Miracle-dz/UniFAR-FTUs huggingface dataset:
The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for the topological analysis of scalar data in scientific visualization. While topological data analysis has gained in popularity over the last two decades, it has not yet been widely adopted as a standard data analysis tool for end users or developers. TTK aims at addressing this problem by providing a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependency-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code. online documentation and video tutorials are available on TTK's website [108].
Profit Maximization for Online Advertising Demand-Side Platforms

We develop an optimization model and corresponding algorithm for the management of a demand-side platform (DSP), whereby the DSP aims to maximize its own profit while acquiring valuable impressions for its advertiser clients. We formulate the problem of profit maximization for a DSP interacting with ad exchanges in a real-time bidding environment in a cost-per-click/cost-per-action pricing model. Our proposed formulation leads to a nonconvex optimization problem due to the joint optimization over both impression allocation and bid price decisions. We use Lagrangian relaxation to develop a tractable convex dual problem, which, due to the properties of second-price auctions, may be solved efficiently with subgradient methods. We propose a two-phase solution procedure, whereby in the first phase we solve the convex dual problem using a subgradient algorithm, and in the second phase we use the previously computed dual solution to set bid prices and then solve a linear optimization problem to obtain the allocation probability variables. On several synthetic examples, we demonstrate that our proposed solution approach leads to superior performance over a baseline method that is used in practice.
Electromagnetic effects in atmosphere, ionosphere and magnetosphere initiated by earthquake preparation process

It was established that the final stage of the earthquake preparation cycle is a complex chain of interactions between the geospheres and energy transformations where the electromagnetic processes play an important role [1]. The main and most important one - it is electromagnetic coupling between the ground surface and ionosphere leading to generation of ionospheric anomalies over the earthquake preparation area through the local modification of the Global Electric Circuit [2]. But on the way from the ground up the ionosphere and magnetosphere a lot of electromagnetic interactions of the smaller scale take place including the generation of electromagnetic emissions at different frequency bands and different altitudes, anomalies of the radio waves propagation of different frequencies, wave-particle interactions, aerosol layers electrification and electric discharges, electromagnetic effects in space plasma, etc. [3, 4]. The present paper concentrates on systematization of these lower scale electromagnetic effects leaving the ionospheric anomalies to other author's discussion.
The attribution of personality traits: the stutterer and nonstutterer.

Three videotaped recordings were made of an adult male speaking in an interview situation. Tapes differed as a function of the fluency exhibited by the interviewed speaker (i.e., fluent speech, primary stuttering, secondary stuttering). Three audiotapes were recorded from the videotapes yielding six stimulus tapes. Independent groups of college students saw and/or heard one of the stimulus tapes, each described as an interview with a "male who stutters. " The fluent audio- and videotapes were replayed to two additional groups but were described only as an interview with a "male. " Groups rated the personality of the speaker after tape presentation. Results revealed no difference in personality trait assignment as a function of experimental variables. However, in a second experiment two groups of college students rated a hypothetical normal speaker and hypothetical stutterer as significantly different in personality attributes. Results are discussed with reference to stereotyping behavior.
Reduced left ventricular relaxation velocity after acute myocardial infarction.

Diastolic left ventricular function is usually described using Doppler recording of the early to atrial (E/A) ratio. However, because of pseudonormalization in patients with moderately impaired diastolic function, the E/A ratio does not allow a meaningful comparison between a group of patients with varying degrees of dysfunction, e.g. after acute myocardial infarction (AMI), and a group of healthy control subjects. In this study, diastolic function was assessed using the E/A ratio, deceleration time of early mitral inflow and maximal longitudinal relaxation velocity. The relaxation velocity was measured using echocardiographic M-mode recording of mitral annulus motion. Mitral annulus motion was recorded in four- and two-chamber views. Relaxation velocities were measured in the septal, lateral, anterior and posterior parts of the mitral annulus and the mean value (RVm) was calculated. Twenty-two consecutive patients were investigated 3-21 days after first transmural AMI. Twenty-two healthy subjects of similar age served as a control group. The group of patients with AMI had an RVm of 40.9 +/- 15.4 mm s-1 compared with 68.5 +/- 12.4 mm s-1 in the control group (P < 0.0001). In contrast, the E/A ratio, deceleration time and heart rate did not differ significantly between the two groups. The results suggest that maximal longitudinal relaxation velocity is a simple and appropriate measure of diastolic function in patients with transmural AMI.
Variations in carotid arterial compliance during the menstrual cycle in young women

