Miracle-dz/UniFAR-FTUs huggingface dataset:
Metabolic pathways and intracellular trafficking of gangliosides

Gangliosides constitute a large and heterogeneous family of acidic glycosphingolipids that contain one or more sialic acid residues and are expressed in nearly all vertebrate cells. Their de novo synthesis starts at the endoplasmic reticulum and is continued by a combination of glycosyltransferase activities at the Golgi complex, followed by vesicular delivery to the plasma membrane. At the cell surface, gangliosides participate in a variety of physiological as well as pathological processes. The cloning of genes for most of the glycosyltransferases responsible for ganglioside biosynthesis has produced a better understanding of the cellular and molecular basis of the ganglioside metabolism. In addition, the ability to delete groups of glycosphingolipid structures in mice has been enormously important in determining their physiological roles. Recently, a number of enzymes for ganglioside anabolism and catabolism have been shown to be associated with the plasma membrane, which might contribute to modulate local glycolipid composition, and consequently, the cell function. © 2011 IUBMB IUBMB Life, 63(7): 513‐520, 2011
ATP hydrolysis provides functions that promote rejection of pairings between different copies of long repeated sequences

Abstract During DNA recombination and repair, RecA family proteins must promote rapid joining of homologous DNA. Repeated sequences with >100 base pair lengths occupy more than 1% of bacterial genomes; however, commitment to strand exchange was believed to occur after testing ∼20–30 bp. If that were true, pairings between different copies of long repeated sequences would usually become irreversible. Our experiments reveal that in the presence of ATP hydrolysis even 75 bp sequence-matched strand exchange products remain quite reversible. Experiments also indicate that when ATP hydrolysis is present, flanking heterologous dsDNA regions increase the reversibility of sequence matched strand exchange products with lengths up to ∼75 bp. Results of molecular dynamics simulations provide insight into how ATP hydrolysis destabilizes strand exchange products. These results inspired a model that shows how pairings between long repeated sequences could be efficiently rejected even though most homologous pairings form irreversible products.
An ab initio Study of the Molecular Electric-field Gradients of the Chlorsilanes

Abstract The electric field gradient (EFG) of chlorine in the chlorine containing silanes (SiCl4 , SiCl3H, SiCl2H2 , and SiClH3) was determined by means of ab initio methods and compared to recent experiments from which nuclear quadrupole moments are extracted. A careful estimation of the AO basis sets and the effect of the electron correlation is undertaken. The results showed the importance of the use of extended basis sets in the calculation of EFGs in second row atoms. Good agreement with deviations less than 5% from the experiments was found. The effect of the electron correlation was found to be small.
The Fecal Viral Flora of Wild Rodents

The frequent interactions of rodents with humans make them a common source of zoonotic infections. To obtain an initial unbiased measure of the viral diversity in the enteric tract of wild rodents we sequenced partially purified, randomly amplified viral RNA and DNA in the feces of 105 wild rodents (mouse, vole, and rat) collected in California and Virginia. We identified in decreasing frequency sequences related to the mammalian viruses families Circoviridae, Picobirnaviridae, Picornaviridae, Astroviridae, Parvoviridae, Papillomaviridae, Adenoviridae, and Coronaviridae. Seventeen small circular DNA genomes containing one or two replicase genes distantly related to the Circoviridae representing several potentially new viral families were characterized. In the Picornaviridae family two new candidate genera as well as a close genetic relative of the human pathogen Aichi virus were characterized. Fragments of the first mouse sapelovirus and picobirnaviruses were identified and the first murine astrovirus genome was characterized. A mouse papillomavirus genome and fragments of a novel adenovirus and adenovirus-associated virus were also sequenced. The next largest fraction of the rodent fecal virome was related to insect viruses of the Densoviridae, Iridoviridae, Polydnaviridae, Dicistroviriade, Bromoviridae, and Virgaviridae families followed by plant virus-related sequences in the Nanoviridae, Geminiviridae, Phycodnaviridae, Secoviridae, Partitiviridae, Tymoviridae, Alphaflexiviridae, and Tombusviridae families reflecting the largely insect and plant rodent diet. Phylogenetic analyses of full and partial viral genomes therefore revealed many previously unreported viral species, genera, and families. The close genetic similarities noted between some rodent and human viruses might reflect past zoonoses. This study increases our understanding of the viral diversity in wild rodents and highlights the large number of still uncharacterized viruses in mammals.
Gray Matter Volume of a Region in the Thalamic Pulvinar Is Specifically Associated with Novelty Seeking

