Miracle-dz/UniFAR-FTUs huggingface dataset:
Methane Leakage From Hydrocarbon Wellbores into Overlying Groundwater: Numerical Investigation of the Multiphase Flow Processes Governing Migration

Methane leakage due to compromised hydrocarbon well integrity can lead to impaired groundwater quality. Here we use a three‐dimensional, multiphase (vapor and aqueous), multicomponent (methane, water, salt), numerical model (TOUGH2 EOS7C) to investigate hydrogeological conditions that could result in groundwater contamination from natural gas wellbore leakage that migrates upward toward a freshwater aquifer. The conceptual model used for the simulations assumes methane leakage at 20–30 m below groundwater. We perform 180 simulations for a sensitivity analysis, examining (1) multiphase flow parameters related to storage, capillarity, and relative permeability, including porosity (ϕ), initial fluid‐phase saturation (SL), and van Genuchten n and α, (2) geostatistical variations in intrinsic permeability (ki), and (3) methane source‐zone pressure. Simulated mean ki values are 10−18 and 10−13 m2 with variances of 1 and 5 m4. Simulated source‐zone pressures range from just over ambient hydrostatic pressure at the depth of leakage (100 kPa) to the maximum pressure that steel casings are commonly rated to withstand (20,340 kPa). ki, initial SL, ϕ, and van Genuchten's n and α were the most important parameters in determining the volume of methane reaching groundwater during a given time period. Multiphase parameterization of formations underlying freshwater aquifers and overlying hydrocarbon production zones is fundamental to assessing aquifer vulnerability to methane leakage.
Transfollicular drug delivery: current perspectives

The pilosebaceous unit is the collective form of a hair follicle, hair shaft, and sebaceous gland. Within the skin, this three-dimensional composite shows a distinctive biochemistry, metabolism, and immunology. Presently, most researchers in this area are focused on the hair follicles, as they see these as a potential pathway for both localized and systemic delivery of various chemotherapeutics. Better understanding of the configuration of the hair follicle is mulled over in order to design rational drug formulations to achieve targeted follicular delivery. Targeted drug delivery may enhance the efficacy of current therapeutics to treat diseases of follicular origin. The present review covers follicular drug delivery with the potential to target the pilosebaceous unit.
Transcriptional control and exploitation of an immune‐responsive family of plant retrotransposons

Mobilization of transposable elements (TEs) in plants has been recognized as a driving force of evolution and adaptation, in particular by providing genes with regulatory modules that impact their transcription. In this study, we employed an ATCOPIA93 long‐terminal repeat (LTR) promoter‐GUS fusion to show that this retrotransposon behaves like an immune‐responsive gene during pathogen defense in Arabidopsis. We also showed that the endogenous ATCOPIA93 copy “EVD”, which is activated in the presence of bacterial stress, is negatively regulated by both DNA methylation and polycomb‐mediated silencing, a mode of repression typically found at protein‐coding and microRNA genes. Interestingly, an ATCOPIA93‐derived soloLTR is located upstream of the disease resistance gene RPP4 and is devoid of DNA methylation and H3K27m3 marks. Through loss‐of‐function experiments, we demonstrate that this soloLTR is required for the proper expression of RPP4 during plant defense, thus linking the responsiveness of ATCOPIA93 to biotic stress and the co‐option of its LTR for plant immunity.
K63-linked polyubiquitin chains bind to DNA to facilitate DNA damage repair

