Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Geospatial Data Sonification for Mobile Augmented Reality Audio Navigation

This paper presents MeanderMaps: a non-speech Augmented Reality Audio (ARA) application for Apple iPhone that aids in navigation purposes by sonifying geospatial data. Users request directions to a specified location on a Google Map overlay, and MeanderMaps uses spatial auditory cues such as distance and direction to guide him/her to the destination. As the user travels to consecutive waypoints known as path nodes , auditory cues indicate whether an incorrect turn has been made or if the user is traveling in the wrong direction. Preliminary findings are reported using qualitative and quantitative methods, evaluating the overall sonification model in addition to individual audio cues that (a) worked, (b) worked somewhat well, and (c) needed to be improved. Future improvements and modifications to MeanderMaps are presented.
NATURAL LANGUAGE INTERFACE TO DATABASES

: In the world of computing, information plays an important role in our lives. One of the major sources of information is database. Database and Database technology are having major impact on the growing use of computers. Almost all IT applications are storing and retrieving the information or data from the database. Database Management Systems (DBMS) have been widely used for storing and retrieving data. However, databases are often hard to use since their interface is quite rigid in co-operating with users. For storing and retrieving the information from database requires the knowledge of database language like SQL. Structured Query Language (SQL) is an ANSI standard for accessing and manipulating the information stored in database. However, everyone may not be able to write the SQL query as they may not be aware of the syntax and structure of SQL and database respectively. The purpose of Natural Language Interface is to allow users to compose questions in Natural Language and receive the response also in Natural Language. The idea of using Natural Language instead of SQL has promoted the development of new type of processing called Natural Language Interface to Database(NLIDB). This paper discuss about an introduction of Intelligent Database System, Natural Language Processing and Natural Language Interface to Database. It also gives a brief overview of subcomponent of NLIDB, techniques used to development of NLIDB along with its architecture.
A DEK domain-containing protein GhDEK2D mediated Gossypium hirsutum enhanced resistance to Verticillium dahliae

ABSTRACT DEK is associated with DNA replication and break repair, mRNA splicing, and transcriptional regulation, which had been studied in humans and mammals. The function of DEK in plants was poorly understood. In this study, GhDEK2D was identified in Gossypium hirsutum by genome-wide and post-translational modifications. GhDEK2D had been phosphorylated, acetylated and ubiquitylated under Verticillium dahliae (Vd) challenge. The GhDEK2D-silenced cotton decreased resistance against Vd. In GhDEK2D-silenced cotton plants, the reactive oxygen species was activated, the callose, xylogen, hypersensitive reaction (HR) and expression levels of defense-related genes were reduced. Homozygous overexpressing-GhDEK2D transgenic Arabidopsis lines were more resistant to Verticillium wilt (Vw). We propose that GhDEK2D was a potential molecular target for improving resistance to Vw in cotton.
Genetics and Molecular Biology

Pseudocercospora ulei is the causal agent of South American Leaf Blight (SALB), the main disease affecting Hevea brasiliensis rubber tree, a native species to the Amazon. Rubber tree is a major crop in South American countries and SALB disease control strategies would benefit from the availability of genomic resources for the fungal pathogen. Here, we assembled and annotated the P. ulei genome. Shotgun sequencing was performed using second and third generation sequencing technologies. We present the first P. ulei high-quality genome assembly, the largest among Mycosphaerellaceae, with 93.8 Mbp, comprising 215 scaffolds, an N50 of 2.8 Mbp and a BUSCO gene completeness of 97.5%. We identified 12,745 protein-coding gene models in the P. ulei genome with 756 genes encoding secreted proteins and 113 genes encoding effector candidates. Most of the genome (80%) is composed of repetitive elements dominated by retrotransposons of the Gypsy superfamily. P. ulei has the largest genome size among Mycosphaerellaceae, with the highest TE content. In conclusion, we have established essential genomic resources for a wide range of studies on P. ulei and related species.
Geometric morphometric analysis of the humerus in New and Old World vultures

The vulture guild is composed of two distinct groups, Old and New World, which provide a unique insight into how morphology varies among convergent species. All vultures are considered to be large birds of prey that utilize a style of flight called thermal soaring to search and feed primarily on carrion. Even though this flight style is exhibited among all 23 species, slight variations in their skeletal morphology may relate to their differences in ecology. We hypothesized that vulture humeral morphology varies in relation to these organisms' habitat, average body mass, courtship displays, and migratory behavior. To address this hypothesis, we used three‐dimensional geometric morphometrics to measure the overall shape differences of vulture humeri. Humeral morphology was found to vary most by habitat association and migratory tendency. The humeri of vultures that inhabit forested areas exhibit features that suggest increased flapping flight compared to those in open and mountainous regions. Migratory species were found to possess more robust features near the glenohumeral joint. We found these (and other features) have some utility for predicting ecology and behavior, but we suggest that further investigation into skeletal and muscular wing elements may reveal greater understanding of the habits of extinct vulture species.
A Serotonin 2A-Receptor Decoy Peptide Potently Lowers Blood Pressure in Male Zucker Diabetic, Fatty, Hypertensive Rats.