Personality reflects the set of psychological traits and mechanisms characteristic for an individual. Geno-neuro-biologically inspired personality accounts have proposed a set of temperaments and characters that jointly compose personality profiles. The present study addresses the link between neurobiology and personality and investigates the association between temperament traits and regional gray matter volume. Furthermore, the specificity of these associations as well as the underlying components that drive the association are addressed. One hundred and four participants completed the Temperament and Character Inventory (TCI) and underwent structural magnetic resonance brain imaging. The participants included premanifest carriers of Huntington's disease, as this population is associated with temperament-related neuropsychiatric symptoms. Whole brain voxel-based multiple regression analyses on gray matter volume revealed a significant specific positive correlation between a region in the left thalamic pulvinar and novelty seeking score, controlled for the other traits (Pheight < 0.05, FWE-corrected). No significant associations were observed for the other temperament traits. Region of interest analyses showed that this association is driven by the subscale NS2: impulsiveness. The results increase the knowledge of the structural neurobiology of personality and indicate that individual differences in novelty seeking reflect the structural differences observed in the brain in an area that is widely and densely connected, which is in line with the typically domain-general behavioral influence of personality traits on a wide range of affective, perceptual, mnemotic, executive, and other cognitive functions.
New features in the Raman spectrum of Silica: Key-points in the improvement on structure knowledge

This paper reports the evidence of new signatures in the low-frequency Raman spectrum of sili-ca, obtained by very high signal-to-noise experiments. Two new Raman lines are observed at 295 and 380 cm-1, and the presence of a third one at 245 cm-1 is needed to account for the experimental spectra. The origin of these supplementary lines is discussed in terms of n-membered rings of [SiO4/2] tetrahedral entities inside the glassy network.
A Novel Approach to Single Cell RNA‐Sequence Analysis Facilitates In Silico Gene Reporting of Human Pluripotent Stem Cell‐Derived Retinal Cell Types

Cell type‐specific investigations commonly use gene reporters or single‐cell analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while single‐cell RNA (scRNA)‐sequencing (seq) frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA‐seq on optic vesicle (OV)‐like structures cultured under cGMP‐compatible conditions. However, efforts to apply traditional scRNA‐seq analytical methods based on unbiased algorithms were unrevealing. Therefore, we developed a simple, versatile, and universally applicable approach that generates gene expression data akin to those obtained from reporter lines. This method ranks single cells by expression level of a bait gene and searches the transcriptome for genes whose cell‐to‐cell rank order expression most closely matches that of the bait. Moreover, multiple bait genes can be combined to refine datasets. Using this approach, we provide further evidence for the authenticity of hPSC‐derived retinal cell types. Stem Cells 2018;36:313–324
Disruption of Microbial Cells by the Flash Discharge of High-pressure Carbon Dioxide

In order to develop a novel sterilization method for heat-sensitive materials, the disruption of microbial cells by the rapid release of gas pressure was examined under various conditions of pressure, temperature, treatment time and water content of the cells. Wet cells of baker’s yeast were completely destroyed, after the microorganisms had been saturated with CO2 gas at 40°C and 40 atm for more than 3h when the pressure was suddenly discharged. On the other hand, dry cells were poorly killed even under the same experimental conditions. In particular, N2 gas with low solubility in water had no effect on the survival ratio of the yeast. From these results, the death of microorganisms may be caused by mechanical breakage and/or physiological damage related to gas sorption and desorption by the cells.
Animal models of dry eye: a critical assessment of opportunities and limitations.

