Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Visualization of Cartilage Canals Using Quantitative Susceptibility Mapping

Purpose Cartilage canal vessels are critical to the normal function of epiphyseal (growth) cartilage and damage to these vessels is demonstrated or suspected in several important developmental orthopaedic diseases. High-resolution, three-dimensional (3-D) visualization of cartilage canals has recently been demonstrated using susceptibility weighted imaging (SWI). In the present study, a quantitative susceptibility mapping (QSM) approach is evaluated for 3-D visualization of the cartilage canals. It is hypothesized that QSM post-processing improves visualization of the cartilage canals by resolving artifacts present in the standard SWI post-processing while retaining sensitivity to the cartilage canals. Methods Ex vivo distal femoral specimens from 3- and 8-week-old piglets and a 1-month-old human cadaver were scanned at 9.4 T with a 3-D gradient recalled echo sequence suitable for SWI and QSM post-processing. The human specimen and the stifle joint of a live, 3-week-old piglet also were scanned at 7.0 T. Datasets were processed using the standard SWI method and truncated k-space division QSM approach. To compare the post-processing methods, minimum/maximum intensity projections and 3-D reconstructions of the processed datasets were generated and evaluated. Results Cartilage canals were successfully visualized using both SWI and QSM approaches. The artifactual splitting of the cartilage canals that occurs due to the dipolar phase, which was present in the SWI post-processed data, was eliminated by the QSM approach. Thus, orientation-independent visualization and better localization of the cartilage canals was achieved with the QSM approach. Combination of GRE with a mask based on QSM data further improved visualization. Conclusions Improved and artifact-free 3-D visualization of the cartilage canals was demonstrated by QSM processing of the data, especially by utilizing susceptibility data as an enhancing mask. Utilizing tissue-inherent contrast, this method allows noninvasive assessment of the vasculature in the epiphyseal cartilage in the developing skeleton and potentially increases the opportunity to diagnose disease of this tissue in the preclinical stages, when treatment likely will have increased efficacy.
Mucosal Escherichia coli bactericidal activity and immune mediators are associated with HIV-1 seroconversion in women participating in the HPTN 035 trial.

The mucosal environment may impact the risk for human immunodeficiency virus type 1 (HIV-1) acquisition. Immune mediators were measured in vaginal fluid collected from HPTN 035 participants who acquired HIV-1 and from those who remained HIV-1 negative (controls). Mediator concentrations were similar in samples obtained before as compared to after HIV-1 acquisition in the 8 seroconverters. Compared with controls, seroconverters were more likely to have detectable levels of HβD-2 (odds ratio [OR], 2.39; P = .005) and greater Escherichia coli bactericidal activity (OR, 1.22; P = .01) prior to seroconversion. E. coli bactericidal activity remained significant in a multivariable analysis (P = .02) and may be a biomarker for HIV-1 acquisition.
Early Cell Cycle Box-Mediated Transcription ofCLN3 and SWI4 Contributes to the Proper Timing of the G1-to-S Transition in Budding Yeast

ABSTRACT The Cln3-Cdc28 kinase is required to activate the Swi4-Swi6 transcription complex which induces CLN1 andCLN2 transcription in late G1 and drives the transition to S. Cln3 and Swi4 are both rate limiting for G1 progression, and they are coordinately transcribed to peak at the M/G1 boundary. Early cell cycle box (ECB) elements, which confer M/G1-specific transcription, have been found in both promoters, and elimination of all ECB elements from the CLN3 promoter causes both a loss of periodicity and Cln3-deficient phenotypes, which include an extended G1interval and increased cell volume. Mutants lacking the ECB elements in both the CLN3 and SWI4 promoters have low and deregulated levels of CLN transcripts, and the G1-to-S transition for these mutants is delayed and highly variable. These observations support the view that the coordinated rise of Cln3 and Swi4 levels mediated by ECB-dependent transcription controls the timing of the G1-to-S phase transition.
Handling dynamic schema change in process models