Aims To test whether a novel 5-hydroxytryptamine 2A decoy receptor peptide, SN.8 (Sertuercept), administered via intraperitoneal injection, acutely lowers arterial blood pressure in obese, hypertensive male Zucker diabetic rats (ZDF). To examine the safety, tolerability and possible reno-protective effects following chronic alternate daily administration of Sertuercept (for 10 weeks) in the male ZDF rat. Methods Systolic and diastolic blood pressure were determined at baseline and regular intervals for up to 48 hours after a single IP administration of either Sertuercept (2 mg/kg), vehicle (saline) or an identical concentration of a scrambled sequence of the decoy receptor peptide, LN…8, in male ZDF and Zucker lean rats using tail cuff plethysmography. Plasma autoantibodies were obtained in thirteen male ZDF rats for determination of 5-hydroxytryptamine 2A receptor-mediated neurotoxicity using an acute neurite retraction assay in mouse neuroblastoma cells. Rats were sacrificed at 25-weeks of age, the kidneys were perfused, fixed and sections were stained using Masson's trichrome for semi-quantitative determination of glomerular and interstitial fibrosis. Results Sertuercept (2 mg/kg IP) potently lowered systolic and diastolic blood pressure in both 11-week-old and 25-week-old male ZDF rats and in a subset of hypertensive Zucker lean rats. There was no significant blood pressure-lowering effect of vehicle (saline) or scrambled peptide sequence (LN.8). Blood pressure-lowering was rapid in onset (15-30 minutes following IP injection) and sustained for at least 24 hours. Alternate daily IP administration of 2 mg/kg dose of Sertuercept vs. scrambled peptide (for 10 weeks) was safe, well-tolerated and associated with a significant decrease in glomerulosclerosis in 25-week-old male ZDF rats. Plasma autoantibody-induced neurotoxicity correlated significantly with the global index of renal fibrosis severity in 25-week-old male ZDF rats. Conclusions These data indicate potent arterial blood pressure-lowering efficacy from a decoy receptor peptide comprised of a second extracellular loop region of the human 5-hydroxytryptamine receptor. Chronic administration of the decoy receptor peptide (10 weeks) was safe, well-tolerated and protected against renal glomerulosclerosis in the male ZDF rat.
Effect of probiotics and dietary fiber combined with pinaverium bromide on intestinal flora in patients with irritable bowel syndrome.

OBJECTIVE To evaluate the clinical efficacy of probiotics and dietary fiber combined with pinaverium bromide in the treatment of irritable bowel syndrome (IBS) and its effect on intestinal flora. METHODS As a prospective study, 180 patients with IBS hospitalized in the gastroenterology department of our hospital from January 2018 to January 2021 were selected and assigned to Group A, Group B, or Group C using the random number table method, with 60 cases in each group. Patients in Group A received conventional treatment with pinaverium bromide tablets. Those in Group B were given bifid triple viable combined with pinaverium bromide, and those in Group C were given bifid triple viable and dietary fiber combined with pinaverium bromide. The treatment spanned 4 weeks. The treatment efficacy, degree of symptom improvement, quality of life, adverse effects, and changes in intestinal flora were compared among the three groups. RESULTS The total treatment efficacy was significantly higher in Group C compared with Group A (χ2=8.711, P=0.003), while it differed insignificantly between Group A and Group B (P>0.05). Groups B and C had a shorter resolution time of abdominal pain, diarrhea, and abdominal distension than Group A (P<0.05). Compared with Group B, Group C experienced a markedly shorter resolution time of abdominal pain (P<0.05). The IBS symptom severity scale (IBS-SSS) and IBS-quality of life (IBS-QOL) scores were the lowest in Group C, followed by Group B, and then Group A (P<0.05). Group A had a significantly higher E. coli count and lower Bifidobacterium and Lactobacillus counts than Groups B and C (P<0.05). Adverse reactions were all within the tolerable range in the three groups, with no difference (P>0.05). CONCLUSION In patients with IBS, treatment with probiotics and dietary fiber combined with pinaverium bromide can significantly improve clinical efficacy, shorten symptom resolution time, reduce calprotectin, and regulate intestinal flora.
Differential Afa/Dr Fimbriae Expression in the Multidrug-Resistant Escherichia coli ST131 Clone

E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. ABSTRACT Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor. We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.
Bacterial Vaginosis: What Do We Currently Know?

