Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Description of Hydrogen Bonding in Chloride−Water Clusters

We have determined the optimal structures, harmonic vibrational frequencies, and incremental association enthalpies for the Cl-(H2O)n, n = 1−4, clusters from first principle calculations and analyzed their structural, spectral, and energetic trends with cluster size. We have found that hydrogen bonding among water molecules plays a significant role in determining the optimal configurations as it becomes more competitive with the chloride−water interaction as the cluster grows. The competition between the different hydrogen bonding networks gives rise to more than one isomer for the n = 3 and 4 clusters that exhibit different structural, spectral, and energetic features. Configurations in which there exists less ordering among water molecules are associated with broader, less intense IR bands. In contrast, narrower bands of larger intensity are signatures of more ordered configurations. The most IR active bands correspond to the motion of the hydrogen bonded to the ion H atom along or perpendicular to the .
Record highest mesophotic fish diversity found in Raja Ampat

Abstract Mesophotic coral ecosystems (MCEs; reefs 30-150 m depth) are poorly studied, with existing research heavily geographically biased away from the most species-rich reef regions. Yet, MCEs are of high interest because of their potential to act as refuges from fisheries impacts. We surveyed MCEs in Raja Ampat, West Papua using baited remote underwater video, representing the largest MCE fish community survey ever conducted in the Coral Triangle region. Here we show that Raja Ampat MCEs are exceptionally fish species rich, with 152 fish species recorded – representing the greatest fish richness of any MCE previously surveyed. We find fish communities are highly depth driven, with declines in fish abundance and biomass at increased depth. In contrast to previous studies elsewhere in the world, we found that planktivores declined as a proportion of MCE community at increased depths. While greater human population density resulted in lower reef fish biomass, we found no evidence that MCEs provide a depth refuge from fisheries impacts. Our results suggest that previously established MCE-depth patterns may not hold true for Raja Ampat and highlight the need for future MCE studies within the Coral Triangle region.
Neo-sex chromosomes and demography shape genetic diversity in the Critically Endangered Raso lark

Generally small effective population sizes expose island species to inbreeding and loss of genetic variation. The Raso lark has been restricted to a single islet for ~500 years, with a population size of a few hundred. To investigate the factors shaping genetic diversity in the species, we assembled a reference genome for the related Eurasian skylark and then assessed genomic diversity and demographic history using RAD-seq data (26 Raso lark samples and 52 samples from its two most closely related mainland species). Genetic diversity in the Raso lark is lower than in its mainland relatives, but is nonetheless considerably higher than anticipated given its recent population size. We found that suppressed recombination on large neo-sex chromosomes maintains divergent alleles across 13% of the genome in females, leading to a two-fold increase in overall diversity in the population. Moreover, we infer that the population contracted from a much larger size recently enough, relative to the long generation time of the Raso lark, that much of the pre-existing genetic variation persists. Nevertheless, the current small population size is likely to lead to considerable inbreeding. Overall, our findings allow for optimism about the ongoing reintroduction of Raso larks to a nearby island, but also highlight the urgency of this effort.
The interpretation of collision‐induced dissociation tandem mass spectra of peptides

