Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of Follow-Up Imaging in Isolated Perimesencephalic Subarachnoid Hemorrhage: A Meta-Analysis

Background and Purpose— Multiple studies have shown that negative computed tomographic angiograms (CTAs) are reliable in excluding aneurysms in patients with isolated perimesencephalic subarachnoid hemorrhage (pSAH). We evaluate the use of digital subtraction angiography versus CTA for initial diagnosis and of angiographic follow-ups in patients with pSAH by performing an institutional analysis and a meta-analysis of literature. Methods— Retrospective institutional analysis of patients with pSAH was performed from 2008 to 2014. The number and types of follow-up imaging studies were tabulated. Initial and follow-up studies were evaluated by an experienced neuroradiologist for intracranial aneurysm. Meta-analysis of literature was performed to assess the use of initial digital subtraction angiography and of follow-up imaging. Results— Our institutional review revealed no additional use of initial digital subtraction angiography or of any angiographic follow-up after initial negative CTA in patients with pSAH on noncontrast CT. Meta-analysis of 40 studies yielded a total of 1031 patients. Only 8 aneurysms were first diagnosed on follow-ups (0.78%). Careful review showed that some of these aneurysms reported on follow-up are of questionable validity. Initial digital subtraction angiography and follow-up imaging after a negative initial CTA showed no statistically significant benefits. Conclusions— In patients meeting the strict imaging criteria of pSAH, initial negative CTA is reliable in excluding aneurysms. A critical review of the literature through meta-analysis shows no foundation for multiple follow-up studies in patients with pSAH.
A Linkage Map of the Zebra Finch Taeniopygia guttata Provides New Insights Into Avian Genome Evolution

Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.
A constructive algorithm for memory-aware task assignment and scheduling

This paper presents a constructive algorithm for memory-aware task assignment and scheduling, which is a part of the prototype system MATAS. The algorithm is well suited for image and video processing applications which have hard memory constraints as well as constraints on cost, execution time, and resource usage. Our algorithm takes into account code and data memory constraints together with the other constraints. It can create pipelined implementations. The algorithm finds a task assignment, a schedule, and data and code memory placement in memory. Infeasible solutions caused by memory fragmentation are avoided. The experiments show that our memory-aware algorithm reduces memory utilization compared to greedy scheduling algorithm which has time minimization objective. Moreover, memory-aware algorithm is able to find task assignment and schedule when time minimization algorithm fails. MATAS can create pipelined implementations, therefore the design throughput is increased.
Quantum model of strategic decision-making in Prisoner ’ s Dilemma game : quantitative predictions and new empirical results

The Disjunction effect introduced in the famous study by Shafir and Tversky (1992) and confirmed by several following studies remains one of key ‘anomalies’ for the standard model of the Prisoner’s Dilemma game. In the last 10 years, new approaches have appeared that explain this effect with the use of quantum probability theory. But the existing results do not allow parameter-free test of these models. This paper introduces a general quantum model of Prisoner’s Dilemma game as well as a new experimental design that enables to test the main quantitative and qualitative predictions of this model. Main findings of the experiment support the viability of the quantum model and challenge the classical solution concept of the Prisoner’s Dilemma game.
Molecular Mechanisms by Which a Fucus vesiculosus Extract Mediates Cell Cycle Inhibition and Cell Death in Pancreatic Cancer Cells

Pancreatic cancer is one of the most aggressive cancer entities, with an extremely poor 5-year survival rate. Therefore, novel therapeutic agents with specific modes of action are urgently needed. Marine organisms represent a promising source to identify new pharmacologically active substances. Secondary metabolites derived from marine algae are of particular interest. The present work describes cellular and molecular mechanisms induced by an HPLC-fractionated, hydrophilic extract derived from the Baltic brown seaweed Fucus vesiculosus (Fv1). Treatment with Fv1 resulted in a strong inhibition of viability in various pancreatic cancer cell lines. This extract inhibited the cell cycle of proliferating cells due to the up-regulation of cell cycle inhibitors, shown on the mRNA (microarray data) and protein level. As a result, cells were dying in a caspase-independent manner. Experiments with non-dividing cells showed that proliferation is a prerequisite for the effectiveness of Fv1. Importantly, Fv1 showed low cytotoxic activity against non-malignant resting T cells and terminally differentiated cells like erythrocytes. Interestingly, accelerated killing effects were observed in combination with inhibitors of autophagy. Our in vitro data suggest that Fv1 may represent a promising new agent that deserves further development towards clinical application.
How the Rgt1 Transcription Factor of Saccharomyces cerevisiae Is Regulated by Glucose