The effect of menstrual cycle phase on arterial elasticity is controversial. In 10 healthy women (20.6 ± 1.5 years old, mean ±s.d.), we investigated the variations in central and peripheral arterial elasticity, blood pressure (carotid and brachial), carotid intima–media thickness (IMT), and serum oestradiol and progesterone concentrations at five points in the menstrual cycle (menstrual, M; follicular, F; ovulatory, O; early luteal, EL; and late luteal, LL). Carotid arterial compliance (simultaneous ultrasound and applanation tonometry) varied cyclically, with significant increases from the values seen in M (0.164 ± 0.036 mm2 mmHg−1) and F (0.171 ± 0.029 mm2 mmHg−1) to that seen in the O phase (0.184 ± 0.029 mm2 mmHg−1). Sharp declines were observed in the EL (0.150 ± 0.033 mm2 mmHg−1) and LL phases (0.147 ± 0.026 mm2 mmHg−1; F= 8.51, P < 0.05). Pulse wave velocity in the leg (i.e. peripheral arterial stiffness) did not exhibit any significant changes. Fluctuations in carotid arterial elasticity correlated with the balance between oestradiol and progesterone concentrations. No significant changes were found in carotid and brachial blood pressures, carotid artery lumen diameter, or IMT throughout the menstrual cycle. These data provide evidence that the elastic properties of central, but not peripheral, arteries fluctuate significantly with the phases of the menstrual cycle.
Context Surrounding Processing Sites Is Crucial in Determining Cleavage Rate of a Subset of Processing Sites in HIV-1 Gag and Gag-Pro-Pol Polyprotein Precursors by Viral Protease*

Background: Processing of HIV-1 Gag/Gag-Pro-Pol polyprotein by viral protease is an essential step to produce infectious virus particle. Results: Processing of CA/SP1, SP1/NC, and SP2/p6 sites by HIV-1 protease are affected by context. Conclusion: Complex substrate interactions beyond the active site of the enzyme define HIV-1 processing rate. Significance: This study helps to understand role of context outside cleavage sites in HIV-1 processing. Processing of the human immunodeficiency virus type 1 (HIV-1) Gag and Gag-Pro-Pol polyproteins by the HIV-1 protease (PR) is essential for the production of infectious particles. However, the determinants governing the rates of processing of these substrates are not clearly understood. We studied the effect of substrate context on processing by utilizing a novel protease assay in which a substrate containing HIV-1 matrix (MA) and the N-terminal domain of capsid (CA) is labeled with a FlAsH (fluorescein arsenical hairpin) reagent. When the seven cleavage sites within the Gag and Gag-Pro-Pol polyproteins were placed at the MA/CA site, the rates of cleavage changed dramatically compared with that of the cognate sites in the natural context reported previously. The rate of processing was affected the most for three sites: CA/spacer peptide 1 (SP1) (≈10-fold increase), SP1/nucleocapsid (NC) (≈10–30-fold decrease), and SP2/p6 (≈30-fold decrease). One of two multidrug-resistant (MDR) PR variants altered the pattern of processing rates significantly. Cleavage sites within the Pro-Pol region were cleaved in a context-independent manner, suggesting for these sites that the sequence itself was the determinant of rate. In addition, a chimera consisting of SP1/NC P4–P1 and MA/CA P1′–P4′ residues (ATIM↓PIVQ) abolished processing by wild type and MDR proteases, and the reciprocal chimera consisting of MA/CA P4–P1 and SP1/NC P1′–4′ (SQNY↓IQKG) was cleaved only by one of the MDR proteases. These results suggest that complex substrate interactions both beyond the active site of the enzyme and across the scissile bond contribute to defining the rate of processing by the HIV-1 PR.
Knowledge, attitudes, and self-efficacy and compliance with medical regimen, number of emergency department visits, and hospitalizations in adults with asthma.

PURPOSE The purpose of this study was to examine the relationship between knowledge, attitudes, and self-efficacy and compliance with prescribed medical regimen, number of emergency department (ED) visits, and hospitalizations in adults with asthma. METHOD The sample consisted of 29 adults with a diagnosis of asthma. The relationship among knowledge, attitudes, self-efficacy, and compliance with medical regimen was explored through use of a survey design. The Knowledge, Attitude, and Self-Efficacy Asthma Questionnaire and the Asthma Management Questionnaire that measured compliance were mailed to subjects' homes. Once completed, questionnaires were returned, and demographic data and number of ED visits and hospitalizations were obtained through a retrospective chart review. RESULTS There was a significant correlation between knowledge and attitudes and knowledge and self-efficacy. The more positive persons' attitudes toward their asthma, the higher their knowledge and self-efficacy scores. There were significant correlations between select demographic variables and knowledge, attitude, and self-efficacy. Women scored higher on attitudes, persons with a college education scored higher on knowledge and attitudes, and persons with mild asthma scored highest on the self-efficacy scale. Compliance with use of peak-flow meters correlated with higher scores on the attitude and self-efficacy scales. The higher total compliance score group had significantly higher self-efficacy scores. In addition, higher self-efficacy scores correlated with lower numbers of hospitalizations. CONCLUSION Attitudes and self-efficacy rather than knowledge had the most significant impact on compliance and number of ED visits and hospitalizations. The Knowledge, Attitude, and Self-Efficacy Asthma Questionnaire provides a means for nurses to assess patients' knowledge, attitudes, and self-efficacy regarding their asthma. Patients with low scores could be channeled into programs that would help them improve their ability to manage their asthma.
Nonlinear Jaynes-Cummings dynamics of a trapped ion.