The introduction of fast atom bombardment (FABJ ionization mass spectrometry (MSJ ( 1 ) in the early 1980s enabled mass spectrometrists to obtain molecular weights of many nonvolatile molecules, including p e p tides comprising 10-20 amino acids, and, by the mid-1980s. small proteins could be desorbed and their molecular weights measured (2-7). FAB (here used generically to include fast atom as well as ion bombardment of the sample dissolved in a liquid matrix such as glycerol), being a ”soft ionization” technique, produces little or no fragmentation of protonated peptide molecules. This characteristic is, certainly, desirable, because it allows for the unambiguous assignment of molecular weights, even in multicomponent mixtures. Nevertheless, fragmentation of a molecule, after ionization in the mass spectrometer, can be used to obtain structural information, often completely and uniquely, and for decades mass spectra of thousands of compounds have been acquired, interpreted, and cataloged. Peptides consisting of as few as several amino acids are nonvolatile and, often, thermally labile and cannot be introduced into the mass spectrometer in the gas phase without prior derivatization. Derivatized peptides have been successfully fragmented, primarily using electron impact (El) ionization, and their amino acid sequence determined (8-1 3). sometimes with the assistance of computer programs ( 1 4). Complex mixtures of protein enzyme digests, often followed by partial acid hydrolysis, were derivatized and introduced into the mass spectrometer after fractionation with a gas chromatograph (GC). The El spectra were used to obtain amino acid sequences for the peptides, which were subsequently combined to arrive at the sequence of the protein. Peptide fragments, which sometimes are produced during FAB ionization, can be correlated to the peptide amino acid sequence ( 15-20). The abundance of such fragment ions, however, is quite low compared with the ions due to the protonated molecule. In addition, in order to obtain reasonably abundant fragment ions, a fairly concentrated sample is required, and even then large peptides (e.9. longer than 10 amino acids) do not fragment efficiently. Also, at lower mass (e.g., below m/z 500). fragment ions are usually difficult to identify, due to the FAB matrix background, and, of course, in mixtures more than one peptide usually fragments, thereby increasing the difficulty of fragment ion assignments to particular precursor ions. The advent of tandem mass spectrometry (MS/MS) (2 1-23) made it possible to analyze complex peptide mixtures (24-34) without the need to separate the individual components, because a mass window narrow enough to exclude all but one of the mixture components can be specified
Kinetics of Carbon Tetrachloride Reduction at an Oxide-Free Iron Electrode

To address some of the fundamental questions regarding the kinetics of reduction of contaminants by zero-valent iron (Fe0), we have taken advantage of the mass transport control afforded by a polished Fe0 rotating disk electrode (RDE) in an electrochemical cell. The kinetics of carbon tetrachloride (CCl4) dechlorination at an Fe0 RDE were studied in pH 8.4 borate buffer at a potential at which an oxide film would not form. In this system, the cathodic current was essentially independent of electrode rotation rate, and the measured first-order heterogeneous rate constant for the chemical reaction (kct = 2.3 × 10-5 cm s-1) was less than the estimated rate constant for mass transfer to the surface. Thus, for the conditions of this study, the rate of reduction of CCl4 by oxide-free Fe0 appears to be dominated by reaction at the metal−water interface rather than by transport to the metal surface. Activation energies for reduction of CCl4 and hexachloroethane by oxide-covered granular Fe0 (measured in batch sys.
Interlocking molecular grid lattices involving weak assembly forces

The X-ray structures of the two diquinoline derivatives 6,13-dihydro-6,13-ethano-5,12-diazapentacene (1) and 6α,13α-dibromo-2,9-dichloro-5bα,6,12bα,13-tetrahydropentaleno[1,2-b:4,5-b′]diquinoline (2) reveal that both crystallise by forming network lattices involving only weak intermolecular forces. These very similar lattices contain no aryl edge–edge C–H⋯N R22(8) dimers or efficient aryl offset face–face interactions, commonly found in related diquinoline crystals. Both lattices arise from multiple interlocking, at an inclined angle, of two identical sets of parallel molecular grids. Each grid connector site comprises a centrosymmetric tetramer of molecules held together by weak intermolecular forces, unlike the metal co-ordination motifs normally used to generate grid structures. Edge–edge C–H⋯N weak hydrogen bonds of various types help stabilise these structures by linking molecules of opposite handedness in neighbouring grids.
Neuronal TLR4 signaling enhances AMPA currents and drives posttraumatic epileptogenesis