Rgt1 is a transcription factor that regulates expression of HXT genes encoding glucose transporters in the yeast Saccharomyces cerevisiae. Rgt1 represses HXT gene expression in the absence of glucose; high levels of glucose cause Rgt1 to activate expression of HXT1. We identified four functional domains of Rgt1. A domain required for transcriptional repression (amino acids 210–250) is required for interaction of Rgt1 with the Ssn6 corepressor. Another region of Rgt1 (320–380) is required for normal transcriptional activation, and sequences flanking this region (310–320 and 400–410) regulate this function. A central region (520–830) and a short sequence adjacent to the zinc cluster DNA-binding domain (80–90) inhibit transcriptional repression when glucose is present. We found that this middle region of Rgt1 physically interacts with the N-terminal portion of the protein that includes the DNA-binding domain. This interaction is inhibited by the Rgt1 regulator Mth1, which binds to Rgt1. Our results suggest that Mth1 promotes transcriptional repression by Rgt1 by binding to it and preventing the intramolecular interaction, probably by preventing phosphorylation of Rgt1, thereby enabling Rgt1 to bind to DNA. Glucose induces HXT1 gene expression by causing Mth1 degradation, allowing Rgt1 phosphorylation, and leading to the intramolecular interaction that inhibits DNA binding of Rgt1.
Prevalence of Genital Mycoplasmas in Women of Various Socio-Economic Status

The prevalence of genital mycoplasma, a sexually transmitted pathogen, was studied in 168 reproductive aged women in Ibadan, Nigeria, using bacteriologic methods. An overall prevalence rate of 35.7% was obtained; with the highest prevalence rate found among artisans (50%) and students (39.1%). Women aged 21 - 25 years and 36 - 40 years had prevalence rates of 41.6 and 47.4%, respectively, while those with parity 4 and above had a higher prevalence rate (52%) as against those with parity 3 and below (33.6%). The educational status of the women revealed a statistically non-significant increase in prevalence of the organism in women who had secondary and tertiary education (36.7%) as against those with primary or no education (p>0.05). The need for health education of women, especially during a younger age is hereby emphasized to enlighten them on the need to avoid the acquisition of these microorganisms as well as other sexually transmitted pathogens which may adversely affect them in future.
Reproductive Biology and Endocrinology Open Access Human Chorionic Gonadotropin Administration Is Associated with High Pregnancy Rates during Ovarian Stimulation and Timed Intercourse or Intrauterine Insemination

Background: There are different factors that influence treatment outcome after ovarian stimulation and timed-intercourse or intrauterine insemination (IUI). After patient age, it has been suggested that timing of insemination in relation to ovulation is probably the most important variable affecting the success of treatment. The objective of this study is to study the value of human chorionic gonadotropin (hCG) administration and occurrence of luteinizing hormone (LH) surge in timing insemination on the treatment outcome after follicular monitoring with timed-intercourse or intrauterine insemination, with or without ovarian stimulation.
Variation in subfertility care measured by guideline-based performance indicators.

BACKGROUND About 30-40% of patients do not receive care based on available scientific evidence. For subfertility, this may imply unnecessary and expensive diagnostic tests and treatments. It is therefore important to identify gaps in performance by monitoring current subfertility care. A set of 39 guideline-based performance indicators was previously developed for this purpose. This study aimed to assess several quality criteria of the indicator-set and to use the set to assess current subfertility care. METHODS A historic cohort study was performed in 16 Dutch subfertility clinics; 2698 couples were invited to participate. Indicator data were gathered by medical record extraction, and patient and professional questionnaires. Quality criteria for each indicator (measurability, reliability, applicability, improvement potential, discriminatory capacity, complexity and case-mix stability) were assessed. Current practice was measured as adherence to the separate indicators. RESULTS One thousand four-hundred and ninety-nine (56%) couples participated. All indicators were measurable, but the results for the other quality criteria varied. In total, 14 of the 39 indicators scored <50% adherence. Variation in performance between the clinics was up to 100%. The highest median adherence (86%) is found within the guideline 'indications for IVF-treatment'. The lowest median adherence is found within the guideline 'initial assessment of fertility' (43%), followed closely by the guideline 'anovulation' (44%). CONCLUSIONS This study shows the quality of the developed indicator-set for monitoring clinical subfertility care. A first assessment in the Netherlands reveals large variation between clinics and ample room for improvement of care.
Intralamellar relationships within the collagenous architecture of the annulus fibrosus imaged in its fully hydrated state

