬂux measurements of ammonia by high temperature chemical ionisation mass spectrometry

A system for fast ammonia (NH 3 ) measurements with chemical ionisation mass spectrometry (CIMS) based on a commercial Proton Transfer Reaction-Mass Spectrometer (PTR-MS) is presented. It uses electron transfer reaction as ionisation pathway and features a drift tube of polyetheretherketone (PEEK) and silica-coated steel. Heating the instrumental inlet and the drift tube to 180 ◦ C en-abled an effective time resolution of ∼ 1 s and made it possible to apply the instrument for eddy covariance (EC) measurements. EC ﬂuxes of NH 3 were measured over two agricultural ﬁelds in Oensingen, Switzerland, following fertilisations with cattle slurry. Air was aspirated close to a sonic anemometer at a ﬂow of 100 STP L min − 1 and was directed through a 23 m long 1/2” PFA tube heated to 150 ◦ C to an air-conditioned trailer where the gas was sub-sampled from the large bypass stream. This setup minimised damping of fast NH 3 concentration changes between the sampling point and the actual measurement. High-frequency attenuation loss of the NH 3 ﬂuxes of 20 to 40% was quantiﬁed and corrected for using an empirical ogive method. The instrumental NH 3 background signal showed a minor interference with H 2 O which was characterised in the laboratory. The resulting correction of the NH 3 ﬂux after slurry spreading was less than 1‰. The ﬂux detection limit of the EC system was about 5 ng m − 2 s − 1 while the accuracy of individual ﬂux measurements was estimated 16% for the high-ﬂux regime during these experiments. The NH 3 emissions after broad spreading of the slurry showed an initial maximum of 150 µg m − 2 s − 1 with a fast decline in the following hours.
A review on various classification algorithms to predict the crime status

- in recent past, crime rate is becoming high in most highly populated country. Security is an aspect which is given higher priority by all governments in the world hence the significant task of to predict the crimes over data history. Now a days increasing user of the internet in the world is going rapidly hence cybercrime rate is also increasing. In data mining lots of algorithms are available to solve the mining problems. The crime profiling and zoning can be modelled with utilization of data mining. The predicted crime status can help to police department for investigation of criminal. Classification and clustering may prove the better methods for predict the crime status in data mining. Naïve Bayesian, k-Nearest Neighbour[3], Neural Networks may prove much better classifiers in comparisons of decision tree and support vector machine in data mining.
in beefburgers produced in the Republic of A quantitative microbial risk assessment

and recover E. coliO157:H7 from beef mince and bovine hide (O’Brien et al.,2005b). Minced beef and bovine hide were inoculated with varying concentrations (log 10 1.58-2.58 CFU g -1 and log 10 2.20-4.49 CFU 100 cm 2 respectively) of E. coliO157:H7 and recovered using an enumeration (direct plate method) or presence /absence method (enrichment / immunomagnetic separation) and then plated onto Sorbitol McConkey Agar (SMAC) or SMAC-Cefixime Tellurite (CT) in both cases. The direct plate method detected the pathogen consistently from minced beef samples with an average recovery of 69.2 - 91.2 %. From faecal material on the bovine hide, the recovery of the pathogen ranged from 1.80 – 64.5 % with fresh faeces, depending on the inoculum, while from dried faeces on hide, the results ranged from no recovery to 25 %. Enrichment/ immunomagnetic separation (IMS) recovered E. coli O157:H7 at all inoculum levels tested in beef mince, while the pathogen was only detected consistently at an average inoculum level of log 10 2.20 CFU 100 cm 2 from fresh faeces and log 10 4.49 cfu 100 cm 2 from dried faeces on bovine hide. These errors (underestimation of counts) associated with the method were included in the developed model.
Surface Magneto Plasmons and Their Applications Surface Magneto Plasmons and Their Applications

Due to their promising properties, surface magneto plasmons have attracted great inter- ests in the field of plasmonics. Apart from flexible modulation of the plasmonic properties by an external magnetic field, surface magneto plasmons also promise nonreciprocal effect and multi-bands of propagation, which can be applied into the design of integrated plasmonic devices for biosensing and telecommunication applications. In the visible fre- quencies, hybrid nanodevices consisting of metals and magnetic materials based on surface magneto plasmon are proposed. In the infrared frequencies, highly-doped semiconductors can replace metals, owning to the lower incident wave frequencies and lower plasma frequencies. Furthermore, a promising 2D material-graphene shows great potential in infra- red magnetic plasmonics. In this book chapter, we will review the magneto plasmonics with a focus on device designs and applications. We will give the basic theory of surface magneto plasmons propagating in different structures, including plane surface structures and slot waveguides. Based on the fundamental investigation and theoretical studies, we will illustrate various magneto plasmonic micro/nanodevices, such as tunable waveguides, filters, and beam-splitters. Novel plasmonic devices such as one-way waveguides and broad-band waveguides will also be introduced.
Cerenkov radiation: time dependent B field over a finite path.