Traumatic brain injury is a major risk factor for acquired epilepsies and understanding the mechanisms underlying the early pathophysiology could yield viable therapeutic targets. Growing evidence indicates a role for inflammatory signaling in modifying neuronal excitability and promoting acquired epilepsies. Here we identify that signaling through an innate immune receptor toll-like receptor 4 (TLR4), in neurons, augments calcium permeable AMPA currents in the hippocampal dentate gyrus after brain injury. Blocking TLR4 signaling in vivo early after brain injury reduced dentate network excitability and seizure susceptibility. TLR4 antagonism suppressed cellular inflammatory responses after injury without impacting sham controls. However, blocking TLR4 signaling augmented both network excitability and seizure susceptibility in uninjured controls. TLR4 antagonists failed to reduce post-injury seizure susceptibility when treatment was delayed and was less efficacious when AMPA currents were transiently enhanced during TLR4 antagonist treatment. These data identify a direct immune receptor regulation of post-traumatic neuronal excitability which is independent of glia. Moreover, the results demonstrate a causal association between TLR4-dependent early increase in dentate excitability and epileptogenesis. The findings suggest that the mechanisms underlying the aberrant TLR4 mediated increase in CP-AMPA after injury could be identified and selectively targeted to prevent epileptogenesis after traumatic brain injury. Graphical Abstract Summary of interactions between TLR4 signaling and brain injury on network excitability and epileptogenesis. Graphic illustration of the effect of injury and early TLR4 antagonist treatment early network excitability and long-term network state. The schematic neurons include TLR4 and GluA subunit expression profile in the acute phase of sham or brain injury. The corresponding early effects on network excitability are depicted by schematic population response traces (Inset on upper left). Note the increase in excitability of the uninjured neuron after TLR4 antagonism without changes in GluA expression. Note also the increase in TLR4, calcium permeable AMPA channels and population excitability after injury and its reduction by TLR4 antagonist treatment. Ampakine enhancement of excitability during TLR4 antagonism is illustrated. The early phase responses and manipulations (including injury, treatments and molecular responses) are superimposed on a two-tone color-coded network state topology where green indicates low-normal network excitability, ensuring network stability and low risk for epilepsy (Inset on upper right). Note the correspondence between early excitability state (population response profile) and long-term seizure susceptibility and the effects of pharmacological manipulations.
KVALITETA PROIZVODA KAO ČIMBENIK STVARANJA MARKE

is and sensitive because brands often reflect consumers' opinions and attitudes. Consumers establish a relationship based on emotions with brands and expect that certain important characteristics that they associate with a brand do not change. In particular, they expect continuity in quality, which is considered to be one of the key determinants of building a successful brand. In today's extremely fast and competitive market, it is more important for brands than ever to maintain continuity of quality and thus meet consumer expectations. The aim of this paper is to explain in more detail the characteristics of a brand, as well as the difference between a brand and a product, and the process of building a brand itself. By reviewing the available and current literature, this paper also aims to examine more closely the importance of quality in the process of creating a successful brand, which then generates positive business results and profits.
Azo Polymers for Reversible Optical Storage. 7. The Effect of the Size of the Photochromic Groups

Poly[(4-nitronaphthyl)[4-[[2-(methacryloyloxy)ethyl]ethylamino]phenyl]diazene] (pNDR1M) was prepared. The effect of the size of the azo moiety in the optical storage properties was studied. Both writing and relaxation processes can be described by biexponential functions. The bulkier pNDR1M exhibits a slower writing rate. However, there is no significant difference in the maximum birefringence achieved and in the relaxation rate when compared with the less bulky poly[(4-nitrophenyl)[4-[[2-(methacryloyoxy)ethyl]ethylamino]phenyl]diazene] (pDR1M).
Three-diodes PV model parameters extraction using PSO algorithm

In this paper, we propose a particle swarm optimization technique for the characterization of the equivalent electrical model of photovoltaic cell. The three diodes model with nine parameters is considered. The particle swarm optimization algorithm is used as a tool for the extraction of the model parameters by reaching the global minimum solution in a few iterations with a very good accuracy and short convergence time based on the minimization of the quadratic error between experimental and theoretical curves. Simulation obtained results show that the proposed approach is effective for modeling the photovoltaic cell as well as the module.
Stable multi-level social structure is maintained by habitat geometry in a wild bird population

