Computer Database Research Articles

Computationally Driven Discovery of T Center-like Quantum Defects in Silicon.

Quantum technologies would benefit from the development of high-performance quantum defects acting as single-photon emitters or spin-photon interfaces. Finding such a quantum defect in silicon is especially appealing in view of its favorable spin bath and high processability. While some color centers in silicon have been emerging in quantum applications, there remains a need to search for and develop new high-performance quantum emitters. By searching a high-throughput computational database of more than 22,000 charged complex defects in silicon, we identify a series of defects formed by a group III element combined with carbon ((A-C)Si with A = B, Al, Ga, In, Tl) and substituting on a silicon site. These defects are analogous structurally, electronically, and chemically to the well-known T center in silicon ((C-C-H)Si), and their optical properties are mainly driven by an unpaired electron on the carbon p orbital. They all emit in the telecom, and some of these color centers show improved properties compared to the T center in terms of computed radiative lifetime, emission efficiency, or smaller optical linewidth. The kinetic barrier computations and previous experimental evidence show that these T center-like defects can be formed through the capture of a diffusing carbon by a substitutional group III atom. We also show that the synthesis of hydrogenated T center-like defects followed by a dehydrogenation annealing step could facilitate the formation of these defects. Our work motivates further studies on the synthesis and control of this new family of quantum defects and demonstrates the use of high-throughput computational screening to discover new color center candidates.

Male factor infertility and implication of fertility treatment in low resource settings

Introduction: The prevalence of infertility has increased worldwide. The etiological factors are also changing in trend and prominence. Male infertility is driving the epidemic in many regions of the world. Therefore, the aim of this study was to explore male factor infertility in the Gambia. Methodology: The design was a longitudinal descriptive study of subfertile couples at a specialist tertiary hospital in Banjul, the Gambia, from August 2022 to May 2023. Data were extracted from patients folders and entered into a computer database. Descriptive statistics were used to analyze the data and results expressed in tables, graphs, and percentages. Results: Total number of subfertile couples analyzed was 152: male factor 69 (45.4%), ovulation disorder 34 (22.4%), tubal factor 20 (13.2%), uterine factor 8 (5.3%), and unexplained 21 (13.8%). The median age of male folk was 50 years, with an age range of 31 to 64 years. The rates of asthenoteratozospermia, oligospermia, and azospermia were 37.8%, 36.2%, and 26%, respectively. In azoospermic males, over 75% had elevated FSH (12–44 miu/mL). Conclusions: The prevalence of male infertility is at 45.4%, which is 3-fold and 2-fold higher than tubal and ovarian factors, respectively. Male infertility is a problem with obvious implications. The predominant types of male infertility we observed in this study will almost always require multidisciplinary care and ICSI.

The prevalence and etiology of infertility in a tertiary specialist hospital in the Gambia

Background: Infertility is a public health problem that has received little or no attention in most sub-Saharan Africa, especially in the Gambia. The prevalence of infertility in the Gambia is increasing from 9.0% in 1998 to 14.3% in 2017. Tubal factor was the predominant leading cause for decades, but recent reviews suggest that male factor is driving the epidermic of infertility worldwide. Therefore, the aim of this study was to determine the prevalence and etiological factors of infertility in our practice. Methodology: The design was a retrospective quantitative study. Data collection tool was developed and variables were retrieved from case notes between August 2022 to March 2023 at a specialist hospital in the Gambia. The data were entered into a computer database and analyzed using descriptive statistics. Results: Total number of women in the reproductive age of 15–49 years that attended gynecology clinic was 1475. Two hundred eighty-five couples (285) had infertility. The prevalence of infertility is 19.3% ~1:5 couples. The causes showed male factor 69 (45.4%), ovulation disorder 34 (22.4%), tubal factor 20 (13.2%), uterine factor 8 (5.3%), and unexplained 21(13.8%). Ovarian factors showed age-related poor ovarian reserve. Overall, male factor infertility was 53%, and female factor infertility was 47%. Conclusions: The prevalence of infertility is increasing and male factor is 3-folds and 2-folds higher than tubal and ovarian factors, respectively. The study observed increasing desire of fertility among female in advanced age. Universal access to assisted reproductive technology is essential.