Abstract : This preliminary study investigated the magnetic field radiated from a passing charge bunch traveling over a finite path. Beginning with the infinite path case for a ramp front charge distribution, limits were derived to solve for the magnetic radiation field over a finite path. Radiation pulses were computed and graphed for many different positions of an observer with respect to the beam line. Comparisons of results show that the similarity in pulse shapes does not depend exclusively on the observer's position with respect to the Cerenkov region, but also on certain time conditions in each case.
The clinical spectrum of the congenital myasthenic syndrome resulting from COL13A1 mutations

Next generation sequencing techniques were recently used to show mutations in COL13A1 cause synaptic basal lamina-associated congenital myasthenic syndrome type 19. Animal studies showed COL13A1, a synaptic extracellular-matrix protein, is involved in the formation and maintenance of the neuromuscular synapse that appears independent of the Agrin-LRP4-MuSK-DOK7 acetylcholine receptor clustering pathway. Here, we report the phenotypic spectrum of 16 patients from 11 kinships harbouring homozygous or heteroallelic mutations in COL13A1. Clinical presentation was mostly at birth with hypotonia and breathing and feeding difﬁculties often requiring ventilation and artiﬁcial feeding. Respiratory crisis related to recurrent apnoeas, sometimes triggered by chest infections, were common early in life but resolved over time. The predominant pattern of muscle weakness included bilateral ptosis (non-fatigable in adulthood), myopathic facies and marked axial weakness, especially of neck ﬂexion, while limb muscles were less involved. Other features included facial dysmorphism, skeletal abnormalities and mild learning difﬁculties. All patients tested had results consistent with abnormal neuromuscular transmission. Muscle biopsies were within normal limits or showed non-speciﬁc changes. Muscle MRI and serum creatine kinase levels were normal. In keeping with COL13A1 mutations affecting both synaptic structure and presynaptic function, treatment with 3,4-diaminopyridine and salbutamol resulted in motor and respiratory function improvement. In non-treated cases, disease severity and muscle strength improved gradually over time and several adults recovered normal muscle strength in the limbs. In summary, patients with COL13A1 mutations present mostly with severe early-onset myasthenic syndrome with feeding and breathing difﬁculties. Axial weakness is greater than limb weakness. Disease course improves gradually over time, which could be consistent with the less prominent role of COL13A1 once the neuromuscular junction is mature. This report emphasizes the role of collagens at the human muscle endplate and should facilitate the recognition of this disorder, which can beneﬁt from pharmacological treatment. We describe the clinical spectrum of disease associated with COL13A1 mutations and report a series of novel pathogenic mutations in this recently described CMS causative gene. Patients with COL13A1 mutations underlie a myasthenic syndrome characterized by early onset muscle weakness with predominantly feeding and breathing difﬁculties often requiring ventilation and artiﬁcial feeding. The pattern of muscle weakness is predominantly axial with marked bulbar, neck and truncal weakness rather than ap-pendicular. Scoliosis can be severe and therefore careful monitoring of the spinal curvature is recommended.
Wireless Relay Communication with Coding

—Wireless communications performance is badly affected by channel fading issue. Some diversity techniques are used to reduce the impact of fading by conveying data over multiple independent fading channel paths and combine them at the receiver side. Cooperative diversity is a novel communication technique where multiple terminals use their resources in cooperative manner to form a virtual array that realizes spatial diversity gain in a distributed fashion. Cooperative relay system can obtain reliable communications, capacity gain and energy saving by mutual relaying among users of wireless network .
BIOINFORMATICS A method of ﬁnding optimal weight factors for compound identiﬁcation in gas chromatography–mass spectrometry

Motivation: The compound identiﬁcation in gas chromatography– mass spectrometry (GC–MS) is achieved by matching the experimental mass spectrum to the mass spectra in a spectral library. It is known that the intensities with higher m / z value in the GC– MS mass spectrum are the most diagnostic. Therefore, to increase the relative signiﬁcance of peak intensities of higher m / z value, the intensities and m / z values are usually transformed with a set of weight factors. A poor quality of weight factors can signiﬁcantly decrease the accuracy of compound identiﬁcation. With the signiﬁcant enrichment of the mass spectral database and the broad application of GC–MS, it is important to re-visit the methods of discovering the optimal weight factors for high conﬁdent compound identiﬁcation. Results: We developed a novel approach to ﬁnding the optimal weight factors only through a reference library for high accuracy compound identiﬁcation. The developed approach ﬁrst calculates the ratio of skewness to kurtosis of the mass spectral similarity scores among spectra (compounds) in a reference library and then considers a weight factor with the maximum ratio as the optimal weight factor. We examined our approach by comparing the accuracy of compound identiﬁcation using the mass spectral library maintained by the National Institute of Standards and Technology. The results demonstrate that the optimal weight factors for fragment ion peak intensity and m / z value found by the developed approach outperform the current weight factors for compound identiﬁcation. Availability: The results and R package are available at http:// stage.louisville. edu/ faculty/ software-development. Supplementary information: Supplementary data are available at Bioinformatics online.
Vaccines Developed for Cancer Immunotherapy Vaccines Developed for Cancer Immunotherapy