Mutations in the DNA-interacting patch of ubiquitin sensitize cells to DNA-damaging agents. DNA-bound ubiquitin coordinates DNA repair Ubiquitylation is a posttranslational modification that reversibly alters protein stability, activity, interactions, or trafficking. The ubiquitylation of histones and various other proteins facilitates the response to DNA damage. However, Liu et al. discovered that ubiquitin also binds directly to DNA. In solution and in live cells, chains of ubiquitin specifically linked through Lys63 residues (referred to as K63-linked polyubiquitin chains) preferentially bound to the free ends of double-stranded DNA through a three-amino acid motif in ubiquitin that the authors call a “DNA-interacting patch” (DIP). These chains appeared to bind the broken ends of DNA and recruit repair proteins. Ubiquitins with mutations in the DIP were found in several types of tumors and, when expressed in cultured cells, impaired the cellular response to DNA-damaging agents, suggesting that these mutations might be exploited for therapeutic benefit in some cancer patients. Polyubiquitylation is canonically viewed as a posttranslational modification that governs protein stability or protein-protein interactions, in which distinct polyubiquitin linkages ultimately determine the fate of modified protein(s). We explored whether polyubiquitin chains have any nonprotein-related function. Using in vitro pull-down assays with synthetic materials, we found that polyubiquitin chains with the Lys63 (K63) linkage bound to DNA through a motif we called the “DNA-interacting patch” (DIP), which is composed of the adjacent residues Thr9, Lys11, and Glu34. Upon DNA damage, the binding of K63-linked polyubiquitin chains to DNA enhanced the recruitment of repair factors through their interaction with an Ile44 patch in ubiquitin to facilitate DNA repair. Furthermore, experimental or cancer patient–derived mutations within the DIP impaired the DNA binding capacity of ubiquitin and subsequently attenuated K63-linked polyubiquitin chain accumulation at sites of DNA damage, thereby resulting in defective DNA repair and increased cellular sensitivity to DNA-damaging agents. Our results therefore highlight a critical physiological role for K63-linked polyubiquitin chains in binding to DNA to facilitate DNA damage repair.
Using GConf as an Example of How to Create an Userspace Object Manager

GConf is a configuration system for GNOME. It does not provide adequate security controls over the configuration data that it manages, which could allow the security goals of the system to be violated. There are various strategies that can be used to provide security controls over an application under SELinux. One strategy, which is a natural part of implementing the Flask architecture on Linux, is to turn the program into a userspace object manager. This paper discusses the general process of providing SELinux controls over a program and the specific steps taken to provide SELinux controls over GConf.
EUS-FNA versus ERCP for tissue diagnosis of suspect malignant biliary strictures: a prospective comparative study

Abstract Background and study aims Biliary strictures are frequently a challenging clinical scenario and the anatomopathological diagnosis is essential in the therapeutic management, whether for curative or palliative purposes. The acquisition of specimens is necessary since many benign diseases mimic biliopancreatic neoplasms. Endscopic retrograde cholangiopancreatography (ERCP) is the traditionally used method despite the low sensitivity of biliary brush cytology and forceps biopsy. On the other hand, several studies reported good accuracy rates using endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA). The aim of this prospective study was to compare, the accuracy of EUS-FNA and ERCP for tissue sampling of biliary strictures. Patients and methods After performing the sample size calculation, 50 consecutive patients with indeterminate biliary strictures were included to undergo ERCP and EUS on the same sedation.The gold-standard was surgery or 6 months’ follow-up. Evaluation of the diagnostic indices (sensitivity, specificity, positive and negative predictive value, positive and negative likelihood ratio), concordance and adverse events among the methods were performed. Also, subtype analyses of the techniques, anatomical localization and size of the lesion were included. Results The final diagnoses reported in 50 patients were 47 malignant, 1 suspicious and 2 benign lesions. 31 lesions were extraductal and 19 intraductal, 35 were distal and 15 proximal strictures. In the intention-to-treat analysis, the sensitivity and accuracy of EUS-FNA were superior than ERCP tissue sampling (93,8 %, 94 % vs. 60,4 %, 62 %, respectively) (P = 0.034), with similar adverse events. There was no concordance between the methods and combining both methods improved the sensitivity and accuracy for 97.9 % and 98 %, respectively. In the subtype analyses, the EUS-FNA was superior, with a higher accuracy than ERCP tissue sampling in evaluating extraductal lesions (100 % vs. 54.8 %, P = 0.019) and in those larger than 1.5 cm (95.8 % vs. 61.9 %, P = 0.031), but were similar in evaluating intraductal lesions and lesions smaller than 1.5 cm. There was no significant difference between the methods in the analyzes of proximal, distal and pancreatic lesions. Conclusion EUS-FNA is better than ERCP with brush cytology and intraductal forceps biopsy in diagnosing malignant biliary strictures, mainly in the assessment of extraductal lesions and in those larger than 1.5 cm. Combining ERCP with tissue sampling and EUS-FNA is feasible, the techniques have similar complication rates, and the combination greatly improves diagnostic accuracy.
Kalman filtering for segment detection: application to music scores analysis