Dry eye syndrome, or keratoconjunctivitis sicca (KCS), affects tens of millions of people worldwide, representing one of the most common ocular diseases. The National Eye Institute Industry Workshop on Clinical Trials in Dry Eyes produced a classification that essentially separates dry eye syndrome into two major types: tear-deficient forms (including Sjögren’s syndrome and non-Sjögren’s tear-deficient) and evaporative forms. Recently, it has become clear that the immunopathogenesis of dry eye is complex and multifactorial. Sjögren’s syndrome, which is the classic form of exocrine deficiency associated with KCS, is characterized by a chronic inflammatory infiltration of the lacrimal and salivary glands. The predominant cell type is CD4 T cells that appear to have a defect in Fas-mediated apoptosis, thereby rendering their infiltration into exocrine tissue damaging. However, exactly what factors incite the infiltration of glands by T cells remains unknown. Recently, the observation that lacrimal gland acinar cells may express class II major histocompatibility complex (MHC) molecules, cathepsins B and D, and ribonucleoprotein particle La/SSB proteins has provided some support (but no definitive proof) for the thesis that these cells may be involved in aberrant presentation of autoantigens, thereby potentially capable of priming autoreactive T cells. But the pathogenic mechanisms in dry eye are not limited to those involved in lacrimal inflammation. Indeed, interruption of neuronal stimulation for tear secretion, defects in transmembrane and secretory mucin expression, and Meibomian gland dysfunction can all lead to various forms of KCS. Numerous animal models have been developed to reflect the multiplicity of pathophysiologic mechanisms involved in KCS. Understanding the unique characteristics of these different models of dry eye, and their limitations, will provide a better insight into their use in mechanistic and therapeutic study design.
Friction, wear, wear debris and functional biocompatibility of cartilage substitution biomaterials

The friction, wear and biological response to hydrogels, thermoset and thermoplastic polyurethanes were investigated in order to determine their suitability as potential cartilage substitution biomaterials. A single station pin-on-plate friction rig was utilised to determine the friction properties of these materials when articulated against articular cartilage plates and stainless steel plates. These materials were also reciprocated against stainless steel plates with smooth and rough surfaces using a six station multidirectional wear rig to generate clinically relevant sized wear particles which were characterised in terms of particle number and area as a function of size. Aseptically generated wear particles from the thermoset and thermoplastic polyurethanes were generated utilising a single station pin-on-plate wear rig and cultured with peripheral blood mononuclear cells to establish their biological activity by assessing the release of four cytokines (tumour necrosis factor-alpha, interleukin-l~, interleukin-6 and interleukin-8) using an enzyme-linked immunosorbent assay. Friction tests demonstrated that articular cartilage (articulated against itself) exhibited a low coefficient of friction which was concurrent with the literature. The thermoplastic polyurethanes and hydrogels (against articular cartilage) exhibited statistically similar friction characteristics compared to articular cartilage against itself, however, the hydrogels generated considerable wear. In contrast, the friction characteristics of the thermoset polyurethanes were significandy higher than the friction of articular cartilage against itself. When wear particles were generated against stainless steel plates with smooth and rough surfaces, it was clear that the largest percentage number of particles were either < 0.1 or 0.1-1.0 11m in size, however, the percentage area of these particles was more variable and was either in the 0.1-1.0 Ilffi, 1-10 11m or > 10 Ilffi size range. Diprane SOD was the least biologically active material, as cells from two donors out of three were stimulated to release elevated levels of cytokines. Diprane SOD and Corethane 5SD were the only two materials to stimulate cells from donors to significandy release three cytokines out of four. All other materials stimulated an elevated level of all four cytokines from cells from all three donors.
Minimally Invasive Distal Metatarsal Diaphyseal Osteotomy (DMDO) for Chronic Plantar Diabetic Foot Ulcers

