Miracle-dz/UniFAR-FTUs huggingface dataset:
Occlusion of Regulatory Sequences by Promoter Nucleosomes In Vivo

Nucleosomes are believed to inhibit DNA binding by transcription factors. Theoretical attempts to understand the significance of nucleosomes in gene expression and regulation are based upon this assumption. However, nucleosomal inhibition of transcription factor binding to DNA is not complete. Rather, access to nucleosomal DNA depends on a number of factors, including the stereochemistry of transcription factor-DNA interaction, the in vivo kinetics of thermal fluctuations in nucleosome structure, and the intracellular concentration of the transcription factor. In vitro binding studies must therefore be complemented with in vivo measurements. The inducible PHO5 promoter of yeast has played a prominent role in this discussion. It bears two binding sites for the transcriptional activator Pho4, which at the repressed promoter are positioned within a nucleosome and in the linker region between two nucleosomes, respectively. Earlier studies suggested that the nucleosomal binding site is inaccessible to Pho4 binding in the absence of chromatin remodeling. However, this notion has been challenged by several recent reports. We therefore have reanalyzed transcription factor binding to the PHO5 promoter in vivo, using ‘chromatin endogenous cleavage’ (ChEC). Our results unambiguously demonstrate that nucleosomes effectively interfere with the binding of Pho4 and other critical transcription factors to regulatory sequences of the PHO5 promoter. Our data furthermore suggest that Pho4 recruits the TATA box binding protein to the PHO5 promoter.
Molecular Characterization of Methicillin Resistant Staphylococcus aureus Isolated from Pediatrics with UTIs

Staphylococcus aureus causes a variety of severe infections such as urinary tract infections. At present, 30–50% of S. aureus isolates from Iran are methicillin resistant (MRSA). The goals of this study were to identify the distribution antibiotic resistance properties in S. aureus isolates of pediatric patients. One-hundred and fifty five urine samples were collected from pediatric patients suffered from UTIs. Samples were cultured immediately and those that were S. aureus -positive were analyzed for the presence of antibiotic resistance genes. We found that 66 out of 155 samples (42.58%) were positive for S. aureus . The highest prevalence of bacterium was seen in the cases of pyelonephritis (43.8%). S. aureus isolates had the highest antibiotic resistance against ampicillin (90.9%), tetracycline (90.9%), erythromycin (87.8%), methicillin (83.3%), oxacillin (78.7%) and trimethoprim - sulfamethoxazole (77.2%). MecA (75.7%) and aacA-D (75.7%) were the most commonly detected antibiotic resistance genes. All of the MRSA strains were also resistant against ampicillin, tetracycline and erythromycin. Totally, 54.5% of strains were PVL positive and 86.1% of PVL positive strains were resistant to methicillin. Although the frequency of MRSA isolates in the current study was intermediate, resistance to other antibiotics was high and most of the isolates were found to be MDR. Regular surveillance of hospital-associated infections and monitoring of their antibiotic sensitivity patterns are required to reduce the prevalence of MRSA.
Sketching Cuts in Graphs and Hypergraphs

Sketching and streaming algorithms are in the forefront of current research directions for cut problems in graphs. In the streaming model, we show that (1--ε)-approximation for Max-Cut must use n{1-O(ε)} space; moreover, beating 4/5-approximation requires polynomial space. For the sketching model, we show that every r-uniform hypergraph admits a (1+ ε)-cut-sparsifier (i.e., a weighted subhypergraph that approximately preserves all the cuts) with O(ε-2n(r+log n)) edges. We also make first steps towards sketching general CSPs (Constraint Satisfaction Problems).
On the formation of massive stellar clusters

Here we report on the properties of the star forming factory, in which the continuous creation of stars results into a highly concentrated, massive (globular cluster-like) stellar system. We show that under very general conditions a large-scale gravitational instability in the ISM, that triggers the collapse of a massive cloud, leads with the aid of a spontaneous rst generation of massive stars, to a standing, small radius, cold and dense shell. Eventually, as more of the collapsing matter is processed and incorporated, the shell becomes gravitationally unstable and begins to fragment, allowing for the formation of new stars. The shell keeps its standing location thanks to a detailed balance established between the ram pressure from the collapsing cloud which, together with the gravitational force excerted on the shell by the forming cluster, act against the mechanical energy deposited by the collection of new stars. The model accounts for a full analysis of feedback, as well as for the mass spectrum of fragments that result from the continuous fragmentation of the standing shell. This matches well, at both ends of the spectrum, the properties of a universal IMF. Other properties of the modelled clusters are here stressed.
Improving Vision Transformers with Novel GLU-Type Nonlinearities