Stability and Electronic Properties of K‐Sb and Na‐Sb Binary Crystals from High‐Throughput Ab Initio Calculations

AbstractThe study of the fundamental properties of alkali antimonide photocathodes for particle accelerators is currently hindered by the limited purity of the samples. First‐principles studies can effectively complement experiments to gain insight into the stability and the electronic structure of these compounds. In this high‐throughput analysis based on density‐functional theory (DFT), two families of binary crystals with K‐Sb and Na‐Sb compositions expected to form during evaporation of multi‐alkali antimonide photocathodes are investigated. Starting from an initial pool of structures mined from existing computational databases, automatized routines included in the in‐house developed library aim2dat are employed to determine the stability and the electronic properties of the aforementioned systems. By analyzing the formation energy, the structures are ranked in a convex hull retaining the information of their crystalline arrangement. Next, the band structure and the projected density of states of selected stable compounds are analyzed. Adopting the r2SCAN functional for the DFT calculations, reliable estimates of the character and size of the bandgaps are obtained and discussed in relation to the relative alkali content in the crystals. These results provide useful indications to predict and characterize binary phases forming during the growth of multi‐alkali antimonide photocathodes.

[Translated article] Basal Cell Carcinoma: Incidence and Trends in Valencia, Spain

BackgroundThere is a need for epidemiological and incidence data on the occurrence of basal cell carcinoma (BCC) in Spain. ObjectivesOur study was designed to retrospectively retrieve cases from our computer databases from 2010 through 2016 to provide updated data on the actual incidence of BCC in Valencia, eastern Spain. Material and methodsThis was an epidemiological study on basal cell carcinoma conducted in Valencia, eastern Spain. We analyzed a total of 2171 patients and 4047 tumors, and gathered data to estimate the actual incidence of BBC in our region. Results and conclusionsOur study confirmed that the incidence of BCC is much higher than previously reported. We calculated a crude incidence of 410.38 BCCs/100 000 person-years, an adjusted rate for the European population of 256.98 BCCs/100 000 person-years, and an adjusted rate for the world population of 196.26 BCCs/100 000 person-years. Risk is up to 29.49% higher for men (464.07 cases/100 000 person-years vs 358.40 cases/100 000 person-years for women). Incidence also increases by an annual 3.91% (a significantly higher annual incidence of 8.28% in women vs a 0.92% annual incidence in men). Overall, the lifetime risk for developing a BCC is 5.8% (5.02% in women and 7% in men).

Orbital magnetization in two-dimensional materials from high-throughput computational screening

Abstract We calculate the orbital magnetization of 822 two-dimensional magnetic materials from the Computational 2D Materials Database (C2DB). For compounds containing 5$d$ elements we find orbital moments of the order of 0.3--0.5 $\mu_\mathrm{B}$, which points to the necessity of including these in any type of magnetic modeling and comparison with experiments. It is also shown that the alignment of orbital moments with respect to the spin largely follows the predictions from Hund's rule and that deviations may be explained by the $d$-band splitting originating from the crystal field - for example in the important case of CrI$_3$. Finally, we show that for certain insulators, Hubbard corrections may lead to large and fully unquenched orbital moments that are pinned to the lattice rather than the spin and that these moments can lead to enormous magnetic anisotropies. Such unquenched ground states are only found from density functional theory calculations that include both Hubbard corrections and self-consistent spin--orbit coupling and largely invalidates the use of the magnetic force theorem for calculating magnetic anisotropies.

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project.

Analysis of microbial content in 5,734 whole-genome sequencing samples from TCGA yields a comprehensive new resource for investigating the role of microbes in cancer.