We show that the vibronic motion of a trapped ion far from the Lamb-Dicke regime can be described, under appropriate resonance conditions, by a strongly nonlinear, multiquantum Jaynes-Cummings model. In contrast to previous nonlinear or multiphoton generalizations of the Jaynes-Cummings model, it could presently be realized in experiments.
Interleukin-1 cluster combined genotype and restenosis after balloon angioplasty

Summary The interleukin-1 system is fundamentally involved in the pathogenesis of restenosis after percutaneous transluminal angioplasty (PTA). In order to further define the clinical impact of genetic variation in this potent proinflammatory pathway we investigated the joint effects of two single nucleotide polymorphisms in the interleukin-1 beta gene [IL-1B(–511) and IL-1B(+3954)] and a variable number tandem repeat polymorphism in intron 2 of the interleukin 1 receptor antagonist gene (IL-1RN VNTR) on postintervention inflammation and occurrence of restenosis in 183 consecutive patients who underwent successful femoropopliteal PTA. C-reactive protein (CRP) and serum amyloid A (SAA) were determined pre- and 48 hours postintervention. Patients were followed up to 12 months for the occurrence of postangioplasty restenosis (≥50 %). When analyzed separately, none of the polymorphisms was associated either with inflammation or restenosis. However, when the IL-1B (–511) and the IL-1RN VNTR genotypes were combined, a highly significant relationship was observed: Non-carriers of the two repeat allele of the IL-1RN VNTR (IL-1RN*2) who were heterozygous and homozygous for the IL-1B (–511)T allele exhibited a gradually increased inflammatory response and a higher restenosis risk. In contrast, carriers of the IL-1RN*2 and the IL-1B (–511)T allele showed a significantly better outcome. This remarkable gene dose-dependent association emphasizes the advantage of considering combinations of genetic markers rather that isolated polymorphisms in the analysis of multifactorial vascular disease.
Avidity as a Determinant of the Protective Efficacy of Human Antibodies to Pneumococcal Capsular Polysaccharides

ABSTRACT Antibodies reactive with capsular polysaccharides are considered the principal mediators of immunity against invasive diseases caused byStreptococcus pneumoniae. In this study, we tested the hypothesis that anti-pneumococcal capsular polysaccharide (PPS) antibody avidity can influence protective efficacy. We measured the avidities of individual adult postvaccination immunoglobulin G2 (IgG2) antibodies to PPS serotypes 6B and 23F and examined the relationship between avidity and opsonophagocytic and mouse-protective activities. The avidities of PPS 6B- and PPS 23F-specific IgG2 antibodies ranged from 6 to 31 nM−1 and from 3 to 20 nM−1, respectively. We observed an inverse correlation between the magnitude of avidity and the amount of antibody required to protect mice against lethal bacteremia caused by serotype 6B pneumococci. Similarly, higher-avidity antibodies were more effective than lower-avidity antibodies in vitro in mediating complement-dependent opsonophagocytosis of both 6B and 23F pneumococci. These data suggest that in adults, PPS antibodies are sufficiently polymorphic to possess biologically significant variations in avidity. We conclude that avidity functions as an important determinant of anticapsular antibody protective efficacy against pneumococci.
Reporting altered test results in hemolyzed samples: is the cure worse than the disease?

Abstract The management of laboratory data in unsuitable (hemolyzed) samples remains an almost unresolved dilemma. Whether or not laboratory test results obtained by measuring unsuitable specimens should be made available to the clinicians has been the matter of fierce debates over the past decades. Recently, an intriguing alternative to suppressing test results and recollecting the specimen has been put forward, entailing the definition and implementation of specific algorithms that would finally allow reporting a preanalytically altered laboratory value within a specific comment about its uncertainty of measurement. This approach carries some advantages, namely the timely communication of potentially life-threatening laboratory values, but also some drawbacks. These especially include the challenging definition of validated performance specifications for hemolyzed samples, the need to producing reliable data with the lowest possible uncertainty, the short turnaround time for repeating most laboratory tests, the risk that the comments may be overlooked in short-stay and frequently overcrowded units (e.g. the emergency department), as well as the many clinical advantages of a direct communication with the physician in charge of the patient. Despite the debate remains open, we continue supporting the suggestion that suppressing data in unsuitable (hemolyzed) samples and promptly notifying the clinicians about the need to recollect the samples remains the most (clinically and analytically) safe practice.
Bit-interleaved coded modulation in linear dispersion coded MIMO system over spatially correlated Rician fading channel