—In this study we systematically investigate a range of nonlinear functions in the fully-connected feed-forward portions of Vision Transformer (ViT) machine learning models. We limit our investigation to only GLU-type nonlinear functions, as the GLU-type function SwiGLU is the current standard in state-of-the-art language and vision models. We identify 21 candidate layer functions with 1, 2, or 3 weight matrices, utilizing the activations: Sigmoid, Tanh, and Sin. ViT-Tiny models are implemented utilizing these functions and benchmarked on the image classification datasets CIFAR10, CIFAR100, and SVHN. Through these experiments we identify several previously uninvestigated functions which consistently outperform SwiGLU on all benchmarks. The most performant of these functions we call SinGLU. We further benchmark SwiGLU and SinGLU on the image classification dataset Imagenet64, and again SinGLU performs better. We note that periodic functions such as Sin are not common in neural networks. We perform a numerical investigation into sinusoidally activated neurons and suggest that their viability in Vision Transformers may be due to the loss-landscape smoothing of Layer Normalization, Multi-Headed Self Attention (MHSA), and modern data augmentations such as label smoothing. However, our experiments on the CIFAR100 dataset indicate that layer nonlinearity remains a hyperparameter, with approximately piecewise-linear functions performing better than more complex functions when the problem space is not densely sampled.
EFFECT OF STATIN THERAPY ON PLASMA HIGH‐DENSITY LIPOPROTEIN–CHOLESTEROL LEVELS IS MODIFIED BY PARAOXONASE 1 IN CHINESE PATIENTS WITH CORONARY HEART DISEASE

1 We sought to determine the effects of Q192R polymorphism of paraoxonase 1 (PON1) gene on plasma high‐density lipoprotein–cholesterol (HDL‐C) levels and the response to statin therapy in Chinese patients with coronary heart disease (CHD). 2 Two hundred and thirty‐six patients with CHD were treated with simvastatin 20 mg/day. Fasting serum lipids were determined before and after 12 weeks of treatment. 3 No significant differences were detected among the PON1 Q192R polymorphism with respect to plasma lipids. In addition, the effects of simvastatin to increase HDL‐C levels were significantly greater in patients with the RR genotype compared with patients with the QR or RR genotypes (P < 0.05). 4 We conclude that the Q192R polymorphism of PON1 significantly modulates the HDL‐C response to simvastatin in Chinese patients with CHD.
Physical Exercise Combined with Whole-Body Cryotherapy in Evaluating the Level of Lipid Peroxidation Products and Other Oxidant Stress Indicators in Kayakers

The influence of exercise combined with whole-body cryotherapy (WBC) on the oxidant/antioxidant balance in healthy men was assessed. The study included 16 kayakers of the Polish National Team, aged 22.7 ± 2.6, subjected to WBC (−120°C–−145°C; 3 min) twice a day for the first 10 days of a 19-day physical training cycle: pre exercise morning stimulation and post exercise afternoon recovery. Blood samples were taken on Day 0 (baseline) and on Days 5, 11 and 19. The serum concentration of malondialdehyde (MDA), conjugated dienes (CD), thiobarbituric acid reactive substances (TBARS), protein carbonyls, vitamin E, urea, cortisol, and testosterone were determined, along with the glutathione peroxidase (GPx) activity, the total antioxidant capacity (TAC), and morphological blood parameters. On 5th day of exercise/WBC, the baseline GPx activity decreased by 15.1% (P < 0.05), while on 19th day, it increased by 19.7% (P < 0.05) versus Day 5. On Day 19 TBARS concentration decreased versus baseline and Day 5 (by 15.9% and 17.4%, resp.; P < 0.01). On 19 Day urea concentration also decreased versus 11 Day; however, on 5th and 11th days the level was higher versus baseline. Combining exercise during longer training cycles with WBC may be advantageous.
The memory glasses: subliminal vs. overt memory support with imperfect information

Wearables are frequently designed to support users engagedin complex "real world" activities, ranging from foodinspection to ground combat. Unfortunately, wearablesalso have the potential to interfere with the very tasks theyare designed to support, either by distracting the user orproviding them with misleading information.In 2002 we published a pilot study suggesting that asubliminal visual cuing system might be an effective low-attentioninteraction strategy for just-in-time memory support.In this paper we present the results of a larger studydemonstrating that not only is wearable subliminal cuingsignificantly effective (increasing performance by a factorof approximately 1.5, p = 0.02), but even incorrect subliminalcues can actually improve performance. By contrast,consciously-visible incorrect cues caused performance todegrade.
Relative Periodicity of Empirical Audio Samples With Application Relative Periodicity of Empirical Audio Samples With Application to Dissonance Perception to Dissonance Perception