The anisotropic, inhomogeneous, multiply collagenous architecture of the annulus reflects the complex pattern of mainly tensile stresses developed in this region of the disc during normal function. Structural and mechanical responses of fully hydrated in‐plane sections taken from within single lamellae of the outer annulus of healthy bovine caudal discs have been investigated using a micromechanical technique in combination with simultaneous high‐resolution differential interference contrast optical imaging. Responses both along and across (i.e. transverse to) the primary direction of the mono‐array of collagen fibres were studied. Stretching along the alignment direction revealed a biomechanical response consistent with the behaviour of an array whose overall strength is governed primarily by the strength of embedding of the fibres in the vertebral endplates, rather than from interfibre cohesion along their length. The mono‐aligned array, even when lacerated, is highly resistant to any further tearing across the alignment direction. Although not visible in the relaxed mono‐arrays, transverse stretching revealed a highly complex set of interconnecting structures embodying hierarchical relationships not previously revealed. It is suggested that these structures might play an important role in the containment under pressure of the nuclear contents. The dramatic differences in rupture behaviour observed along vs. across the primary fibre direction are consistent with the known clinical consequences arising from varying degrees of annular wall damage, and might also explain various types of disc herniation. The lamellar architecture of the healthy disc revealed by this investigation provides an important reference framework for exploring structural changes associated with disc trauma and degeneration.
Primal-Dual Rates and Certificates

We propose an algorithm-independent framework to equip existing optimization methods with primal-dual certificates. Such certificates and corresponding rate of convergence guarantees are important for practitioners to diagnose progress, in particular in machine learning applications. We obtain new primal-dual convergence rates, e.g., for the Lasso as well as many L1, Elastic Net, group Lasso and TV-regularized problems. The theory applies to any norm-regularized generalized linear model. Our approach provides efficiently computable duality gaps which are globally defined, without modifying the original problems in the region of interest.
Brain surface electrode co-registration using MRI and x-ray

Electrocorticographic recording is now being used in a wide variety of experimental settings. We present a simple method which can be used to estimate electrode position with respect to brain gyral anatomy using a pre-implantation MRI and post-implantation coronal and sagittal x-rays. It is semi-automated, with the user manually rotating and scaling an x-ray to fit brain outline, identifying threshold values for brain surface rendering, and clicking on electrodes on an x-ray. Electrode positions can be rapidly identified and rendered in about 20 minutes from start to finish. This approach is useful when the MRI quality is poor, there is no quality CT, but one would like to understand the relationship between experimental result and brain anatomy.
A multifactor regulatory circuit involving H-NS, VirF and an antisense RNA modulates transcription of the virulence gene icsA of Shigella flexneri

The icsA gene of Shigella encodes a structural protein involved in colonization of the intestinal mucosa by bacteria. This gene is expressed upon invasion of the host and is controlled by a complex regulatory circuit involving the nucleoid protein H-NS, the AraC-like transcriptional activator VirF, and a 450 nt antisense RNA (RnaG) acting as transcriptional attenuator. We investigated on the interplay of these factors at the molecular level. DNase I footprints reveal that both H-NS and VirF bind to a region including the icsA and RnaG promoters. H-NS is shown to repress icsA transcription at 30°C but not at 37°C, suggesting a significant involvement of this protein in the temperature-regulated expression of icsA. We also demonstrate that VirF directly stimulates icsA transcription and is able to alleviate H-NS repression in vitro. According to these results, icsA expression is derepressed in hns- background and overexpressed when VirF is provided in trans. Moreover, we find that RnaG-mediated transcription attenuation depends on 80 nt at its 5′-end, a stretch carrying the antisense region. Bases engaged in the initial contact leading to sense–antisense pairing have been identified using synthetic RNA and DNA oligonucleotides designed to rebuild and mutagenize the two stem–loop motifs of the antisense region.
Spatial mixture relative risk models applied to disease mapping

An important issue within health services research is the correct allocation of resources within health authority regions and the capability of public health professionals to make such allocation appropriately. This allocation is often based on a mapping of relevant disease incidence and the assessment of the geographical distribution of relative risk of disease in small areas within the health authority administrative domain. Existing methods for the statistical analysis of small area risk are mostly based on smoothing methods. However, these methods often smooth over large discontinuities in the risk surface which might be important to maintain for the purposes of resource allocation. In this paper we propose a method that involves the use of spatial mixtures of components that can provide a balance between smoothness and the maintenance of discontinuity. The method is applied to a sudden infant death incidence data set. Copyright © 2002 John Wiley & Sons, Ltd.
HARDNESS OF COOKED MILLED RICE BY INSTRUMENTAL AND SENSORY METHODS

