Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns of modeling tree structures. Case study: MongoDB database

This work includes the analysis and evaluation of the use of different patterns to store data structures that are conceptually organized as a tree and generally can be populating database tables not normalized relational data or other sources of unstructured data such as spreadsheets, text files and more. The type of storage that has been chosen is a NoSQL database-oriented documents, specifically MongoDB it is an early and popular alternative within its scope. Our analysis considers five patterns: Parent References, Child References, Array of Ancestors, Materialized Paths and Nested Sets. An experiment was designed to measure the performance of the database regarding the speed of insert operations, query and indexing as well as the required storage capacity according to each standard used. The database was deployed in the cloud provider as a service MongoLab. The results of the experiment along with their analysis are presented separately showing two tables and 3 graphs appropriately to contrast the differences and approaches between the yield between different patterns.
Uterine artery flow velocity waveform (FVW) type and subednometrial vascularity in recurrent pregnancy loss

Abstract Purpose: To assess the subendometrial and uterine artery blood flow and pattern of the waveform of the uterine artery in cases of recurrent pregnancy loss compared with normal controls. Subjects and methods: Fifty women with a history of two or more successive pregnancy losses were investigated by Doppler transvaginal ultrasound to assess the subendometrial blood flow resistance index (RI), type of Doppler waveform of the uterine artery, and uterine artery pulsatility index (PI) in the mid-luteal phase. Fifty normal women acted as controls. Results: Subendometrial blood flow RI and uterine artery PI were higher in cases than controls. The majority of cases of recurrent pregnancy loss had a waveform pattern of A, or loss of diastolic flow, whereas the controls were mainly C wave. Conclusions: Some sort of endometrial and subendometrial ischemia can be suggested in cases of recurrent pregnancy loss, waveform pattern of uterine artery changes may be used to monitor changes in vascularity of endometrium if vascular enhancers are given in such cases.
Phylogenetic analysis and genetic structure of the seahorse, Hippocampus fuscus from the Arabian and Red Sea based on mitochondrial DNA sequences

Abstract The unique body morphology and specialized life history traits make seahorses excellent flagship species for many issues in marine conservation and biological evolution. In this study, the complete mitochondrial genome of Hippocampus fuscus was determined. Phylogenetic analyses showed that H. fuscus had a close genetic relationship to Hippocampus reidi, which give us a new insight into the speciation and dispersal among seahorse genus. A total of 843 base pairs of cytochrome b (Cytb) gene and a 646 base pairs of cytochrome oxidase I (COI) gene were obtained from 36 H. fuscus and 26 H. reidi from three populations. Population genetic analysis revealed a relatively high genetic diversity across the populations of H. fuscus compared with H. reidi. Neighbour-joining (NJ) tree of COI and Cytb gene sequences showed that H. fuscus haplotypes formed one cluster. The result of median-joining network of haplotypes based on COI and Cytb indicated a lack of structure in populations of H. fuscus. This study addressed the information about the evolution history and genetic structure of an Arabian seahorse H. fuscus, which provides insight into the genetic conservation and sustainable management for this species.
Similar controls on calcification under ocean acidification across unrelated coral reef taxa

Ocean acidification (OA) is a major threat to marine ecosystems, particularly coral reefs which are heavily reliant on calcareous species. OA decreases seawater pH and calcium carbonate saturation state (Ω), and increases the concentration of dissolved inorganic carbon (DIC). Intense scientific effort has attempted to determine the mechanisms via which ocean acidification (OA) influences calcification, led by early hypotheses that calcium carbonate saturation state (Ω) is the main driver. We grew corals and coralline algae for 8–21 weeks, under treatments where the seawater parameters Ω, pH, and DIC were manipulated to examine their differential effects on calcification rates and calcifying fluid chemistry (Ωcf, pHcf, and DICcf). Here, using long duration experiments, we provide geochemical evidence that differing physiological controls on carbonate chemistry at the site of calcification, rather than seawater Ω, are the main determinants of calcification. We found that changes in seawater pH and DIC rather than Ω had the greatest effects on calcification and calcifying fluid chemistry, though the effects of seawater carbonate chemistry were limited. Our results demonstrate the capacity of organisms from taxa with vastly different calcification mechanisms to regulate their internal chemistry under extreme chemical conditions. These findings provide an explanation for the resistance of some species to OA, while also demonstrating how changes in seawater DIC and pH under OA influence calcification of key coral reef taxa.
Nonalcoholic fatty liver disease burden – Saudi Arabia and United Arab Emirates, 2017–2030