Vaccines have been successfully used for prophylaxis of infectious diseases for a long time and in the last decades have inspired researchers to make products with similar immunological mechanisms for cancer immunotherapy, which has been developed rap- idly into clinical applications and has shown remarkable therapeutic efficacy, as exempli fied by chimeric Ag receptor T cell (CAR-T cell) and immune checkpoint inhibitor-based therapies which can efficiently strengthen the body’s immune system to fight against cancer, but they are also expensive. Therefore, encouraged by recent success of cancer immunotherapy, scientists are actively developing the low-cost tumor Ag-based vac cines, which, however, usually exhibit weak immunostimulating effects and, therefore, are often formulated with nanoparticulate carriers to form a vaccine adjuvant-delivery system (VADS), which can not only enhance the efficacy but also mitigate the off-target toxicity associated with conventional anticancer vaccines. These nanoparticulate carrier-based VADSs have demonstrated multiple functions, such as targetedly triggering Ag-presenting cells, reeducating tumor-associated macrophages (TAM) to function as tumor suppressor agent, and eliciting robust cytotoxic T lymphocytes (CTLs) to kill tumor cells. This chapter introduces multifunctional VADS that have been engineered with nanoparticulate carriers, including polymeric-, lipid-, metallic-, and cell-based nanoparticles, and used as an alternative to the existent tools for cancer immunotherapy.
A fundamental relation between mass, SFR and metallicity in local and high redshift galaxies

We show that the mass-metallicity relation observed in the local universe is due to a more general relation between stellar mass M*, gas-phase metallicity and SFR. Local galaxies define a tight surface in this 3D space, the Fundamental Metallicity Relation (FMR), with a small residual dispersion of ~0.05 dex in metallicity, i.e, ~12%. At low stellar mass, metallicity decreases sharply with increasing SFR, while at high stellar mass, metallicity does not depend on SFR. High redshift galaxies, up to z~2.5 are found to follow the same FMR defined by local SDSS galaxies, with no indication of evolution. The evolution of the mass-metallicity relation observed up to z=2.5 is due to the fact that galaxies with progressively higher SFRs, and therefore lower metallicities, are selected at increasing redshifts, sampling different parts of the same FMR. By introducing the new quantity mu_alpha=log(M*)-alpha log(SFR), with alpha=0.32, we define a projection of the FMR that minimizes the metallicity scatter of local galaxies. The same quantity also cancels out any redshift evolution up to z~2.5, i.e, all galaxies have the same range of values of mu_0.32. At z>2.5, evolution of about 0.6 dex off the FMR is observed, with high-redshift galaxies showing lower metallicities. The existence of the FMR can be explained by the interplay of infall of pristine gas and outflow of enriched material. The former effect is responsible for the dependence of metallicity with SFR and is the dominant effect at high-redshift, while the latter introduces the dependence on stellar mass and dominates at low redshift. The combination of these two effects, together with the Schmidt-Kennicutt law, explains the shape of the FMR and the role of mu_0.32. The small metallicity scatter around the FMR supports the smooth infall scenario of gas accretion in the local universe.
Kaposi’s Sarcoma-Associated Herpesvirus/Human Herpesvirus 8 K-bZIP Modulates Latency-Associated Nuclear Protein-Mediated Suppression of Lytic Origin-Dependent DNA Synthesis (cid:1)

The original cotransfection replication assay identiﬁed eight human herpesvirus 8 (HHV8)-encoded proteins required for origin-dependent lytic DNA replication. Previously, we demonstrated that under conditions where K-Rta is overexpressed, a K-bZIP knockout bacmid displayed an aberrant subcellular localization pattern for the latency-associated nuclear protein (LANA). Additionally, these same studies demonstrated that K-bZIP interacts with LANA in the absence of K-Rta and that K-bZIP does not directly participate in, but may facilitate, the initiation of lytic DNA synthesis. We developed a modiﬁcation of the transient cotransfection replication assay wherein both lytic (oriLyt) and latent (terminal repeat) DNA replication are evaluated simultaneously. We now show that LANA represses origin-dependent lytic DNA replication in a dose dependent manner when added to the cotransfection replication assay. This repression was overcome by increasing amounts of a K-bZIP expression plasmid in the cotransfection mixture or by dominant-negative inhibition of the interaction of LANA with K-bZIP by the overexpression of the K-bZIP-LANA binding domain. Chromatin immunoprecipitation assays show that LANA interacts with oriLyt in the absence of K-bZIP expression, suggesting that suppression of lytic replication by LANA is mediated by direct binding. The interaction of K-bZIP with oriLyt was dependent upon the of These data suggest that the interaction of with modulates and and that facilitates and modulates the switch from of