Workflow technology has emerged as an appropriate platform for consolidating the distributed information resources of an enterprise, promoting interoperability across cross-platform systems and for providing a global view and understanding of business process models. However, the business processes that workflows represent, are dynamic by nature, that is, they encounter frequent and unavoidable changes. It is through this dynamism that organizations maintain their competitive edge. Workflow technology to date does not provide sufficient support for dynamically changing processes. Managing schema change of workflow processes with multiple active instances is a complex issue. In this paper, we present an analysis of workflow changes in relation to business process change, and present a classification of workflow changes that dictate the scope of the problem. Based on this classification we lay the foundation for a generic framework to support dynamically changing workflow processes.
Can Strategic Uncertainty Help Deter Tax Evasion? An Experiment on Auditing Rules

This paper adds to the economic-psychological research on tax compliance by experimentally testing a simple auditing rule that induces strategic uncertainty among taxpayers. Under this rule, termed the bounded rule, taxpayers are informed of the maximum number of audits by a tax authority, so that the audit probability depends on the joint decisions among the taxpayers. We compare the bounded rule to the widely studied flat-rate rule, where taxpayers are informed that they will be audited with a constant probability. The experimental evidence shows that, as theoretically predicted, the bounded rule induces the same level of compliance as the flat-rate rule when strategic uncertainty is low, and a higher level of compliance when strategic uncertainty is high. The bounded rule also suppresses the "bomb crater" effect often observed in prior studies. The results suggest that strategic uncertainty due to interactions among taxpayers could be an effective device to deter tax evasion.
Availability-Aware VNF Placement for uRLLC Applications in MEC-Enabled 5G Networks

In this paper, we study the VNF placement problem in MEC-enabled 5G networks to meet the stringent reliability and latency requirements of uRLLC applications. We pose it as a constrained optimization problem, which is NP-hard, to maximize the total reward obtained by a network service provider by serving uRLLC service requests. We propose an approximated randomized rounding approach to solve the NP-hard optimization problem in polynomial time. We prove that the proposed randomized approach achieves performance guarantees while violating the resource constraints in a bounded way. Furthermore, we present a greedy-heuristic approach to tackle the violations in the resource constraints. Simulation results show the proposed approach yields close-to-optimal performance. Specifically, the total reward is within 5% and 10% of the optimal solution using the proposed randomized rounding and greedy approaches, respectively.
The effect of swimming activity and section of the vagus nerves on heart rate in rainbow trout.

1. Heart rates associated with swimming activity were measured in intact and vagotomized fish at 6.5 and 15 °C. 2. Low swimming speeds had no effect on heart rate but above a threshold speed it increased logarithmically with swimming speed up to the critical speed and maximum heart rate. 3. Times for recovery after exercise increased rapidly above the critical speed. 4. Bilaterally vagotomized fish at 6.5 °C showed high resting heart rates and erratic cardiac responses to exercise. 5. In bilaterally vagotomized fish at 15 °C heart rates were normal except for a low maximum rate. 6. It is concluded that the vagus nerve can function differently at different temperatures.
Lack of K-Dependent Oxidative Stress in Cotton Roots Following Coronatine-Induced ROS Accumulation

Coronatine [COR] is a novel type of plant growth regulator with similarities in structure and property to jasmonate. The objective of this study was to examine the relationship between increased root vitality induced by 10nM COR and reactive oxygen species scavenging under potassium (K)-replete (2.5mM) and K-deficient (0.05mM) conditions in hydroponic cultured cotton seedlings. K-replete and K-deficient conditions increased root vitality by 2.7- and 3.5-fold, respectively. COR treatment significantly decreased lipid peroxidation in cotton seedlings determined by reduction in MDA levels. These results suggest that COR improves the functioning of both enzymatic and non-enzymatic antioxidant systems. Under K-replete and K-deficient conditions, COR significantly increased the activities of antioxidant enzymes SOD (only for K-repletion), CAT, GPX, and APX comparing; COR also significantly increased DPPH-radical scavenging activity. However, COR led to 1.6- and 1.7-fold increases in superoxide anion (O2 •-) concentrations, and 5.7- and 2.1-fold increases in hydrogen peroxide (H2O2) levels, respectively. Additionally, COR intensified the DAB staining of H2O2 and the NBT staining of O2 •-. Therefore, our results reveal that COR-induced ROS accumulation stimulates the activities of most antioxidant enzymes but does not induce oxidative stress in cotton roots.
Gait mechanics after ACL reconstruction: implications for the early onset of knee osteoarthritis