Many symbols in music scores are linear segments. In this context, we designed an extractor of segments. It is robust towards problems of quality within binary images (scale factor, curvature, bias and noises). It is based on Kalman filtering technique. By splitting music scores into layers of detectable symbols and by applying methodically to the defined layers both this extractor and simple rules of classification for the detected segments, we were able to recognize staves, stems, slurs, beams, bar lines, black note heads and then quarters and note groups.
Attention Effects on Neural Population Representations for Shape and Location Are Stronger in the Ventral than Dorsal Stream

Abstract We examined how attention causes neural population representations of shape and location to change in ventral stream (AIT) and dorsal stream (LIP). Monkeys performed two identical delayed-match-to-sample (DMTS) tasks, attending either to shape or location. In AIT, shapes were more discriminable when directing attention to shape rather than location, measured by an increase in mean distance between population response vectors. In LIP, attending to location rather than shape did not increase the discriminability of different stimulus locations. Even when factoring out the change in mean vector response distance, multidimensional scaling (MDS) still showed a significant task difference in AIT, but not LIP, indicating that beyond increasing discriminability, attention also causes a nonlinear warping of representation space in AIT. Despite single-cell attentional modulations in both areas, our data show that attentional modulations of population representations are weaker in LIP, likely due to a need to maintain veridical representations for visuomotor control.
Job Seekers' Acceptance of Job Recommender Systems: Results of an Empirical Study

Based on UTAUT2 and the importance of trust to explain user behavior in relation to recommender systems, we focus on job recommender systems by developing and validating a job recommender system acceptance model. The results of our empirical, survey-based study with 440 job seekers indicate that beside performance expectancy and habit, trust is among the three most important determinants and it is especially relevant for women, passive job seekers and those without experience in using job recommender systems. The paper extends general trust and recommender system research by revealing three moderators for the trust and intention relationship. It contextualizes the UTAUT2 by incorporating trust as an antecedent of a consumer’s intention to use and by revealing three moderating effects for this relationship. Hence, it is the basis for further studies investigating the acceptance of job recommender system, which has rather been neglected by prior research.
Boosting Black Box Variational Inference

Approximating a probability density in a tractable manner is a central task in Bayesian statistics. Variational Inference (VI) is a popular technique that achieves tractability by choosing a relatively simple variational approximation. Borrowing ideas from the classic boosting framework, recent approaches attempt to \emph{boost} VI by replacing the selection of a single density with an iteratively constructed mixture of densities. In order to guarantee convergence, previous works impose stringent assumptions that require significant effort for practitioners. Specifically, they require a custom implementation of the greedy step (called the LMO) for every probabilistic model with respect to an unnatural variational family of truncated distributions. Our work fixes these issues with novel theoretical and algorithmic insights. On the theoretical side, we show that boosting VI satisfies a relaxed smoothness assumption which is sufficient for the convergence of the functional Frank-Wolfe (FW) algorithm. Furthermore, we rephrase the LMO problem and propose to maximize the Residual ELBO (RELBO) which replaces the standard ELBO optimization in VI. These theoretical enhancements allow for black box implementation of the boosting subroutine. Finally, we present a stopping criterion drawn from the duality gap in the classic FW analyses and exhaustive experiments to illustrate the usefulness of our theoretical and algorithmic contributions.
Age and area predict patterns of species richness in pumice rafts contingent on oceanic climatic zone encountered