The vaginal microbiome is a well-defined compartment of the human microbiome. It has unique conditions, characterized by the dominance of one bacterial species, the Lactobacilli. This microbiota manifests itself by a low degree of diversity and by a strong dynamic of change in its composition under the influence of various exogenous and endogenous factors. The increase in diversity may paradoxically be associated with dysbiosis, such as bacterial vaginosis (BV). BV is the result of a disturbance in the vaginal ecosystem; i.e., a sudden replacement of Lactobacilli by anaerobic bacteria such as Gardnerella vaginalis, Atopobium vaginae, Ureaplasma urealyticum, Mycoplasma hominis, and others. It is the most common cause of vaginal discharge in women of childbearing age, approximately 30% of all causes. The etiology of this dysbiosis remains unknown, but its health consequences are significant, including obstetrical complications, increased risk of sexually transmitted infections and urogenital infections. Its diagnosis is based on Amsel’s clinical criteria and/or a gram stain based on the Nugent score. While both of these methods have been widely applied worldwide for approximately three decades, Nugent score are still considered the “gold standard” of BV diagnostic tools. Given the limitations of these tools, methods based on molecular biology have been developed as alternative rational strategies for the diagnosis of BV. The treatment of BV aims at restoring the balance of the vaginal flora to stop the proliferation of harmful microorganisms. Prescription of antibiotics such as metronidazole, clindamycin, etc. is recommended. Faced with the considerable uncertainty about the cause of BV, the high rate of recurrence, the unacceptable treatment options, and clinical management which is often insensitive and inconsistent, research on this topic is intensifying. Knowledge of its composition and its associated variations represents the key element in improving the therapeutic management of patients with the most suitable treatments possible.
Evolution of Somite Compartmentalization: A View From Xenopus

Somites are transitory metameric structures at the basis of the axial organization of vertebrate musculoskeletal system. During evolution, somites appear in the chordate phylum and compartmentalize mainly into the dermomyotome, the myotome, and the sclerotome in vertebrates. In this review, we summarized the existing literature about somite compartmentalization in Xenopus and compared it with other anamniote and amniote vertebrates. We also present and discuss a model that describes the evolutionary history of somite compartmentalization from ancestral chordates to amniote vertebrates. We propose that the ancestral organization of chordate somite, subdivided into a lateral compartment of multipotent somitic cells (MSCs) and a medial primitive myotome, evolves through two major transitions. From ancestral chordates to vertebrates, the cell potency of MSCs may have evolved and gave rise to all new vertebrate compartments, i.e., the dermomyome, its hypaxial region, and the sclerotome. From anamniote to amniote vertebrates, the lateral MSC territory may expand to the whole somite at the expense of primitive myotome and may probably facilitate sclerotome formation. We propose that successive modifications of the cell potency of some type of embryonic progenitors could be one of major processes of the vertebrate evolution.
Imaging Approaches for the Study of Metabolism in Real Time Using Genetically Encoded Reporters

Metabolism comprises of two axes in order to serve homeostasis: anabolism and catabolism. Both axes are interbranched with the so-called bioenergetics aspect of metabolism. There is a plethora of analytical biochemical methods to monitor metabolites and reactions in lysates, yet there is a rising need to monitor, quantify and elucidate in real time the spatiotemporal orchestration of complex biochemical reactions in living systems and furthermore to analyze the metabolic effect of chemical compounds that are destined for the clinic. The ongoing technological burst in the field of imaging creates opportunities to establish new tools that will allow investigators to monitor dynamics of biochemical reactions and kinetics of metabolites at a resolution that ranges from subcellular organelle to whole system for some key metabolites. This article provides a mini review of available toolkits to achieve this goal but also presents a perspective on the open space that can be exploited to develop novel methodologies that will merge classic biochemistry of metabolism with advanced imaging. In other words, a perspective of “watching metabolism in real time. ”
Cationic Polymer Brush-Modified Carbon Nanotube-Meditated eRNA LINC02569 Silencing Attenuates Nucleus Pulposus Degeneration by Blocking NF-κB Signaling Pathway and Alleviate Cell Senescence

