Miracle-dz/UniFAR-FTUs huggingface dataset:
New, extended hairpin form of the TAR-2 RNA domain points to the structural polymorphism at the 5′ end of the HIV-2 leader RNA

The HIV-2 TAR RNA domain (TAR-2) plays a key role in the trans-activation of HIV-2 transcription as it is the target for the Tat-2 protein and several cell factors. Here, we show that the TAR-2 domain exists in vitro in two global, alternative forms: a new, extended hairpin form with two conformers and the already proposed branched hairpins form. This points strongly to the structural polymorphism of the 5′ end of the HIV-2 leader RNA. The evidence comes from the non-denaturing PAGE mobility assay, 2D structure prediction, enzymatic and Pb2+- or Mg2+-induced RNA cleavages. Existence of the TAR-2 extended form was further proved by the examination of engineered TAR-2 mutants stabilized either in the branched or extended structure. The TAR-2 extended form predominates with an increasing magnesium concentration. Gel retardation assays reveal that both TAR-2 wt and its mutant, unable to form branched structure, bind Tat-2 protein with comparable, high affinity, while RNA hairpins I and II, derived from TAR-2 branched structure model, show much less protein binding. We propose that an internal loop region of the TAR-2 extended hairpin form is a potential Tat-2 binding site.
Exploring Peripheral Physiology as a Predictor of Perceived Relevance in Information Retrieval

Peripheral physiological signals, as obtained using electrodermal activity and facial electromyography over the corrugator supercilii muscle, are explored as indicators of perceived relevance in information retrieval tasks. An experiment with 40 participants is reported, in which these physiological signals are recorded while participants perform information retrieval tasks. Appropriate feature engineering is defined, and the feature space is explored. The results indicate that features in the window of 4 to 6 seconds after the relevance judgment for electrodermal activity, and from 1 second before to 2 seconds after the relevance judgment for corrugator supercilii activity, are associated with the users' perceived relevance of information items. A classifier verified the predictive power of the features and showed up to 14% improvement predicting relevance. Our research can help the design of intelligent user interfaces for information retrieval that can detect the user's perceived relevance from physiological signals and complement or replace conventional relevance feedback.
Genetic analysis of the human Insulin‐like 3 gene: absence of mutations in a Greek paediatric cohort with testicular maldescent

This study investigated the hypothesis that genetic alterations of the human insulin‐like 3 (INSL3) gene are associated with testicular maldescent (TMD). Genomic DNA was extracted and amplified from peripheral blood samples of 170 unrelated children with all possible phenotypical expressions of TMD and 50 volunteers with normal external genitalia from the general paediatric population (controls). PCR‐single strand conformation polymorphism analysis was used to screen INSL3 gene for genetic variants. For rapid screening of a detected nonsilent genetic alteration, restriction assay using endonuclease Eag I was further employed. Products were analysed on 2% agarose gel and restriction patterns were visualised by ethidium bromide. Differences in genotype and allelic distributions of nonsilent genetic alterations were evaluated between (i) patients–controls, (ii) familial–sporadic, (iii) bilateral–unilateral and (iv) intra‐abdominal–inguinal cases of TMD. No mutations were detected. Three common INSL3 gene polymorphisms (27G>A, 126G>A, 178G>A) unrelated to any particular phenotype of TMD were detected both in patients and controls. These results indicate that INSL3 gene mutations are not a common cause of TMD in the human.
The Incidence of Stroke by Socioeconomic Status, Age, Sex, and Stroke Subtype: A Nationwide Study in Korea