Abstract The theory of island biogeography predicts that area and age explain species richness patterns (or alpha diversity) in insular habitats. Using a unique natural phenomenon, pumice rafting, we measured the influence of area, age, and oceanic climate on patterns of species richness. Pumice rafts are formed simultaneously when submarine volcanoes erupt, the pumice clasts breakup irregularly, forming irregularly shaped pumice stones which while floating through the ocean are colonized by marine biota. We analyze two eruption events and more than 5,000 pumice clasts collected from 29 sites and three climatic zones. Overall, the older and larger pumice clasts held more species. Pumice clasts arriving in tropical and subtropical climates showed this same trend, where in temperate locations species richness (alpha diversity) increased with area but decreased with age. Beta diversity analysis of the communities forming on pumice clasts that arrived in different climatic zones showed that tropical and subtropical clasts transported similar communities, while species composition on temperate clasts differed significantly from both tropical and subtropical arrivals. Using these thousands of insular habitats, we find strong evidence that area and age but also climatic conditions predict the fundamental dynamics of species richness colonizing pumice clasts.
Nasal colonisation, antimicrobial susceptibility and genotypic pattern of Staphylococcus aureus among agricultural biotechnology students in Besut, Terengganu, east coast of Malaysia

This study aimed to profile the antimicrobial susceptibility and presence of resistance and virulence genes of methicillin‐susceptible Staphylococcus aureus (MSSA) and MRSA nasal carriage, by means of genotypic analyses, in students of a tertiary institution in the state of Terengganu, east coast of Malaysia.
Linguistic Validation and Cultural Adaptation of Bulgarian Version of Hospital Survey on Patient Safety Culture (HSOPSC)

BACKGROUND: Patient safety (PS) is one of the essential elements of health care quality and a priority of healthcare systems in most countries. Thus the creation of validated instruments and the implementation of systems that measure patient safety are considered to be of great importance worldwide. AIM: The present paper aims to illustrate the process of linguistic validation, cross-cultural verification and adaptation of the Bulgarian version of the Hospital Survey on Patient Safety Culture (B-HSOPSC) and its test-retest reliability. METHODS: The study design is cross-sectional. The HSOPSC questionnaire consists of 42 questions, grouped in 12 different subscales that measure patient safety culture. Internal consistency was assessed using Cronbach’s alpha. The Wilcoxon signed-rank test and the split-half method were used; the Spearman-Brown coefficient was calculated. RESULTS: The overall Cronbach’s alpha for B-HSOPSC is 0.918. Subscales 7 Staffing and 12 Overall perceptions of safety had the lowest coefficients. The high reliability of the instrument was confirmed by the Split-half method (0.97) and ICC-coefficient (0.95). The lowest values of Spearmen-Broun coefficients were found in items A13 and A14. CONCLUSION: The study offers an analysis of the results of the linguistic validation of the B-HSOPSC and its test-retest reliability. The psychometric characteristics of the questions revealed good validity and reliability, except two questions. In the future, the instrument will be administered to the target population in the main study so that the psychometric properties of the instrument can be verified.
Focal Visual-Text Attention for Visual Question Answering

Recent insights on language and vision with neural networks have been successfully applied to simple single-image visual question answering. However, to tackle real-life question answering problems on multimedia collections such as personal photos, we have to look at whole collections with sequences of photos or videos. When answering questions from a large collection, a natural problem is to identify snippets to support the answer. In this paper, we describe a novel neural network called Focal Visual-Text Attention network (FVTA) for collective reasoning in visual question answering, where both visual and text sequence information such as images and text metadata are presented. FVTA introduces an end-to-end approach that makes use of a hierarchical process to dynamically determine what media and what time to focus on in the sequential data to answer the question. FVTA can not only answer the questions well but also provides the justifications which the system results are based upon to get the answers. FVTA achieves state-of-the-art performance on the MemexQA dataset and competitive results on the MovieQA dataset.
Creatine kinase, neuromuscular fatigue, and the contact codes of football: A systematic review and meta-analysis of pre- and post-match differences