Social structure can have profound evolutionary and ecological implications for animal populations. Structure can arise and be maintained via social preferences or be indirectly shaped by habitat structure. Understanding how social structure emerges is important for understanding the potential links between social structure and evolutionary and ecological processes. Here, we study a large community of wild birds fitted with uniquely-coded passive integrated transponder (PIT) tags and recorded on a grid of automated feeders fitted with radio frequency identification (RFID) antennae. We show that both large-scale and fine-scale network communities are consistent across years in this population, despite high generational turn-over. Studying the process that generates community structure, here the movement of individual birds across the woodland, suggests an important role of habitat geometry in shaping population-level social community structure. Our study highlights how relatively simple factors can produce apparent emergent social structure at the population scale, which has widespread implications for understanding eco-evolutionary dynamics.
Role of probiotics Bifidobacterium breve and Lactobacillus rhamnosus on inflammation lung in an experimental model of chronic obstructive pulmonary disease

Chronic pulmonary obstructive disease (COPD) is defined as an abnormal inflammatory response of the lungs to noxious particles or gases, mainly cigarette smoke. Thus, new therapeutic approaches are of unquestionable relevance. Without a specific treatment for COPD patients the use of probiotics via supplementation of diet can be a promising target. This project aims to investigate the beneficial effects of Bifidobacterium breve (Bb) and Lactobacillus rhamnosus (Lr) probiotics in lung inflammatory process in mice in a model of lung emphysema.
Traces of past transposable element presence in Brassicaceae genome dark matter

Transposable elements (TEs) are mobile, repetitive DNA sequences that have been found in every branch of life. In many organisms TEs are the primary contributors to the genome bulk. They invade genomes recurrently by wave of transposition bursts that ceased rapidly as repressed by host defense mechanisms subsequently triggered. The sequences become immobile and start to degrade, fading away in the genome sequence so that it cannot be recognized as such. It contributes then to the so-called "dark matter of the genome", this part of the genome where nothing can be recognized as biologically functional in first instance. We developed a new method able to find these old and degenerated TE sequences. With the new algorithm we implemented, we detect up to 10% of the A. thaliana genome deriving from TEs not yet identified. Altogether we bring to 50% the part of the genome deriving from TE in this species. Interestingly these sequences are generally very short, about 500bp, and found in the upstream 500pb of genes. Their epigenetic status and their nucleotide composition suggest an old TE origin.
Formulation and Evaluation of Herbal Drug Loaded Self Nano Emulsifying Drug Delivery System (SNEDDS)

The goal of this research was to formulate and test invitro the self-nano emulsifying drug delivery system (SNEDDS) of poorly water-soluble herbal material. Linalool, an essential of Coriandrum sativum with anti-epileptic activity, was isolated from Coriandrum sativum by using Soxhlet extraction method followed by column chromatography and fractionates are concentrated under reduced pressure by using rotary flash evaporator. It is low water soluble material; unpredictable dissolution and low bioavailability make it very difficult to administer linalool orally.The captex-200 oil was exhibited maximum solubility of linalool. Thus, it was chosen as the oil phase, while Tween 80 and PEG-200 were chosen as surfactant and co-surfactant respectively for the preparation of linalool SNEDDS. For the determination of existence zone of nanoemulsion, pseudo ternary phase diagram was developed using the Prism Software by using water titration method. Self-nanoemulsion are evaluated for scanning electron microscopy (SEM), particle size analysis, polydispersity index, zeta potential and invitro drug release.The s9 formulation showed 97.72% cumulative release higher than other selected formulations(S4-S8). The S9 formulation showed promising result on droplet size, zeta potential, polydispersity index, invitro drug dissolution. It was concluded that SNEDDS formation from captex-200, tween 80, PEG-200, Smix (4:1), is a promising approach to enhancing substance solubility and the pace of dissolution.
Conformation-Induced Electrostatic Gating of the Conduction of Spiropyran-Coated Organic Thin-Film Transistors