Enhancer RNAs (eRNAs) are noncoding RNAs that synthesized at active enhancers. eRNAs have important regulatory characteristics and appear to be significant for maintenance of cell identity and information processing. Series of functional eRNAs have been identified as potential therapeutic targets for multiple diseases. Nevertheless, the role of eRNAs on intervertebral disc degeneration (IDD) is still unknown yet. Herein, we utilized the nucleus pulposus samples of patients and identified a key eRNA (LINC02569) with the Arraystar eRNA Microarray. LINC02569 mostly locates in nucleus and plays an important role in the progress of IDD by activating nuclear factor kappa-B (NF-κB) signaling pathway. We used a cationic polymer brush coated carbon nanotube (oCNT-pb)-based siRNA delivery platform that we previously designed, to transport LINC02569 siRNA (si-02569) to nucleus pulposus cells. The siRNA loaded oCNT-pb accumulated in nucleus pulposus cells with lower toxicity and higher transfection efficiency, compared with the traditional siRNA delivery system. Moreover, the results showed that the delivery of si-02569 significantly alleviated the inflammatory response in the nucleus pulposus cells via inhibiting P65 phosphorylation and preventing its transfer into the nucleus, and meanwhile alleviated cell senescence by decreasing the expression of P21. Altogether, our results highlight that eRNA (LINC02569) plays important role in the progression of IDD and could be a potential therapeutic target for alleviation of IDD.
sgRNA Knock-in Mouse Provides an Alternative Approach for In Vivo Genetic Modification

Functional genomics in a mammalian model such as mice is fundamental for understanding human biology. The CRISPR/Cas9 system dramatically changed the tempo of obtaining genetic mouse models due to high efficiency. However, experimental evidence for the establishment of sgRNA knock-in animals and analyses of their value in functional genomics are still not sufficient, particularly in mammalian models. In this study, we demonstrate that the establishment of sgRNA knock-in mice is feasible, and more importantly, crosses between sgRNA knock-in mice and the Cas9 constitutively expressing mice result in complete deletion of the target gene. Such sgRNA knock-in provides an alternative approach for in vivo genetic modification and can be useful in multiple circumstances, such as maintenance of genetically modified animals, which are difficult to breed as homozygotes, and cross of such mice to diverse genomic backgrounds to obtain genetically modified animals.
Son or Daughter Care in Relation to Self-Reported Health Outcomes for Older Adults in China

Objectives Parental care in China is traditionally provided by sons. In recent decades—partly due to the One-Child Policy but also economic development and urbanization—significant changes have occurred with more and more parents receiving care from daughters. We investigate the disparities in outcomes of eldercare provided by son(s) and daughter(s). Methods Our study compares the self-reported health (SRH) status of parents who receive eldercare from daughters and sons in China, analyzing the harmonized 2013, 2015, and 2018 waves of CHARLS with random-effects logistic estimates. Results Our results show that the SRH status of parents who receive care from their sons is greater than those cared for by their daughters. This disparity is greater in rural areas, for mothers, and poorer families. Discussion The One-Child Policy was more effective in urban areas, reducing both the availability of sons and cultural son preference. Higher levels of education received by girls in urban settings increases their employability and thus their ability to materially care for their parents. However, traditional norms and gender differences in social economic statuses still persist in rural areas, leading to higher SRH status of those cared for by sons, especially amongst those who are heavily dependent on their children: mothers or parents with less wealth.
Distinct Features of Cerebral Blood Flow and Spontaneous Neural Activity as Integrated Predictors of Early Response to Antidepressants

Aims The purpose of this study is to explore whether pre-treatment features of brain function can discriminate non-responders to antidepressant medication in the early phase. Methods Forty-four treatment-responsive depressed (RD) patients, 36 non-responsive depressed (NRD) patients, and 42 healthy controls (HCs) were recruited. Regional cerebral blood flow (CBF) and amplitude of low-frequency fluctuation (ALFF) values were calculated for all subjects. Correlation analyses were used to explore the relationship between symptom improvement and CBF/ALFF. Receiver operating characteristics (ROC) and the 10-fold cross-validation support vector machine (SVM) classifier were applied for the discrimination of treatment response. Results Compared with the HCs, the RD and NRD groups exhibited lower CBF and ALFF in the right posterior lobe of the cerebellum. Compared with the NRD group, the RD group showed distinct CBF patterns in the left frontal striatal regions and right frontal cerebellar regions, as well as distinct ALFF features in the left frontoparietal striatum and right frontotemporal striatal cerebellar regions. The ROC and SVM classifier revealed the optimal power to distinguish the RD and NRD groups based on the combined measures (i.e., CBF and ALFF). Conclusion Distinct features of CBF and ALFF in the frontal striatal network may serve as promising neuroimaging predictors for identifying patients with blunted responsiveness, which may facilitate personalized antidepressant treatment.