Fifteen milled rice varieties covering the usual range of amylose content and cooked rice hardness were used in a collaborative study to verify the sensitivity of the present objective method for measuring cooked rice hardness. The grains were cooked either in a rice cooker using a fixed water:rice ratio of 2:1, or by boiling in excess water for the predetermined optimum cooking time for each sample followed by draining. Hardness of cooked rice was measured in an Instron Universal Testing Machine (UTM) using two methods: (1) puncture of 100 individual grains and (2) extrusion through a 30 cm2 Ottawa Texture Measuring System (OTMS) cell with either a 3.2- or 4.8-mm-diam. holes plate. Hardness values were compared with sensory scores by a trained panel composed of 11 members. Sensory hardness of the rices cooked in a fixed amount of water showed very good correlation with puncture force (r = 0.94, P < 0.01) and with extrusion force through a 3.2-mm-diam. holes plate (r = 0.94). The correlation coefficient between puncture force and extrusion force was 0.97. Paired comparison test by the sensory panel on three pairs of rices verified consumers’ claims with respect to preference between members of each pair and agreed with results of ranking test.
An RPTPα/Src family kinase/Rap1 signaling module recruits myosin IIB to support contractile tension at apical E-cadherin junctions

The role of myosin IIB in junctional contractility and its mode of regulation are not well understood. It is demonstrated that junctional recruitment of myosin IIB requires the activation of a receptor-type protein tyrosine phosphatase alpha–Src family kinase–Rap1 pathway. This reinforces the concept that E-cadherin–based signaling recruits distinct myosin II paralogues to generate contractile tension.
The Endoplasmic Reticulum (ER)-associated Degradation System Regulates Aggregation and Degradation of Mutant Neuroserpin*

Familial encephalopathy with neuroserpin inclusion bodies is a neurodegenerative disorder characterized by the accumulation of neuroserpin polymers in the endoplasmic reticulum (ER) of cortical and subcortical neurons in the CNS because of neuroserpin point mutations. ER-associated degradation (ERAD) is involved in mutant neuroserpin degradation. In this study, we demonstrate that two ER-associated E3 ligases, Hrd1 and gp78, are involved in the ubiquitination and degradation of mutant neuroserpin. Overexpression of Hrd1 and gp78 decreases the mutant neuroserpin protein level, whereas Hrd1 and gp78 knockdown increases mutant neuroserpin stability. Moreover, ERAD impairment by mutant valosin-containing protein increases the mutant neuroserpin protein level and aggregate formation. Thus, these findings identify mutant neuroserpin as an ERAD target and show that Hrd1 and gp78 mediate mutant neuroserpin turnover through the ERAD pathway.
Automatic early defects detection in use case documents

Use cases, as the primary techniques in the user requirement analysis, have been widely adopted in the requirement engineering practice. As developed early, use cases also serve as the basis for function requirement development, system design and testing. Errors in the use cases could potentially lead to problems in the system design or implementation. It is thus highly desirable to detect errors in use cases. Automatically analyzing use case documents is challenging primarily because they are written in natural languages. In this work, we aim to achieve automatic defect detection in use case documents by leveraging on advanced parsing techniques. In our approach, we first parse the use case document using dependency parsing techniques. The parsing results of each use case are further processed to form an activity diagram. Lastly, we perform defect detection on the activity diagrams. To evaluate our approach, we have conducted experiments on 200+ real-world as well as academic use cases. The results show the effectiveness of our method.
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

The transcriptional landscape in embryonic stem cells (ESCs) and during ESC differentiation has received considerable attention, albeit mostly confined to the polyadenylated fraction of RNA, whereas the non-polyadenylated (NPA) fraction remained largely unexplored. Notwithstanding, the NPA RNA super-family has every potential to participate in the regulation of pluripotency and stem cell fate. We conducted a comprehensive analysis of NPA RNA in ESCs using a combination of whole-genome tiling arrays and deep sequencing technologies. In addition to identifying previously characterized and new non-coding RNA members, we describe a group of novel conserved RNAs (snacRNAs: small NPA conserved), some of which are differentially expressed between ESC and neuronal progenitor cells, providing the first evidence of a novel group of potentially functional NPA RNA involved in the regulation of pluripotency and stem cell fate. We further show that minor spliceosomal small nuclear RNAs, which are NPA, are almost completely absent in ESCs and are upregulated in differentiation. Finally, we show differential processing of the minor intron of the polycomb group gene Eed. Our data suggest that NPA RNA, both known and novel, play important roles in ESCs.
Clinical research and trials in developing countries

Over 80 per cent of the global disease burden occurs in developing countries. Yet the proportion of research conducted in these countries is less than 10 per cent of the global research activity. This article emphasizes the need to conduct research in developing countries on locally relevant questions, provides general principles that may assist in establishing such studies, and describes some experiences in the cardiovascular area. Copyright © 2002 John Wiley & Sons, Ltd.