Objectives To date, studies have not comprehensively demonstrated the relationship between stroke incidence and socioeconomic status. This study investigated stroke incidence by household income level in conjunction with age, sex, and stroke subtype in Korea. Methods Contributions by the head of household were used as the basis for income levels. Household income levels for 21 766 036 people were classified into 6 groups. The stroke incidences were calculated by household income level, both overall within income categories and further by age group, sex, and stroke subtype. To present the inequalities among the six ranked groups in a single value, the slope index of inequality and relative index of inequality were calculated. Results In 2005, 57 690 people were first-time stroke patients. The incidences of total stroke for males and females increased as the income level decreased. The incidences of stroke increased as the income level decreased in those 74 years old and under, whereas there was no difference by income levels in those 75 and over. Intracerebral hemorrhage for the males represented the highest inequality among stroke subtypes. Incidences of subarachnoid hemorrhage did not differ by income levels. Conclusions The incidence of stroke increases as the income level decreases, but it differs according to sex, age, and stroke subtype. The difference in the relative incidence is large for male intracerebral hemorrhage, whereas the difference in the absolute incidence is large for male ischemic stroke.
The Effects of TMT Demographics on Large Traditional Firms' E-Business Strategy

The Internet has been changing the current ways of doing business in traditional firms. Not all the traditional firms show the same enthusiasm in e-business. Some firms’ e-business strategies are more aggressive while other firms’ e-business strategies are more conservative. This study proposes a framework to investigate whether or not the demographic characteristics of top management team (TMT) influence the aggressiveness of the large traditional firms’ e-business strategy. This study contributes to the research about the effects of TMT on IT strategy.
Age- and Sex-Dependency of Laser Speckle Flowgraphy Measurements of Optic Nerve Vessel Microcirculation

Purpose To investigate the relationship between various characteristics of a normal population and laser speckle flowgraphy (LSFG) measurements of mean blur rate (MBR) in the optic nerve head (ONH). Methods A total of 189 eyes of 189 normal subjects (93 male, 96 female, mean age 45 ± 14 years old, age range: 20–72) without any history of hypertension, hyperlipidemia or diabetes were enrolled. ONH microcirculation was measured with LSFG and overall MBR (MA), vessel-area MBR (MV), and tissue-area MBR (MT) were derived from these measurements. The statistical association of these measurements with characteristics such as sex, age, intraocular pressure (IOP) and systolic blood pressure (SBP) was then determined. Results There was a trend towards decreased IOP and MV and increased SBP with age (P = 0.002, P = 0.035, and P = 0.006, respectively). Furthermore, IOP, MV and SBP were correlated with age (r = -0.23, P = 0.011; r = -0.24, P < 0.001; and r = 0.30, P < 0.001, respectively). Separate multiple regression analyses of independent contributing factors revealed that sex and IOP contributed to MA (P < 0.001 and P = 0.002, respectively), sex, IOP, and age contributed to MV (P < 0.001, P = 0.003, and P = 0.024, respectively), while only IOP contributed to MT (P = 0.003). Conclusion In a normal population, MBR was affected by IOP in both the large vessel and capillary areas of the ONH, but not by SBP. MV was also affected by age and sex, while MT was stable independent of age or sex.
Towards appearance-based methods for lidar sensors

Cameras have emerged as the dominant sensor modality for localization and mapping in three-dimensional, unstructured terrain, largely due to the success of sparse, appearance-based techniques, such as visual odometry. However, the Achilles' heel for all camera-based systems is their dependence on consistent ambient lighting, which poses a serious problem in outdoor environments that lack adequate or consistent light, such as the Moon. Actively illuminated sensors on the other hand, such as a light detection and ranging (lidar) device, use their own light source to illuminate the scene, making them a favourable alternative in light-denied environments. The purpose of this paper is to demonstrate that the largely successful appearance-based methods traditionally used with cameras can be applied to laser-based sensors, such as a lidar. We present two experiments that are vital to understanding and enabling appearance-based methods for lidar sensors. In the first experiment, we explore the stability of a representative keypoint detection and description algorithm on both camera images and lidar intensity images collected over a 24 hour period. In the second experiment, we validate our approach by implementing visual odometry based on sparse bundle adjustment on a sequence of lidar intensity images.
Pan-Immune-Inflammation Value Could Be a New Marker to Predict Amyloidosis and Disease Severity in Familial Mediterranean Fever