Background/Aim: Due to epidemic levels of obesity and type 2 diabetes mellitus (DM), nonalcoholic fatty liver disease (NAFLD) and resulting nonalcoholic steatohepatitis (NASH) will be driving factors in liver disease burden in the coming years in Saudi Arabia and United Arab Emirates (UAE). Materials and Methods: Models were used to estimate NAFLD and NASH disease progression, primarily based on changes in adult prevalence rates of adult obesity and DM. The published estimates and expert interviews were used to build and validate the model projections. Results: In both countries, the prevalence of NAFLD increased through 2030 parallel to projected increases in the prevalence of obesity and DM. By 2030, there were an estimated 12,534,000 NAFLD cases in Saudi Arabia and 372,000 cases in UAE. Increases in NASH cases were relatively greater than the NAFLD cases due to aging of the population and disease progression. Likewise, prevalent cases of compensated cirrhosis and advanced liver disease are projected to at least double by 2030, while annual incident liver deaths increase in both countries to 4800 deaths in Saudi Arabia and 140 deaths in UAE. Conclusions: Continued high rates of adult obesity and DM, in combination with aging populations, suggest that advanced liver disease and mortality attributable to NAFLD/NASH will increase across both countries. Reducing the growth of the NAFLD population, along with potential therapeutic options, will be needed to reduce liver disease burden.
Development and Application of Computational Methods in Phage Display Technology.

BACKGROUND Phage display is a powerful and versatile technology for the identification of peptide ligands binding to multiple targets, which has been successfully employed in various fields, such as diagnostics and therapeutics, drug-delivery and material science. The integration of next generation sequencing technology with phage display makes this methodology more productive. With the widespread use of this technique and the fast accumulation of phage display data, databases for these data and computational methods have become an indispensable part in this community. This review aims to summarize and discuss recent progress in the development and application of computational methods in the field of phage display. METHODS We undertook a comprehensive search of bioinformatics resources and computational methods for phage display data via Google Scholar and PubMed. The methods and tools were further divided into different categories according to their uses. RESULTS We described seven special or relevant databases for phage display data, which provided an evidence-based source for phage display researchers to clean their biopanning results. These databases can identify and report possible target-unrelated peptides (TUPs), thereby excluding false-positive data from peptides obtained from phage display screening experiments. More than 20 computational methods for analyzing biopanning data were also reviewed. These methods were classified into computational methods for reporting TUPs, for predicting epitopes and for analyzing next generation phage display data. CONCLUSION The current bioinformatics archives, methods and tools reviewed here have benefitted the biopanning community. To develop better or new computational tools, some promising directions are also discussed.
Discovering the CIO from the organizational cognition: A research with RepGrid

The purpose of this article is to identify qualities that define a successful CIO, based on organizational cognition, and contingent on context and organizational maturity. A qualitative approach is used based on the Theory of Personal Constructs and the cognitive mapping tool called Repertory Grid. Three dimensions of qualities were identified, prominent among them the personal and interpersonal type. The study confirms the importance of the understanding of assumptions, values, expectations and individual beliefs in the interpretation and meaning of constructs related to the impact of information technologies in the organization.
Analyzing CO2 concentration changes and their influencing factors in Indonesia by OCO-2 and other multi-sensor remote-sensing data

ABSTRACT We used OCO-2 products and considered three factors that potentially affect CO2 concentration in Indonesia: sea surface temperature (SST), forest fires and vegetation. From 2014 to 2016, CO2 concentration in Indonesia showed a trend of increase, which is consistent with the global increase reported by the Greenhouse Gases Observing Satellite (GOSAT) Project. As an archipelago country, the results indicate that SST has a direct effect on the CO2 concentration in Indonesia. Their changing exhibits similar fluctuations; meanwhile, CO2 concentration and SST also presented positive correlation. In 2015, the number of fire hotspots suddenly increased to 140,699, because of occurrence of the worst forest fire. Due to special geographic conditions, forest fires did not induce CO2 concentration changes in Indonesia, but CO2 concentration in the corresponding islands showed a trend of increase. CO2 concentration increased in Kalimantan during the occurrence of forest fire in September–October 2014, and CO2 concentration increased in Kalimantan and Sumatra during the occurrence of forest fire in September–October 2015. Vegetation indices were stable and presented no correlation with CO2 concentration. This study demonstrated that OCO-2 is capable of monitoring CO2 concentration at a regional scale; additionally, an effective method for using OCO-2 Level 2 products is proposed.
Peri-implant Tissue Health and Bone Resorption in Patients with Immediately Loaded, Implant-Supported, Full-Arch Prostheses.