Beast DB: A Computational Electrocatalysis Database with Solvation, Grand-Canonical Applied Potential, and Beyond-DFT Reaction Energetics

Electrocatalytic reactions are key to decarbonizing the world economy, but progress in understanding electrocatalytic systems is often hindered by the diversity of conditions under which experiments are run and calculations are performed. This diversity is most often a result of experimental innovation to achieve better electrocatalyst performance, but nonetheless makes it difficult to establish clear baselines for electrocatalytic performance and to understand the fundamental factors that govern changes in performance. In order to make clear comparisons between different electrochemical configurations routine, we have constructed BEAST DB: the Beyond-DFT Electrochemistry with Accelerated and Solvated Techniques database. BEAST DB contains the most promising electrocatalysts for CO2reduction (CO2RR), the oxygen reduction reaction (ORR), the oxygen evolution reaction (OER), the hydrogen evolution reaction (HER), and nitrogen reduction reaction (NRR). For each electrocatalyst and chemistry, we have computed the adsorption energies, 𝛥Gads, and electronic properties for the most relevant catalyst facets and applied potentials. In this talk, we discuss general trends observed from this high-throughput database approach, and examine a few catalysts and chemistries in detail. Additionally, we describe our delta learning approach to learn high-fidelity reaction energetics from less expensive, lower-fidelity DFT calculations and applications of it to electrocatalytic systems. We illustrate how calculations of potential-dependent reaction energetics, as well as observables such as oxidation state and vibrational frequencies, allows for detailed comparisons to experiments such as X-ray absorption spectroscopy (XAS), Surface-enhanced infrared absorption spectroscopy (SEIRAS), and cyclic voltammetry. BEAST DB provides a wealth of information for both computationalists and experimentalists in the field of electrocatalysis, and provides a foundation for exploration of the underlying factors that govern electrocatalytic performance across a wide range of catalysts and chemistries.

Perancangan Aplikasi Pengarsipan Surat Berbais Web pada PT. Perkebunan Nusantara IV Medan

Archiving is the task of storing highly important data. All recorded data must be accurate and accessible whenever needed, enabling employees to provide effective services. Manual archiving of letters often leads to errors in data storage and retrieval. Therefore, there is a need for a web-based letter archiving application system to address these issues. This research employs the waterfall method, where the developed system is web-based using HTML, Xampp, MySQL manages the database, and PHP programming language is utilized with the assistance of Visual Studio Code text editor. The goal of this research is to design an archiving system that can be managed effectively and efficiently. Letter archiving is done electronically, where documents are stored in softcopy form and equipped with incoming and outgoing letter reports. This approach reduces the risk of errors in data storage and letter retrieval, as the data is stored in a computer database.

Magnetic order in the computational 2D materials database (C2DB) from high throughput spin spiral calculations

We report high throughput computational screening for magnetic ground state order in 2D materials. The workflow is based on spin spiral calculations and yields the magnetic order in terms of a two-dimensional ordering vector Q. We then include spin-orbit coupling to extract the easy and hard axes for collinear structures and the orientation of spiral planes in non-collinear structures. Finally, for all predicted ferromagnets we compute the Dzyaloshinskii-Moriya interactions and determine whether or not these are strong enough to overcome the magnetic anisotropy and stabilise a chiral spin spiral ground state. We find 58 ferromagnets, 21 collinear anti-ferromagnets, and 85 non-collinear ground states of which 15 are chiral spin spirals driven by Dzyaloshinskii-Moriya interactions. The results show that non-collinear order is in fact as common as collinear order in these materials and emphasise the need for detailed investigation of the magnetic ground state when reporting magnetic properties of new materials.

Computer Simulation for Effective Pharmaceutical Kinetics and Dynamics: A Review.

Computer-based modelling and simulation are developing as effective tools for supplementing biological data processing and interpretation. It helps to accelerate the creation of dosage forms at a lower cost and with the less human effort required to conduct the work. This paper aims to provide a comprehensive description of the different computer simulation models for various drugs along with their outcomes. The data used are taken from different sources, including review papers from Science Direct, Elsevier, NCBI, and Web of Science from 1995-2020. Keywords like - pharmacokinetic, pharmacodynamics, computer simulation, whole-cell model, and cell simulation, were used for the search process. The use of computer simulation helps speed up the creation of new dosage forms at a lower cost and less human effort required to complete the work. It is also widely used as a technique for researching the structure and dynamics of lipids and proteins found in membranes. It also facilitates both the diagnosis and prevention of illness. Conventional data analysis methods cannot assess and comprehend the huge amount, size, and complexity of data collected by in vitro, in vivo</i>, and ex vivo</i> experiments. As a result, numerous in silico</i> computational e-resources, databases, and simulation software are employed to determine pharmacokinetic (PK) and pharmacodynamic (PD) parameters for illness management. These techniques aid in the provision of multiscale representations of biological processes, beginning with proteins and genes and progressing through cells, isolated tissues and organs, and the whole organism.