Familial Mediterranean fever (FMF) is characterized by recurrent episodes of fever and serositis. Blood-based biomarkers determined in FMF patients during attack-free periods could be used to predict the risk of amyloidosis and the severity of the disease. The recently defined pan-immune-inflammation value (PIV) comprises four distinct subsets of blood cells and serves as an easily accessible and cost-effective marker. The objective of this study was to assess the role of PIV in predicting amyloidosis and moderate-to-severe disease. Clinical characteristics and laboratory values during the attack-free period were retrospectively analyzed in 321 patients over 18 years of age diagnosed with familial Mediterranean fever (FMF). In our tertiary adult rheumatology outpatient clinic, disease severity and laboratory markers were evaluated during the first attack-free interval. At baseline, patients with amyloidosis were excluded. Patients were categorized based on the presence of amyloidosis and the severity of the disease. When focusing on amyloidosis in receiver operating characteristic (ROC) analysis, optimal cut-off values for pan-immune-inflammation value (PIV), neutrophil-to-lymphocyte ratio (NLR), and platelet-to-lymphocyte ratio were determined as ≥518.1, ≥2.3, and ≥127.2, respectively. In multivariate analysis, PIV, C-reactive protein (CRP), and the presence of the M694V homozygous mutation emerged as independent risk factors for both amyloidosis and moderate-to-severe disease. Additionally, NLR was identified as an independent risk factor for amyloidosis, while red blood cell distribution width was associated with moderate-to-severe disease. In patients with FMF, especially in the presence of the M694V homozygous mutation, CRP and PIV may be useful in predicting both amyloidosis and moderate-to-severe disease.
Involvement of Polyamine Oxidase-Produced Hydrogen Peroxide during Coleorhiza-Limited Germination of Rice Seeds

Seed germination is a complicated biological process that requires regulated enzymatic and non-enzymatic reactions. The action of polyamine oxidase (PAO) produces hydrogen peroxide (H2O2), which promotes dicot seed germination. However, whether and, if so, how PAOs regulate monocot seed germination via H2O2 production is unclear. Herein, we report that the coleorhiza is the main physical barrier to radicle protrusion during germination of rice seed (a monocot seed) and that it does so in a manner similar to that of dicot seed micropylar endosperm. We found that H2O2 specifically and steadily accumulated in the coleorhizae and radicles of germinating rice seeds and was accompanied by increased PAO activity as the germination percentage increased. These physiological indexes were strongly decreased in number by guazatine, a PAO inhibitor. We also identified 11 PAO homologs (OsPAO1–11) in the rice genome, which could be classified into four subfamilies (I, IIa, IIb, and III). The OsPAO genes in subfamilies I, IIa, and IIb (OsPAO1–7) encode PAOs, whereas those in subfamily III (OsPAO8–11) encode histone lysine-specific demethylases. In silico-characterized expression profiles of OsPAO1–7 and those determined by qPCR revealed that OsPAO5 is markedly upregulated in imbibed seeds compared with dry seeds and that its transcript accumulated to a higher level in embryos than in the endosperm. Moreover, its transcriptional abundance increased gradually during seed germination in water and was inhibited by 5 mM guazatine. Taken together, these results suggest that PAO-generated H2O2 is involved in coleorhiza-limited rice seed germination and that OsPAO5 expression accounts for most PAO expression and activity during rice seed germination. These findings should facilitate further study of PAOs and provide valuable information for functional validation of these proteins during seed germination of monocot cereals.
Hereditary thrombophilia among 217 consecutive patients with thromboembolic disease in Jordan

This is a four‐year prospective study on patients admitted or referred with thromboembolic disease to Jordan University Hospital or to the Thrombosis/Haemostasis Laboratory at the University of Jordan. The aim of the study was to find the relative prevalence of hereditary thrombophilia. For the purpose of this work, hereditary thrombophilia was diagnosed in the absence of an acquired cause of thrombophilia in addition to two of the following: 1) positive family history of thrombophilia, 2) confirmed same deficiency in a closely related family member, 3) the deficient protein is constantly below 2 SD of the normal mean on repeated testing. All ages were admitted to the study. Acquired systemic factors or local factors known to cause thrombosis or affect the levels of proteins opposing thrombosis were excluded.
Non-Q-wave versus Q-wave myocardial infarction after thrombolytic therapy: angiographic and prognostic insights from the global utilization of streptokinase and tissue plasminogen activator for occluded coronary arteries-I angiographic substudy. GUSTO-I Angiographic Investigators.