Background: Individuals who sustain a rupture of the anterior cruciate ligament (ACL) are at an increased risk for developing early-onset knee osteoarthritis (OA). The mechanism behind the early onset of the disease is still unknown. Knee OA progression has been previously examined by calculating the internal knee-abduction moment during gait. However, knee-joint moments have not been examined in individuals after ACL reconstruction as a potential mechanism for disease progression in early knee OA. Objective: To determine if individuals who have undergone ACL reconstruction exhibit altered gait mechanics that may be associated with knee OA progression. Methods: In total, 17 people who had previously undergone ACL reconstruction were enrolled in the study. A matched control group was recruited for comparison. All participants underwent gait analysis at an intentional walking speed to examine variables previously associated with knee OA progression, primarily the internal peak knee-abduction moment, during gait. One way ANOVAs were performed to examine differences in gait mechanics between the two groups. All joint moments were calculated as internal moments. Results: The peak knee-abduction moment was increased by 21% in the ACL compared with the control group (p = 0.04). No other differences were seen in frontal plane knee or hip mechanics. Conclusion: It seems that individuals who have undergone ACL reconstruction exhibit an increased peak knee-abduction moment that may establish a potential mechanism of the earlier onset of knee OA in this population.
Subclonal variant calling with multiple samples and prior knowledge

Motivation: Targeted resequencing of cancer genes in large cohorts of patients is important to understand the biological and clinical consequences of mutations. Cancers are often clonally heterogeneous, and the detection of subclonal mutations is important from a diagnostic point of view, but presents strong statistical challenges. Results: Here we present a novel statistical approach for calling mutations from large cohorts of deeply resequenced cancer genes. These data allow for precisely estimating local error profiles and enable detecting mutations with high sensitivity and specificity. Our probabilistic method incorporates knowledge about the distribution of variants in terms of a prior probability. We show that our algorithm has a high accuracy of calling cancer mutations and demonstrate that the detected clonal and subclonal variants have important prognostic consequences. Availability: Code is available as part of the Bioconductor package deepSNV. Contact: mg14@sanger.ac. uk; pc8@sanger.ac. uk
Towards Distributed and Adaptive Detection and Localisation of Network Faults

We present a statistical probing-approach to distributed fault-detection in networked systems, based on autonomous configuration of algorithm parameters. Statistical modelling is used for detection and localisation of network faults. A detected fault is isolated to a node or link by collaborative fault-localisation. From local measurements obtained through probing between nodes, probe response delay and packet drop are modelled via parameter estimation for each link. Estimated model parameters are used for autonomous configuration of algorithm parameters, related to probe intervals and detection mechanisms. Expected fault-detection performance is formulated as a cost instead of specific parameter values, significantly reducing configuration efforts in a distributed system. The benefit offered by using our algorithm is fault-detection with increased certainty based on local measurements, compared to other methods not taking observed network conditions into account. We investigate the algorithm performance for varying user parameters and failure conditions. The simulation results indicate that more than 95% of the generated faults can be detected with few false alarms. At least 80% of the link faults and 65% of the node faults are correctly localised. The performance can be improved by parameter adjustments and by using alternative paths for communication of algorithm control messages.
Combining Two And Three-Way Embeddings Models for Link Prediction in Knowledge Bases