PURPOSE To evaluate plaque accumulation, peri-implant soft tissue inflammation, and bone resorption in patients with immediately loaded implants supporting fixed full-arch prostheses. MATERIALS AND METHODS A convenience sample of 72 patients treated with fixed full-arch prostheses supported by four to six immediately loaded implants was selected. Bleeding on probing (BOP), Plaque Index (PI), and peri-implant bone loss were measured. The Sixth European Workshop on Periodontology definitions of mucositis and peri-implantitis were used, and collected data were analyzed using a nonparametric test (Spearman's rank correlation). Correlation coefficients (ρ) were defined as follows: < 0.2 = very weak; 0.2 to 0.39 = weak; 0.4 to 0.59 = moderate; 0.6 to 0.79 = strong; 0.8 to 1.0 = very strong. RESULTS A total of 331 implants were analyzed. The mean follow-up observation time was 5.8 years (range: 1 to 14 years); mean PI and BOP were 61.7% and 21.1%, respectively; and mean bone loss was 0.89 mm (standard deviation [SD] 1.09). The mean probing depth was 1.8 mm (range: 0.5 to 5 mm). Five patients presented with one implant each affected by peri-implantitis (6.9%), and 15 patients presented with at least one implant affected by mucositis (20.8%). No correlation was found between PI and bone resorption (P = .08). Very weak correlations were found between BOP and bone resorption (ρ = 0.18; P = .001) and between PI and BOP (ρ = 0.13, P = .019). CONCLUSION The results suggest that plaque accumulation is correlated with peri-implant mucositis; however, plaque accumulation alone does not appear to be associated with bone resorption.
A hybrid technique for annotating book tables

Table extraction is usually complemented with the table annotation to find the hidden semantics in a particular piece of document or a book. These hidden semantics are determined by identifying a type for each column, finding the relationships between the columns, if any, and the entities in each cell. Though used for the small documents and web-pages, these approaches have not been extended to the table extraction and annotation in the book tables. This paper focuses on detecting, locating and annotating entities in book tables. More specifically it contributes algorithms for identifying and locating the tables in books and annotating the table entities by using the online knowledge source DBpedia Spotlight. The missing entities from the DBpedia Spotlight are then annotated using Google Snippets. It was found that the combined results give higher accuracy and superior performance over the use of DBpedia alone. The approach is a complementary one to the existing table annotation approaches as it enables us to discover and annotate entities that are not present in the catalogue. We have tested our scheme on Computer Science books and got promising results in terms of accuracy and performance.
Natural Language Processing for the Long Tail

Natural language processing (NLP) is a research area that stands at the intersection of linguistics and computer science; its focus is the development of automatic methods that can reason about the internal structure of text. This includes part-of-speech tagging (which, for a sentence like John ate the apple , infers that John is a noun
Growth Hormone Deficiency Causing Micropenis: Lessons Learned From a Well-Adjusted Adult

We describe the outcome of a 46,XY patient with a micropenis resulting from GH deficiency consistent with prenatal androgen CNS exposure impact on male gender identity development. This report of a 46,XY patient born with a micropenis consistent with etiology from isolated congenital growth hormone deficiency is used to (1) raise the question regarding what degree testicular testosterone exposure to the central nervous system during fetal life and early infancy has on the development of male gender identity, regardless of gender of rearing; (2) suggest the obligatory nature of timely full disclosure of medical history; (3) emphasize that virtually all 46,XY infants with functional testes and a micropenis should be initially boys except some with partial androgen insensitivity syndrome; and (4) highlight the sustaining value of a positive long-term relationship with a trusted physician (R.M.B.). When this infant presented, it was commonly considered inappropriate to gender assign an infant male whose penis was so small that an adult size was expected to be inadequate, even if the karyotype was 46,XY, and testes were functional. Concomitantly, female gender assignment was considered the appropriate decision, believing that parental rearing in the assigned gender was considered the major factor determining established adult gender identity. Full disclosure of medical information was considered inappropriate. Progress in appreciating the complexities of gender identity development, which is not yet completely understood, and sexuality, coping ability, and outcome data has resulted in a change of practice in initial gender assignment. A 46,XY individual with functional testes and verified androgen responsiveness should be assigned and reared as male, regardless of penis size. Without androgen responsiveness, the multiple factors must be carefully considered and disclosed.
Podocyte injury elicits loss and recovery of cellular forces

ERISM continuously maps dynamic changes in the forces podocytes exert on their substrate in a model of acute kidney damage. In the healthy kidney, specialized cells called podocytes form a sophisticated blood filtration apparatus that allows excretion of wastes and excess fluid from the blood while preventing loss of proteins such as albumin. To operate effectively, this filter is under substantial hydrostatic mechanical pressure. Given their function, it is expected that the ability to apply mechanical force is crucial to the survival of podocytes. However, to date, podocyte mechanobiology remains poorly understood, largely because of a lack of experimental data on the forces involved. We perform quantitative, continuous, nondisruptive, and high-resolution measurements of the forces exerted by differentiated podocytes in real time using a recently introduced functional imaging modality for continuous force mapping. Using an accepted model for podocyte injury, we find that injured podocytes experience near-complete loss of cellular force transmission but that this loss of force is reversible under certain conditions. The observed changes in force correlate with F-actin rearrangement and reduced expression of podocyte-specific proteins. By introducing robust and high-throughput mechanical phenotyping and by demonstrating the significance of mechanical forces in podocyte injury, this research paves the way to a new level of understanding of the kidney. In addition, in an advance over established force mapping techniques, we integrate cellular force measurements with immunofluorescence and perform continuous long-term force measurements of a cell population. Hence, our approach has general applicability to a wide range of biomedical questions involving mechanical forces.
Platform Flexibility Strategies: R&D Investment versus Production Customization Tradeoff