The Pathological Pattern of Breast Cancer in the Najran Region of Saudi Arabia: A Retrospective Study.

Background Breast cancer (BC) is the most widespread cancer on a global scale, and its prevalence is likewise significant in the Kingdom of Saudi Arabia. Nevertheless, the data accessible regarding the epidemiology and histopathological characteristics of BC in clinical practice is restricted and primarily confined to research endeavors. Aim This study aims to investigate the histopathological profile of women diagnosed with BC seeking treatment at King Khalid Hospital in the Najran region of the Kingdom of Saudi Arabia. Methods In this retrospective study, BC biopsies performed on Saudi patients at King Khalid Hospital between January 2018 and December 2022 were examined. All records of breast biopsies from this timeframe were extracted from the hospital's histopathology laboratory computer database after written permission from the head of the laboratory department. For all neoplastic lesions, the World Health Organization's 2012 categorization of breast tumors was applied. Results A total of 61 women with BC were included. Women's age ranged from 30 to 89 years, with a mean age of 49.6 ± 12.3 years. The most reported BC was invasive ductal carcinoma (IDC; 70.5%). Other types reported included invasive papillary carcinoma (8.2%), ductal carcinoma in situ (4.9%), and invasive lobular carcinoma (3.3%). A total of 14 (23%) of the study women had multifocal cancer. Ki-67 was high in 19 cases (31.1%); six (9.8%) had BRCA1 mutations, and six (9.8%) had BRCA2 mutations. Conclusion The current study revealed that BC was frequent among young females, mainly IDC, which was reported on both sides at different sizes and grades. Breast lump was the most commonly presented symptom and had a high representation in women with hormonal receptors, mainly estrogen receptors, but positive genetic testing was infrequent.

Bioinformatics tools and resources for cancer and application.

Tumor bioinformatics plays an important role in cancer research and precision medicine. The primary focus of traditional cancer research has been molecular and clinical studies of a number of fundamental pathways and genes. In recent years, driven by breakthroughs in high-throughput technologies, large-scale cancer omics data have accumulated rapidly. How to effectively utilize and share these data is particularly important. To address this crucial task, many computational tools and databases have been developed over the past few years. To help researchers quickly learn and understand the functions of these tools, in this review, we summarize publicly available bioinformatics tools and resources for pan-cancer multi-omics analysis, regulatory analysis of tumorigenesis, tumor treatment and prognosis, immune infiltration analysis, immune repertoire analysis, cancer driver gene and driver mutation analysis, and cancer single-cell analysis, which may further help researchers find more suitable tools for their research.

Rare correlation of somatic PRKACA mutations with pregnancy-associated aldosterone- and cortisol-producing adenomas: a case report and literature review

BackgroundSomatic mutations have been observed to induce aldosterone-producing adenomas (APAs). These may be accelerated during pregnancy. Somatic PRKACA mutations are common in cortisol-producing adenomas (CPAs). However, their role in APAs, particularly aldosterone- and cortisol-producing adenomas (A/CPAs), is not well understood. This study aims to investigate the association between PRKACA mutations and the accelerated development of A/CPAs during pregnancy.Case presentationA patient with primary aldosteronism (PA) associated with severe Cushing’s syndrome (CS) underwent surgical resection of an adrenal tumor one year after delivery. Pathologic examination revealed an adrenocortical adenoma characterized primarily by zona glomerulosa hyperplasia. Somatic mutation analysis revealed the presence of the somatic PRKACA mutation, which was validated as a deleterious mutation by various computational databases. Immunohistochemical results showed positive staining for cytochrome P450 family 11 subfamily B member 1 (CYP11B1), cytochrome P450 family 11 subfamily B member 2 (CYP11B2), and luteinizing hormone/chorionic gonadotropin receptor (LHCGR). Our study included a review of 20 previously documented cases of aldosterone- and cortisol-producing adenomas (A/CPAs), two of which were concurrently positive for both CYP11B1 and CYP11B2, consistent with our findings.ConclusionSomatic mutations in PRKACA may correlate with the upregulation of LHCGR, which synergistically drives the accelerated growth of co-secretion tumors during pregnancy, thereby exacerbating disease progression.