Background: The aims of this prospective study were first to evaluate the safety and effectiveness of minimally invasive distal metatarsal diaphyseal osteotomies (DMDOs) for treating a consecutive series of diabetic patients with chronic plantar diabetic foot ulcers (CPDFUs) and second to assess their clinical-functional and radiographic outcomes. Methods: A consecutive series of patients affected by diabetes mellitus with CPDFUs, not responsive to previous nonoperative management, underwent DMDO. The CPDFUs were evaluated using the University of Texas Diabetic Wound Classification System (UTDWC). Demographic parameters, Foot & Ankle Society (AOFAS) scores, visual analog scale (VAS) scores, healing times, and complications were recorded. Maestro et al criteria and bone callus formation were analyzed radiologically. Statistical analysis was carried out (P < .05). Thirty consecutive enrolled patients with a mean age of 66.7 (range, 53-75) years presented 35 CPDFUs with a mean diameter of 16.3 mm and a mean duration of 10.3 months. The most frequent grade of the UTDWC was IIIB (42.9%). Results: All ulcers recovered with a mean healing time of 7.9 ± 4.0 (range, 4-17) weeks. AOFAS scores improved significantly from 55.3 to 81.4 points (P < .001). At a mean follow-up of 25.3 months (range, 18-71), no cases of ulcer recurrence were recorded, while a major complication or a wound infection required longer healing time. Conclusion: Minimally invasive DMDO was a safe and effective method in promoting CPDFU healing, regardless of the grade of severity, by the reduction of the high plantar pressure under the metatarsal heads. This technique improved functional and radiographic outcomes with few complications. Level of Evidence: IV, case series.
Secure Android-based Mobile Banking Scheme

Smartphones and other mobile computing devices are being widely adopted globally [1]. The increasing popularity of smart devices has led users to perform all their day to day activities using these devices [2]. Hence, M-banking has become more convenient, effective and reliable [3]. It is extremely necessary to provide the security services including; confidentiality, integrity, and authentication between the financial institutions‟ servers and the mobile device used by the customer, as their communications are through unsecured networks such as the Internet [4]. Users‟ confidential information may be at risk due to fixed valuesbased security schemes, one level authentication, separate hard token-based authentication, hardware stealing, and Android-Based attacks. This paper specifies a comprehensive sought of how M-banking schemes can be assessed. Also it introduces a solution to mitigate most of these risks.
Throughput Maximization for Mobile Relaying Systems

This paper studies a novel mobile relaying technique, where relays of high mobility are employed to assist the communications from source to destination. By exploiting the predictable channel variations introduced by relay mobility, we study the throughput maximization problem in a mobile relaying system via dynamic rate and power allocations at the source and relay. An optimization problem is formulated for a finite time horizon, subject to an information-causality constraint, which results from the data buffering employed at the relay. It is found that the optimal power allocations across the different time slots follow a "stair-case" water filling (WF) structure, with non-increasing and non- decreasing water levels at the source and relay, respectively. For the special case where the relay moves unidirectionally from source to destination, the optimal power allocations reduce to the conventional WF with constant water levels. Numerical results show that with appropriate trajectory design, mobile relaying is able to achieve tremendous throughput gain over the conventional static relaying.
Human-Debugging of Machines

We have proposed the human-debugging paradigm, where human involvement is leveraged to identify bottlenecks in existing computational AI systems. We introduce this paradigm, and brieﬂy describe two instances of our prior work on using this paradigm for computer vision tasks. We then describe some interesting challenges involved in employing this paradigm in practice
A Frequency-Domain Adaptive Matched Filter for Active Sonar Detection