Product platforms are assets that are shared by multiple products. We study the optimal investment in platform flexibility. Each platform type is characterized by its functionality that determines its R&D investment and unit production cost, as well as the customization cost to produce the end products from the platform. The firm can invest in a portfolio of specialized platforms that align with the functionalities of a specific product and flexible platforms that cover the functionalities of a product range at lower customization cost. We characterize the optimal platform portfolio strategy using an ex-ante investment versus ex-post production customization tradeoff curve and show comparative statics of these costs, demand forecast, and the decision maker’s regret and risk attitude. Flexible platforms provide operational hedging for risk-averse decision makers who thus should invest more than risk-neutral counterparts. In contrast to manufacturing flexibility, the regret of sub-optimal investments increases as demand is more negatively correlated.
Authors’ Reply to Comments on ASHAs’ Perceptions on Depression

Another forewarning for future researchers is that the study used the directed content analysis method, which is more structured than conventional content analysis. Hence, the authors would have used the blind coding system in the methodology and that should have directly contributed to more robust and refined consensus in the initial coding of this study with the Directed content analysis. Thus, the authors might have used blinding but eschewed to report it in the article.
An Improved Symmetric H-Bridge Multilevel Converter Topology; An Attempt to Reduce Power Losses

In this paper, a new structure for multilevel converter based on improved H-bridge converter is presented. The proposed topology is a symmetric topology since the values of all voltage sources are equal. The proposed symmetric structure is a general topology which can be extended for any number of voltage levels at output voltage waveform to obtain the least value of total harmonic distortion (THD). Reduction of switching losses, conduction losses, the number of on-state switches in the current path, utilized DC voltage sources, and gate driver circuits are the main advantages of proposed symmetric structures in comparison with other symmetric topologies. All mathematical analysis on the proposed structure is presented in terms of power losses and maximum blocked voltage by switches. The comparison results with other recently presented symmetric topologies and traditional multilevel converter structures are provided. Experimental results for a thirteen-level converter based on presented structure are provided to validate the practicality of the suggested multilevel structure.
Hormonal regulation of spermatogenesis: mutant mice challenging old paradigms

The two pituitary gonadotrophins, luteinizing hormone (LH) and follicle-stimulating hormone (FSH), and in particular LH-stimulated high intratesticular testosterone (ITT) concentration, are considered crucial for spermatogenesis. We have revisited these concepts in genetically modified mice, one being the LH receptor (R)-knockout mouse (LuRKO), the other a transgenic mouse expressing in Sertoli cells a highly constitutively active mutated Fshr (Fshr-CAM). It was found that full spermatogenesis was induced by exogenous testosterone treatment in LuRKO mice at doses that restored ITT concentration to a level corresponding to the normal circulating testosterone level in WT mice, ≈5 nmol/L, which is 1.4% of the normal high ITT concentration. When hypogonadal LuRKO and Fshr-CAM mice were crossed, the double-mutant mice with strong FSH signaling, but minimal testosterone production, showed nearnormal spermatogenesis, even when their residual androgen action was blocked with the strong antiandrogen flutamide. In conclusion, our findings challenge two dogmas of the hormonal regulation of male fertility: (1) high ITT concentration is not necessary for spermatogenesis and (2) strong FSH stimulation can maintain spermatogenesis without testosterone. These findings have clinical relevance for the development of hormonal male contraception and for the treatment of idiopathic oligozoospermia.
Twitter user geolocation by filtering of highly mentioned users

Geolocated social media data provide a powerful source of information about places and regional human behavior. Because only a small amount of social media data have been geolocation‐annotated, inference techniques play a substantial role to increase the volume of annotated data. Conventional research in this area has been based on the text content of posts from a given user or the social network of the user, with some recent crossovers between the text‐ and network‐based approaches. This paper proposes a novel approach to categorize highly‐mentioned users (celebrities) into Local and Global types, and consequently use Local celebrities as location indicators. A label propagation algorithm is then used over the refined social network for geolocation inference. Finally, we propose a hybrid approach by merging a text‐based method as a back‐off strategy into our network‐based approach. Empirical experiments over three standard Twitter benchmark data sets demonstrate that our approach outperforms state‐of‐the‐art user geolocation methods.