Fast predicting the trajectory of chip-like particles by integrating a discrete element method model with a computational fluid dynamics-based aerodynamic database

The accumulation of ice within aircraft engines poses a significant safety concern, necessitating effective and accessible methods to predict ice particle shedding trajectories. This study develops a novel method by integrating the discrete element method with a computational fluid dynamics (CFD)-based aerodynamic database, aiming to accurately predict the trajectories of chip-like ice particles under various conditions. The accuracy of the CFD-based aerodynamic database is validated through a quantitative comparison with experimental data, and the predicted trajectories align well with the experimental trajectories under varied conditions following a database-independence analysis. The results indicate that aerodynamic coefficients are independent of both the relative velocity and the scaling factor (k) for chip-like particles. Moreover, the initial angle of attack significantly influences the translational and rotational dynamics of chip-like particles. Furthermore, the chip-like ice particles released closer to the engine inlet exhibit a more uniform distribution of landing points, whereas those released at longer distances from the engine inlet tend to converge toward the central area of the engine. The methodology developed in this paper is expected to be a promising tool for fast predicting the trajectories of chip-like particles, thereby enhancing engine protection against ice impacts and improving overall operational safety.

Utilizing indicator functions with computational data to confirm nature of overlap in normal turbulent stresses: Logarithmic or quarter-power

Indicator functions of the streamwise normal-stress profiles (NSP), based on careful differentiation of some of the best direct numerical simulations (DNS) data from channel and pipe flows, over the range 550&amp;lt;Reτ&amp;lt;16 000, are examined to establish the existence and range in wall distances of either a logarithmic-trend segment or a 1/4-power region. For nine out of 15 cases of DNS data we examined where Reτ&amp;lt;2000, the NSP did not contain either of the proposed trends. As Reτ exceeds around 2000 a 1/4-power, reflecting the “bounded-dissipation” predictions of Chen and Sreenivasan [“Law of bounded dissipation and its consequences in turbulent wall flows,” J. Fluid Mech. 933, A20 (2022); “Reynolds number asymptotics of wall-turbulence fluctuations,” J. Fluid Mech. 976, A21 (2023)] and data analysis of Monkewitz [“Reynolds number scaling and inner-outer overlap of stream-wise Reynoldss stress in wall turbulence,” arXiv:2307.00612 (2023)], develops near y+=1000 and expands with Reynolds numbers extending to 1000&amp;lt;y+&amp;lt;10 000 for Reτ around 15 000. This range of 1/4-power NSP corresponds to a range of outer-scaled Y between around 0.3 and 0.7. The computational database examined did not include the zero-pressure-gradient boundary layer experiments at higher Reynolds numbers where the logarithmic trend in the NSP has been previously reported around y+ of 1000 by Marusic et al. [“Attached eddy model of wall turbulence,” Annu. Rev. Fluid Mech. 51, 49–74 (2019); “The logarithmic variance of streamwise velocity and conundrum in wall turbulence,” J. Fluid Mech. 933, A8 (2022)] according to a “wall-scaled eddy model.”

Ab initio property characterisation of thousands of previously unexplored 2D materials

We perform extensive density functional theory calculations to determine the stability and elementary properties of 4249 previously unexplored monolayer crystals. The monolayers comprise the most stable subset (energy within 0.1 eV/atom of the convex hull) of a larger portfolio of two-dimensional (2D) materials recently discovered using a deep generative model and systematic lattice decoration schemes. The relaxed 2D structures are run through the basic property workflow of the Computational 2D Materials Database (C2DB) to evaluate the dynamical stability and obtain the stiffness tensor, piezoelectric tensor, deformation potentials, Born and Bader charges, electronic band structure, effective masses, plasma frequency, Fermi surface, projected density of states, magnetic moments, magnetic exchange couplings, magnetic anisotropy, topological indices, optical- and infrared polarisability. We provide statistical overviews of the property data and highlight a few specific examples of interesting materials. Our work exposes previously unknown parts of the 2D chemical space and provides a basis for the discovery of 2D materials with specific properties. All data is available in the C2DB.