The most classical detector of active sonar and radar is the matched filter (MF), which is the optimal processor under ideal conditions. Aiming at the problem of active sonar detection, we propose a frequency-domain adaptive matched filter (FDAMF) with the use of a frequency-domain adaptive line enhancer (ALE). The FDAMF is an improved MF. In the simulations in this paper, the signal to noise ratio (SNR) gain of the FDAMF is about 18.6 dB higher than that of the classical MF when the input SNR is −10 dB. In order to improve the performance of the FDAMF with a low input SNR, we propose a pre-processing method, which is called frequency-domain time reversal convolution and interference suppression (TRC-IS). Compared with the classical MF, the FDAMF combined with the TRC-IS method obtains higher SNR gain, a lower detection threshold, and a better receiver operating characteristic (ROC) in the simulations in this paper. The simulation results show that the FDAMF has higher processing gain and better detection performance than the classical MF under ideal conditions. The experimental results indicate that the FDAMF does improve the performance of the MF, and can adapt to actual interference in a way. In addition, the TRC-IS preprocessing method works well in an actual noisy ocean environment.
How Do Shellfisheries Influence Genetic Connectivity in Metapopulations? A Modeling Study Examining the Role of Lower Size Limits in Oyster Fisheries

Fisheries can potentially alter evolutionary processes such as genetic connectivity and lead to genotypic changes in stocks. Using an individual-based metapopulation genetics model, we examined the possible influence of oyster (Crassostrea virginica) fisheries on genetic connectivity. We simulated a range of realistic fishing pressures, with and without a minimum size limit (limit = 63.5 mm), over a range of fishing scenarios including single-area and stock-wide fisheries. Movement of a neutral marker gene provided an indicator of gene transfer between populations. Simulations showed that fishing may alter genetic connectivity. Increasing fishing pressure tended to decrease potential for fished populations to export genes in fisheries with and without size limits. On average, when instantaneous fishing mortality, location, and time period are held constant, fishing unrestricted by size results in a 3.5% lower allele export. Depression of the spawning potential ratio by unrestricted fishing relative to siz.
Towards Player Preference Modeling for Drama Management in Interactive Stories

There is a growing interest in producing story based game experiences that do not follow fixed scripts predefined by the author, but change the experience based on actions performed by the player during his interaction. In order to achieve this objective, previous approaches have employed a drama management component that produces a narratively pleasing arc based on an author specified aesthetic value of a story, ignoring a player’s personal preference for that story path. Furthermore, previous approaches have used a simulated player model to assess their approach, ignoring real human players interacting with the story based game. This paper presents an approach that uses a case based player preference modeling component that predicts an interestingness value for a particular plot point within the story. These interestingness values are based on real human players’ interactions with the story. We also present a drama manager that uses a search process (based on the expectimax algorithm) and combines the author specified aesthetic values with the player model.
Predilation, sizing and post-dilation scoring in patients undergoing everolimus-eluting bioresorbable scaffold implantation for prediction of cardiac adverse events: development and internal validation of the PSP score.

AIMS The aim of the study was to develop a scoring model to evaluate the quality of bioresorbable vascular scaffold (BVS) implantation and determine the model's usefulness in predicting adverse cardiac events. METHODS AND RESULTS The implantation technique and clinical outcomes of 1,736 lesions treated with BVS were analysed using the GHOST-EU registry. Predilation, scaffold sizing, and post-dilation (PSP) were scored according to the hazard model derived from the weight of these variables. The primary endpoint was a one-year device-oriented composite endpoint (DoCE) composed of cardiac death, target vessel myocardial infarction, and clinically driven target lesion revascularisation. Definite/probable scaffold thrombosis was also evaluated as defined by the Academic Research Consortium. The PSP model performance was evaluated by internal validation. Predilation, correct scaffold sizing, and post-dilation with a non-compliant balloon were performed in 95.7%, 50.2%, and 26.2% of the cases and scored 0.63, 1.96 and 1.93 points, respectively, in the PSP-1 model. PSP-1 was an independent predictor of one-year DoCE (HR 0.75, 95% CI: 0.61-0.93; p=0.007), but with poor calibration and discrimination (AUC 0.611, 95% CI: 0.545-0.677). No patient with a maximum PSP-1 score had scaffold thrombosis, compared to those with a non-maximum PSP-1 score (0% vs. 2.3%; p=0.095). CONCLUSIONS At one-year follow-up, the PSP-1 score was an independent predictor of DoCE. External validation and prospective studies are needed to determine the clinical usefulness of this score.