A facile method to make optoelectronic devices formed from organic thin-film transistors that are functionalized by photochromic spiropyran dyes in a nondestructive manner has been developed. When PDMS stamps are employed, alkane-containing spiropyran molecules can be coated simply onto the surface of organic thin films in a noninvasive manner. Upon UV irradiation, the molecules undergo isomerization from the neutral closed form to the charge-separated merocyanine form, producing the local electrostatic environment. This photoinduced electrostatic environment can function as a local negative gate voltage, thus increasing the electrical conductivity in p-type devices and decreasing the electrical conductivity in n-type devices. Further irradiation with visible light or keeping the devices in the dark can switch the device conductance back to their initial value. This method is reversible and reproducible on different devices with different thickness over a long period of time.
Time dependent quantum propagation in phase space

Numerical solutions of the quantum time-dependent integro-differential Schrodinger equation in a coherent state Husimi representation are investigated. Discretization leads to propagation on a grid of nonorthogonal coherent states without the need to invert an overlap matrix, with the further advantage of a sparse Hamiltonian matrix. Applications are made to the evolution of a Gaussian wave packet in a Morse potential. Propagation on a static rectangular grid is fast and accurate. Results are also presented for a moving rectangular grid, guided at its center by a mean classical path, and for a classically guided moving grid of individual coherent states taken from a Monte Carlo ensemble.
Accelerating Optimal Elemental Configuration Search in Crystal using Ising Machine

This research demonstrates that Ising machines can effectively solve optimal elemental configuration searches in crystals, with Au-Cu alloys serving as an example. The energy function is derived using the cluster expansion method in the form of a QUBO function, enabling efficient problem-solving via Ising machines. We have successfully obtained reasonable solutions for crystal structures consisting of over 10,000 atoms. Notably, we have also obtained plausible solutions for optimization problems with constrained solutions, such as situations where the composition ratio of atomic species is predetermined. These findings suggest that Ising machines can be valuable tools for addressing materials science challenges.
Automatic log analysis with NLP for the CMS workflow handling

The central Monte-Carlo production of the CMS experiment utilizes the WLCG infrastructure and manages daily thousands of tasks, each up to thousands of jobs. The distributed computing system is bound to sustain a certain rate of failures of various types, which are currently handled by computing operators a posteriori. Within the context of computing operations, and operation intelligence, we propose a Machine Learning technique to learn from the operators with a view to reduce the operational workload and delays. This work is in continuation of CMS work on operation intelligence to try and reach accurate predictions with Machine Learning. We present an approach to consider the log files of the workflows as regular text to leverage modern techniques from Natural Language Processing (NLP). In general, log files contain a substantial amount of text that is not human language. Therefore, different log parsing approaches are studied in order to map the log files’ words to high dimensional vectors. These vectors are then exploited as feature space to train a model that predicts the action that the operator has to take. This approach has the advantage that the information of the log files is extracted automatically and the format of the logs can be arbitrary. In this work the performance of the log file analysis with NLP is presented and compared to previous approaches.
Inference of Nonlinear Spatial Subunits by Spike-Triggered Clustering in Primate Retina

Integration of rectified synaptic inputs is a widespread nonlinear motif in sensory neuroscience. We present a novel method for maximum likelihood estimation of nonlinear subunits by soft-clustering spike-triggered stimuli. Subunits estimated from parasol ganglion cells recorded in macaque retina partitioned the receptive field into compact regions, likely representing bipolar cell inputs. Joint clustering with multiple RGCs revealed shared subunits in neighboring cells, producing a parsimonious population model. Closed-loop subunit validation was then performed by projecting white noise into the null space of the linear receptive field. Responses to these null stimuli were more accurately explained by a model with multiple subunits, and were stronger in OFF cells than ON cells. Presentation of natural stimuli containing jittering edges and textures also revealed greater response prediction accuracy with the subunit model. Finally, the generality of the approach was demonstrated by application to V1 data.