BACKGROUND Although the stratification of patients with myocardial infarction into ECG subsets based on the presence or absence of new Q waves has important clinical and prognostic utility, systematic evaluation of the impact of thrombolytic therapy on the subsequent development and prognosis of non-Q-wave infarction has been limited to date. METHODS AND RESULTS We examined 12-lead ECG, coronary anatomy, left ventricular function, and mortality among 2046 patients with ST-segment elevation infarction from the Global Utilization of Streptokinase and Tissue Plasminogen Activator for Occluded Coronary Arteries angiographic subset to gain further insight into the pathophysiology and prognosis of Q- versus non-Q-wave infarction in the thrombolytic era. Non-Q-wave infarction developed in 409 patients (20%) after thrombolytic therapy. Compared with Q-wave patients, non-Q-wave patients were more likely to present with lesser ST-segment elevation in a nonanterior location. The infarct-related artery in non-Q-wave patients was more likely to be nonanterior (67% versus 58%, P=.012) and distally located (33% versus 39%, P=.021). Early (90-minute, 77% versus 65%, P=.001) and complete (54% versus 44%, P<.001) infarct-related artery patency was greater among the non-Q-wave group. Non-Q-wave patients had better global (ejection fraction, 66% versus 57%; P<.0001) and regional left ventricular function (10 versus 24 abnormal chords, P=.0001). In-hospital, 30-day, 1-year, and 2-year (6.3% versus 10.1%, P=.02) mortality rates were lower among non-Q-wave patients. CONCLUSIONS The excellent prognosis among the subgroup of patients who develop non-Q-wave infarction after thrombolysis is related to early, complete, and sustained infarct-related artery patency with resultant limitation of left ventricular infarction and dysfunction.
Brain Abscess

The epidemiology of brain abscess has changed with the increasing incidence of this infection in immunocompromised patients, particularly solid organ and bone marrow transplant recipients, and the decreasing incidence of brain abscess related to sinusitis and otitis. A number of new neuroimaging modalities, including single photon emission computed tomography, positron emission tomography, perfusion magnetic resonance imaging, and magnetic resonance spectroscopy, provide an initial noninvasive approach to diagnosis. The recommendations for the management of intracranial mass lesions in human immunodeficiency virus-infected individuals has changed as the incidence of toxoplasmic encephalitis has decreased with the use of trimethoprim-sulfamethoxazole prophylaxis. The epidemiology, pathogenesis, microbiology, clinical presentation, diagnosis, treatment and prognosis of brain abscess in the beginning of the 21 st century are provided in this review.
Homo floresiensis Contextualized: A Geometric Morphometric Comparative Analysis of Fossil and Pathological Human Samples

The origin of hominins found on the remote Indonesian island of Flores remains highly contentious. These specimens may represent a new hominin species, Homo floresiensis, descended from a local population of Homo erectus or from an earlier (pre-H. erectus) migration of a small-bodied and small-brained hominin out of Africa. Alternatively, some workers suggest that some or all of the specimens recovered from Liang Bua are pathological members of a small-bodied modern human population. Pathological conditions proposed to explain their documented anatomical features include microcephaly, myxoedematous endemic hypothyroidism (“cretinism”) and Laron syndrome (primary growth hormone insensitivity). This study evaluates evolutionary and pathological hypotheses through comparative analysis of cranial morphology. Geometric morphometric analyses of landmark data show that the sole Flores cranium (LB1) is clearly distinct from healthy modern humans and from those exhibiting hypothyroidism and Laron syndrome. Modern human microcephalic specimens converge, to some extent, on crania of extinct species of Homo. However in the features that distinguish these two groups, LB1 consistently groups with fossil hominins and is most similar to H. erectus. Our study provides further support for recognizing the Flores hominins as a distinct species, H. floresiensis, whose affinities lie with archaic Homo.
Formation in Macrophages with WASP Interacting Protein in Podosome Wiskott-Aldrich Syndrome Protein (WASP) Requirement for a Complex of