Abstract Physiological or performance tests are routinely utilised to assess athletes’ recovery. At present, the ideal tool to assess recovery remains unknown. Therefore, the aim of this systematic review was to examine the change in creatine kinase (CK) and neuromuscular function as measured via a countermovement jump (CMJ) following a match in the contact codes of football. A comprehensive search of databases was undertaken with RevMan (V 5.3) used for statistical analysis. Our results demonstrated that CK pre- versus post-match (standardised mean difference (SMD) = 0.90, 95% CI = 0.50 to 1.31, p < . 0001), CK pre- versus 24 h post-match (SMD = 1.50, 95% CI = 1.12 to 1.88, p < .00001), and CK pre- versus 48 h post-match all increased significantly (SMD = 0.90, 95% CI = 0.50 to 1.31, p < .0001), while CMJ peak power (PP) pre- versus post-match (SMD = −0.59, 95% CI = −1.12 to −0.06, p = .03), and pre- versus 24 h post-match (SMD = −0.80, 95% CI = −1.31 to −0.28, p = .002) decreased significantly. There was a significant relationship between the change in CK and the change in CMJ PP from immediately pre to immediately post (r = −0.924, p = .025), and between CMJ immediately following a match and 24 h CK change (r = −0.983, p = .017). In conclusion, CK levels increase and performance in the CMJ decreases following a match of a contact code of football. The identification of this relationship may allow coaching staff to implement a standalone measure of recovery.
Says Who?: How News Presentation Format Influences Perceived Believability and the Engagement Level of Social Media Users

We investigate whether the news presentation format affects the believability of a news story and the engagement level of social media users. Specifically, we test to see if highlighting the source delivering the story can nudge the users to think more critically about the truthfulness of the story that they see, and for obscure sources, whether source ratings can affect how the users evaluate the truthfulness. We also test whether the believability can influence the users’ engagement level for the presented news post (e.g., read, like, comment, and share). We find that such changes in the news presentation format indeed have significant impacts on how social media users perceive and act on news items.
Role of religion, spirituality, and faith in assisted reproduction

Abstract Purpose: The purpose of this study is to evaluate the impact of the patient’s faith, religion, and spirituality on the outcomes of intracytoplasmic sperm injection (ICSI) cycles. Materials and methods: Eight hundred and seventy-seven patients received a questionnaire containing information on faith, religiosity, and spirituality and the results of the questionnaires were correlated with ICSI outcomes. Patients stated to be Catholic (n = 476), spiritists (n = 93), Evangelical (n = 118), and other religion (n = 32), and 78 did not identify with any religious group. Results: A significant increase in fertilization, high-quality embryos, and pregnancy rate was found among Spiritists and Evangelicals. Patients who included the infertility diagnosis and treatment in their prayers showed an increased pregnancy rate, and those who reported their faith to be affected by the infertility diagnosis presented a decreased high-quality embryos rate. The high-quality embryos rate was increased among patients who answered that their faith contributed to their decision to undergo infertility treatment. The cycle’s cancelation was negatively correlated with the frequency of religious meetings, and the frequency of prayers was positively correlated with the response to ovarian stimulation. Finally, belief in treatment success positively influenced the embryo quality. Conclusion: The findings suggest that spirituality plays a role in adjusting the psychological aspects of an infertile patient.
Transforming temporary organizations to permanence: Examining the role of information systems

Temporary organizations might not remain such in perpetuity. They may transform into permanent form over time. Information systems are pivotal to such transformation. In this study, we examine such transformation using an exploratory case study of a firm operating in the domain of disaster management. We examine the changing role of information systems in driving such transformation. In this regard, we propose a dynamic framework for examining these dynamics across different phases of this transformation. This study concludes that information systems hold significant influence on communication, coordination, and control of various teams in such temporary organizations. When implemented appropriately, it reflects variedly at different stages of such organizational transformation. This study helps develop a vocabulary for future research on the theme of transformation for such organizations.