Intimate Partner Violence during pregnancy: Impact on women and children: A Review

Background: Intimate partner violence (IPV) is one of the major causes of anxiety, depression, and post-traumatic stress disorder and can have a negative impact on the mother during pregnancy. This review aims to understand the health consequences of IPV on maternal mental health so that effective interventions and policies can be developed and implemented to provide support to victims, promote gender equality, and prevent adverse maternal outcomes. Methods: A systematic search was conducted as per the PRISMA guidelines. Computer database researches were conducted using the following databases: Google Scholar, Psych INFO, Medline, Scopus, Web of Science, and PubMed. The literature was screened by titles and abstracts and by applying keyword search. The following keywords were searched: women, violence, domestic violence, intimate partner violence, IPV, pregnancy, antenatal, conception, maternal health, child health, mental health, and maternal mental health. The literature search was done from 2014 to 2024. Results: IPV not only poses adverse effects on the well-being of the victim but also disrupts the stability of the environment of the home. It impacts the health, nurturing care, and overall development of the child. Children born to mothers exposed to violence during pregnancy may have lower birth weights and experience higher rates of mortality, preterm births, and lower Apgar scores. The negative effects of IPV on child health also extend beyond the child's cognitive development, impacting the academic performance of their peers. Conclusion: A vast majority of the incidents involving IPV go unreported due to fear, shame, stigma, or lack of awareness. This can affect the accuracy of the actual data of prevalence. In addition, societal norms, gender stereotypes, and male dominance may add to the effects of IPV, making it difficult for the victims to seek help.

Compilation of resources on subcellular localization of lncRNA

Long non-coding RNAs (lncRNAs) play a vital role in biological processes, and their dysfunctions lead to a wide range of diseases. Due to advancements in sequencing technology, more than 20,000 lncRNA transcripts have been identified in humans, almost equivalent to coding transcripts. One crucial aspect in annotating lncRNA function is predicting their subcellular localization, which often determines their functional roles within cells. This review aims to cover the experimental techniques, databases, and in silico tools developed for identifying subcellular localization. Firstly, we discuss the experimental methods employed to determine the subcellular localization of lncRNAs. These techniques provide valuable insights into the precise cellular compartments where lncRNAs reside. Secondly, we explore the available computational resources and databases contributing to our understanding of lncRNAs, including information on their subcellular localization. These computational methods utilize algorithms and machine learning approaches to predict lncRNA subcellular locations using sequence and structural features. Lastly, we discuss the limitations of existing methodologies, future challenges, and potential applications of subcellular localization prediction for lncRNAs. We highlight the need for further advancements in computational methods and experimental validation to enhance the accuracy and reliability of subcellular localization predictions. To support the scientific community, we have developed a platform called LncInfo, which offers comprehensive information on lncRNAs, including their subcellular localization. This platform aims to consolidate and provide accessible resources to researchers studying lncRNAs and their functional roles (http://webs.iiitd.edu.in/raghava/lncinfo).

EFFECTIVENESS OF CORE STABILITY EXERCISES TO IMPROVE THE BALANCE AMONG ELDERLY PEOPLE - A NARRATIVE REVIEW

In this study the literature review focus on the available evidence for physiotherapy intervention to improve the balance among elderly people. Research involved a computerized data base pertaining to studies that include the physiotherapy among elderly people seven articles that showed outcome relative to improve balance, physiotherapy intervention to improve the balance among elderly patient, in among elderly people are at an impaired balance especially when walking, due to age related changes reduce in sensory perception, muscle strength coordination vestibular system and proprioception. In this literature review explained physiotherapy intervention core stability exercises improve balance among elderly people, affect balance leads to difficult of walking and difficult functional activity minimal literatures on improve balance there is scarcity of study which intervention among core stability exercises and Cawthorne Cooksey exercises. AIM – The Study Aimed to Find the Effectiveness of Core Stability Exercises to Improve the Balance Among Elderly People KEY WORDS: Balance, Elderly People, Intervention, Sensory Perception, Proprioception.