This paper tackles the problem of endogenous link prediction for knowledge base completion. Knowledge bases can be represented as directed graphs whose nodes correspond to entities and edges to relationships. Previous attempts either consist of powerful systems with high capacity to model complex connectivity patterns, which unfortunately usually end up overfitting on rare relationships, or in approaches that trade capacity for simplicity in order to fairly model all relationships, frequent or not. In this paper, we propose TATEC, a happy medium obtained by complementing a high-capacity model with a simpler one, both pre-trained separately and then combined. We present several variants of this model with different kinds of regularization and combination strategies and show that this approach outperforms existing methods on different types of relationships by achieving state-of-the-art results on four benchmarks of the literature.
Probabilistic Cause-of-Death Assignment Using Verbal Autopsies

ABSTRACT In regions without complete-coverage civil registration and vital statistics systems there is uncertainty about even the most basic demographic indicators. In such regions, the majority of deaths occur outside hospitals and are not recorded. Worldwide, fewer than one-third of deaths are assigned a cause, with the least information available from the most impoverished nations. In populations like this, verbal autopsy (VA) is a commonly used tool to assess cause of death and estimate cause-specific mortality rates and the distribution of deaths by cause. VA uses an interview with caregivers of the decedent to elicit data describing the signs and symptoms leading up to the death. This article develops a new statistical tool known as InSilicoVA to classify cause of death using information acquired through VA. InSilicoVA shares uncertainty between cause of death assignments for specific individuals and the distribution of deaths by cause across the population. Using side-by-side comparisons with both observed and simulated data, we demonstrate that InSilicoVA has distinct advantages compared to currently available methods. Supplementary materials for this article are available online.
A Mouse Model of Human Primitive Neuroectodermal Tumors Resulting from Microenvironmentally-Driven Malignant Transformation of Orthotopically Transplanted Radial Glial Cells

There is growing evidence and a consensus in the field that most pediatric brain tumors originate from stem cells, of which radial glial cells constitute a subtype. Here we show that orthotopic transplantation of human radial glial (RG) cells to the subventricular zone of the 3rd ventricle - but not to other transplantation sites - of the brain in immunocompromised NOD-SCID mice, gives rise to tumors that have the hallmarks of CNS primitive neuroectodermal tumors (PNETs). The resulting mouse model strikingly recapitulates the phenotype of PNETs. Importantly, the observed tumorigenic transformation was accompanied by aspects of an epithelial to mesenchymal transition (EMT)-like process. It is also noteworthy that the tumors are highly invasive, and that they effectively recruit mouse endothelial cells for angiogenesis. These results are significant for several reasons. First, they show that malignant transformation of radial glial cells can occur in the absence of specific mutations or inherited genomic alterations. Second, they demonstrate that the same radial glial cells may either give rise to brain tumors or differentiate normally depending upon the microenvironment of the specific region of the brain to which the cells are transplanted. In addition to providing a prospect for drug screening and development of new therapeutic strategies, the resulting mouse model of PNETs offers an unprecedented opportunity to identify the cancer driving molecular alterations and the microenvironmental factors that are responsible for committing otherwise normal radial glial cells to a malignant phenotype.
The effects of stimulus-response mapping and irrelevant stimulus-response and stimulus-stimulus overlap in four-choice Stroop tasks with single-carrier stimuli.

The purpose of this study was to investigate whether and how stimulus-stimulus (SS) and stimulus-response (SR) consistency and SR congruence effects combine to produce the Stroop effect. Two experiments were conducted with 4-choice tasks in which SS and SR consistency and SR congruence effects were examined in isolation as well as in the Stroop task. The experiments were so designed as to remove the confound between SS and SR consistency that is ordinarily found in standard Stroop tasks and to pit SS consistency against the logical recording hypothesis (A. Hedge & N. W. A. Marsh, 1975). The results indicate that SS and SR consistency both contribute to the Stroop effect and that they interact. This finding supports models such as the dimensional overlap model (e.g., S. Kornblum & J. W. Lee, 1995) that distinguish between SS and SR overlap. Simulation results from an interactive activation network, modeled after the dimensional overlap model, provide reasonable fits to the experimental data.
Patterns of Congenital Heart Diseases at Sohag University Hospital