Chemotactic migration of macrophages is critical for the recruitment of leukocytes to inﬂamed tissues. Macrophages use a specialized adhesive structure called a podosome to migrate. Podosome formation requires the Wiskott-Aldrich syndrome protein (WASP), which is a product of the gene defective in an X-linked inherited immunodeﬁciency disorder, the Wiskott-Aldrich syndrome. Macrophages from WASP-deﬁcient Wiskott-Aldrich syndrome patients lack podosomes, resulting in defective chemotactic migration. However, the molecular basis for podosome formation is not fully understood. I have shown that the WASP interacting protein (WIP), a binding partner of WASP, plays an important role in podosome formation in macrophages. I showed that WASP bound WIP to form a complex at podosomes and that the knockdown of WIP impairs podosome formation. When WASP binding to WIP was blocked, podosome formation was also impaired. When WASP expression was reduced by small interfering RNA transfection, the amount of the complex of WASP with WIP decreased, resulting in reduced podosome formation. Podosomes were restored by reconstitution of the WASP-WIP complex in WASP knockdown cells. These results indicate that the WASP-WIP complex is required for podosome formation in macrophages. When podosome formation was reduced by blocking WASP binding to WIP, transendothelial migration of macrophages, the most crucial process in macrophage trafﬁcking, was impaired. These results suggest that a complex of WASP with WIP plays a critical role in podosome formation, thereby mediating efﬁcient transendothelial migration of macrophages. The Journal of Immunology, 2007, 178: 2987–2995.
piggyBac transposase tools for genome engineering

Significance DNA transposons that translocate by excision from a donor site and insertion into a target site are often used for genome engineering by insertional mutagenesis and transgenesis. The piggyBac element is especially useful because it can excise precisely from an insertion site, restoring the site to its pretransposon state. Precise excision is particularly useful when transient transgenesis is needed, for example, in the transient introduction of transcription factors for induced pluripotent stem cell production. We have used mutagenesis to generate an Excision+ Integration− transposase that allows piggyBac excision without potentially harmful reintegration. These mutations likely lie in a target DNA-binding domain. The transposon piggyBac is being used increasingly for genetic studies. Here, we describe modified versions of piggyBac transposase that have potentially wide-ranging applications, such as reversible transgenesis and modified targeting of insertions. piggyBac is distinguished by its ability to excise precisely, restoring the donor site to its pretransposon state. This characteristic makes piggyBac useful for reversible transgenesis, a potentially valuable feature when generating induced pluripotent stem cells without permanent alterations to genomic sequence. To avoid further genome modification following piggyBac excision by reintegration, we generated an excision competent/integration defective (Exc+Int−) transposase. Our findings also suggest the position of a target DNA–transposase interaction. Another goal of genome engineering is to develop reagents that can guide transgenes to preferred genomic regions. Others have shown that piggyBac transposase can be active when fused to a heterologous DNA-binding domain. An Exc+Int− transposase, the intrinsic targeting of which is defective, might also be a useful intermediate in generating a transposase whose integration activity could be rescued and redirected by fusion to a site-specific DNA-binding domain. We show that fusion to two designed zinc finger proteins rescued the Int− phenotype. Successful guided transgene integration into genomic DNA would have broad applications to gene therapy and molecular genetics. Thus, an Exc+Int− transposase is a potentially useful reagent for genome engineering and provides insight into the mechanism of transposase–target DNA interaction.
An analog VLSI multilayer perceptron and its application towards built-in self-test in analog circuits

A proof-of-concept hardware neural network for the purpose of analog built-in self-test is presented. The network is reconfigurable into any one-hidden-layer topology within the constraints of the number of inputs and neurons. Analog operation domain of synapses and neurons in conjunction with the digital weight storage allow fast computational time, low power consumption and fast training cycle. The network is trained in the chip-in-the-loop fashion with the simulated annealing-based parallel weight perturbation training algorithm. Its effectiveness in learning how to separate nominal from faulty circuits is investigated on two case studies: a Butterworth filter and an operational amplifier. The results are compared to those of the software neural networks of equivalent topologies and limitations concerning the practical applicability are discussed.