A multiple-input multiple-output (MIMO) system with serially concatenated bit-interleaved coded modulation (BICM) and linear dispersion code (LDC) is investigated. LDC is a member of the family of linear space-time block codes STBC. A tight upper bound for this system over a spatially correlated Rician fading channel is derived, based on the moment generation function (MGF) approach. We utilize this bound to study the impact of the propagation environment features, such as the Rician factor, geometry of the Rician component, and transmit and receive antenna correlation, on the performance of a bit-interleaved convolutional-coded LDC MIMO system.
The importance of hygiene in the domestic kitchen: Implications for preparation and storage of food and infant formula

Aims: Public concerns relating to food safety remain high with most attention focused on manufactured foods and those served in catering operations. However, previous data have suggested that the home may be the main location for cases of food-borne disease. The aim of this paper is to review the microbiological risks associated with hygiene in the domestic kitchen related to food and infant formula safety. Methods: Compared to other food sectors, research on consumer food hygiene, domestic food-handling and preparation of infant formula is relatively understudied. Behavioural and microbiological studies of consumer hygiene and the domestic kitchen have been reviewed to incorporate research relating to the safety of infant formula. Results: Incidence data identify the home as an important location for acquiring food-borne disease. The domestic kitchen can be used for a variety of purposes and is often contaminated with potentially harmful micro-organisms such as Campylobacter and Salmonella. Consumer hygiene habits have frequently been found to be inadequate and relate both to microbial growth, survival and cross-contamination. Due to the reduced immune response of infants, the activities associated with the preparation of infant formula and associated bottles and equipment are of particular concern. Conclusions: Cumulatively, the data suggest that more effort should be made to educate the consumer in food hygiene, especially when the kitchen is used to reconstitute infant formula. This information needs to be provided in a form appropriate for use by consumers.
Evidence for different aetiologies of low estradiol response to FSH: age-related accelerated luteinization of follicles or presence of ovarian autoantibodies.

BACKGROUND We found granulosa cells of low responders (LR) expressed more LH receptors, suggesting that follicles were more luteinized than normal responders (NR). The objectives were to test the hypothesis that follicles of LR were more luteinized than follicles of NR, and to determine if LR with (LR+) and without (LR-) ovarian antibodies differed. METHODS Hormone levels and ovarian autoantibodies (OVAB) were measured in follicular fluid from mature follicles (>17 mm), and in serum obtained on the day of oocyte retrieval during controlled ovarian stimulation. The gonadotrophin response was defined as a ratio of peak estradiol/number of FSH ampoules. RESULTS NR (32.5 +/- 4.6 years; n = 11) were similar in age to LR+ (33.4 +/- 4.2 years; n = 9) and were younger than LR- (37.1 +/- 3.8 years; n = 12) (P = 0.03). Likewise, dehydroepiandrosterone sulphate was lower in LR- compared with LR+ or NR (P < 0.01). FSH, progesterone, inhibin-A and vascular endothelial growth factor levels were higher in follicular fluid of LR than NR. LR- and LR+ differed. For example, the follicular fluid progesterone/estradiol ratio was similar in NR (11.1 +/- 8.9) and LR+ (9.8 +/- 6.6) but was lower than LR- (22.9 +/- 19.6) (P = 0.05). Serum hormone levels did not reflect follicular fluid hormone profiles. CONCLUSIONS In the absence of ovarian antibodies, low responses are associated with higher age and accelerated luteinization of mature follicles, rather than diminished responsiveness. Ovarian antibody may be an additional tool to predict and individualize treatment regimens in poor responders.
Mechanomyography and electromyography during and after fatiguing shoulder eccentric contractions in males and females

The aim of this study was to investigate changes in mechanomyographic (MMG) and the surface electromyographic (EMG) signals during and after fatiguing shoulder eccentric contractions in a group consisting of 12 males and 12 females. Exerted force, MMG, EMG, pain and rate of perceived exertion were assessed before, during and after repeated high‐intensity eccentric exercises. Bouts of eccentric contractions caused a decrease in the exerted force for males (P<0.05) and an increase in the rate of perceived exertion and pain for both genders (P<0.05). During eccentric exercise, the root mean square (RMS) values of the MMG signal increased (P<0.05). The mean power frequency (MPF) values of the EMG signal decreased at the end of each eccentric bout for both genders (P<0.05); the decrease was higher for females compared with males (P<0.05). Immediately after eccentric exercise in static abduction of the upper limbs, the MMG RMS and MPF values increased (P<0.05). The present study showed that (1) neuromuscular changes associated with pain and changes in muscle stiffness and (2) changes in motor units strategy during fatigue development in shoulder muscle are reflected in the MMG and EMG signals.