Background: Congenital heart diseases (CHD) are structural or functional heart diseases that present at birth even if it is discovered later in life . Aim: to study Patterns of CHD in children at Sohag University Hospital. Methods: This was a Prospective and cross sectional study done in pediatric department at Sohag University Hospital with all its divisions. Results: Total cases of congenital heart diseases were 900 patients, of them 650 (72.2) Acyanotic CHD and 250 (27.8) Cyanotic CHD, regarding acyanotic CHDs the commonest isolated defects were ASD in 181 (20.1) , VSD in 142 (15.78), followed by PDA in 78 (8.67), P.S in 55 (6.11), Then AS in 45 (5). Less common CoA in 20 (2.22), complete AV Canal Defect in 13 (1.44), partial AV Canal Defect in 6 (0.67), combined defects detected in 110 (12.22) . As regard Cyanotic CHDs the commonest were TOF in 97 (10.78) , D-TGA in 57 (6.33) , followed by P.A. in 27 (3) T.A. in 20 (2.22) LHHS in 17 (1.89) , less common were Ebestien anomaly in 12 (1.33) , Single Ventricle in 10 (1.11) other complex cyanotic CHD in 10 (1.11). CHDs were commonest in infants (53.33%) followed by neonates (37.22%) then preschool children (7.222%) then school children (2.22%). Conclusion : the trends of CHD observed in our study were different from the other national and international studies as the most common type observed in this study was ASD followed by VSD, PDA, and TOF.
Genetic analysis of alpha 4 integrin functions in the development of mouse skeletal muscle

It has been suggested, on the basis of immunolocalization studies in vivo and antibody blocking experiments in vitro, that alpha 4 integrins interacting with vascular cell adhesion molecule 1 (VCAM-1) are involved in myogenesis and skeletal muscle development. To test this proposal, we generated embryonic stem (ES) cells homozygous null for the gene encoding the alpha 4 subunit and used them to generate chimeric mice. These chimeric mice showed high contributions of alpha 4- null cells in many tissues, including skeletal muscle, and muscles lacking any detectable (< 2%) alpha 4-positive cells did not reveal any gross morphological abnormalities. Furthermore, assays for in vitro myogenesis using either pure cultures of alpha 4-null myoblasts derived from the chimeras or alpha 4-null ES cells showed conclusively that alpha 4 integrins are not essential for muscle cell fusion and differentiation. Taking these results together, we conclude that alpha 4 integrins appear not to play essential roles in normal skeletal muscle development.
HIV–A prognostic factor of tuberculous meningitis: A retrospective cohort study among adults in peninsular Malaysia

Background: Tuberculous meningitis is a major public health issue, despite showing low incidence, tuberculous meningitis causes substantial mortality. For better clinical management, identification of prognostic factors is crucial to reduce health risk of Malaysian society. Therefore, the aim of this study was to determine the prognostic factors of adult tuberculous meningitis in peninsular Malaysia. Materials & methods: Initially, a retrospective cohort study and one-year of follow-up period was carried out. In addition, a total of 217 adult tuberculous meningitis patients treated or had follow-up in four tertiary hospitals in peninsular Malaysia were recruited. Cox proportional hazards regression was employed to perform multivariable analysis. Results: The overall survival probability of adult tuberculous meningitis was 36.8% with median survival time 244 days. Significant prognostic factors were Glasgow coma scale score (aHR=0.71, 95% CI=0.65, 0.76; p<0.001), HIV status (aHR=1.94, 95% confidence interval [CI]=1.19, 3.15; p=0.008), headache (aHR=0.48, 95% CI=0.31, 0.76; p=0.002) and meningeal enhancement (aHR=0.47, 95% CI=0.30, 0.74; p=0.001), nausea (aHR=2.21, 95% CI=1.33, 3.66; p=0.002), and vomit (aHR=0.58, 95% CI=0.36, 0.93; p=0.023). Conclusions: Evidently, the survival of among adults with tuberculous meningitis was low. Since HIV positive has a significant influence in mortality; early screening, diagnosis, and prompt treatment in this subgroup of patients play a key role in survival.