The concept of dissonance in music perception has been variously associated with the physical concepts of roughness, instability, and tension by appealing to a subjective cross-sensory analogy. For all the subjectivity around the term, it is noteworthy that non-musical test subjects in clinical experiments have produced remarkably consistent rank-orderings of musical sounds, according to the perceived dissonance of those sounds. Further studies in psychology, neuroscience, and mathematics show that consonance perception appears to be influenced not only by convention and culture but by the psychoacoustics of sound perception, likely by some combination of the Helmholtz theory of roughness and the theory of harmonicity originally contemplated by Galilei. In this work, we elaborate on Stolzenburg’s relative periodicity, a harmonicity metric that can be computed in the time domain by neuronal systems. We aim to determine whether relative periodicity can be extended from pure sinusoids to empirical audio signals, and whether such extension would still yield dissonance rankings that comport with the known experimental perceptions of dissonance. By drawing on the theory of quasi-periodic signals, we show that the relative periodicities of many familiar dyads and triads agree with Stolzenburg’s calculations and experimental dissonance rankings. However, we also observe substantial departures from Stolzen-burg’s work in the case of the most highly empirically dissonant dyads and the diminished triads. This discrepancy likely supports the work of Masina et al. that found periodicity unable to fully explain empirical studies of dyad dissonance.
Speaking and listening on the run: design for wearable audio computing

The use of speech and auditory interaction on wearable computers can provide an awareness of events and personal messages, without requiring one's full attention or disrupting the foreground activity. A passive "hands-and-eyes-free" approach is appropriate when users need convenient and timely access to remote information and communication services. Nomadic Radio is a distributed computing platform for wearable access to unified messaging via an auditory interface. We demonstrate the use of auditory cues, spatialized audio, and speech I/O in the wearable interface for passive awareness, scaleable notification and navigation/control. The architecture is designed for wired audio wearables and has been extended for distributed wireless operation.
Performance in the Wisconsin Card Sorting Test and the C957T Polymorphism of the DRD2 Gene in Healthy Volunteers

Introduction: Previous studies have associated a decreased striatal D2 dopamine receptor (DRD2) binding with impaired performance in cognitive tasks. In vivo studies have found a lower DRD2 binding associated with the CC genotype of the C957T single nucleotide polymorphism (SNP) of the DRD2 gene. Objective: The aim of this study was to investigate the relationship between executive functions and the C957T DRD2 SNP. We hypothesized that the CC genotype would be associated with a poorer executive functioning. Methods: Our sample consisted of 83 healthy volunteers (28 males and 55 females; mean age 25.2, SD 1.7 years). To assess executive functions, the Wisconsin Card Sorting Test was used, considering the variables perseverative errors, perseverative responses, and number of categories achieved. The genotype distribution was 13 CC, 41 CT, and29 TT, satisfying Hardy-Weinberg equilibrium. Results: Carriers of the CC genotype, compared with carriers of the CT/TT genotypes, achieved significantly fewer categories (5.00 vs. 5.81; p = 0.004), made a greater number of perseverative errors (13.46 vs. 8.39; p = 0.018), and had a greater number of perseverative responses (14.92 vs. 8.94; p = 0.014). Conclusions: Our results support the hypothesis that the C957T DRD2 SNP may influence cognitive performance through its repercussions on central dopaminergic function.
Assessment of Some Physiological Parameters and HAK1-type Transporter Transcriptional Changes in Aeluropus littoralis under NaCl Stress

Maintenance of internal status of K + ion is one of the important mechanisms for regulation of potassium balance under salt stress. In the present study, we use Aeluropus littoralis as a halophytic monocot model to investigate transcriptional changes in HAK1 gene that code a H + -K + transporter for acquire potassium under condition of limited availability of K + and also measurement of some physiological parameters such as Dry weight, Ash and K + content, Photosynthetic pigments and Carbohydrate content under salt stress. The Comparison of HAK1 gene expression in pattern in shoot and root revealed that transcript levels of HAK1 in shoot induced by salt androot contained less levels of HAK1 mRNA than shoot at high concentrations of NaCl. Our results suggest that HAK1-type transporters can play an important role in potassium uptake and cell internal diffusion of K + ion to tissue that can be effective in salt tolerance in this grass.
Effect of a combined education and eHealth programme on the control of oral anticoagulation patients (PORTALS study): a parallel cohort design in Dutch primary care

Objectives To analyse the effect on therapeutic control and self-management skills of the implementation of self-management programmes, including eHealth by e-learning versus group training. Setting Primary Care Thrombosis Service Center. Participants Of the 247 oral anticoagulation therapy (OAT) patients, 63 started self-management by e-learning, 74 self-management by group training and 110 received usual care. Intervention and methods Parallel cohort design with two randomised self-management groups (e-learning and group training) and a group receiving usual care. The effect of implementation of self-management on time in therapeutic range (TTR) was analysed with multilevel linear regression modelling. Usage of a supporting eHealth platform and the impact on self-efficacy (Generalised Self-Efficacy Scale (GSES)) and education level were analysed with linear regression analysis. After intervention, TTR was measured in three time periods of 6 months. Main outcome measures (1) TTR, severe complications,(2) usage of an eHealth platform,(3) GSES, education level. Results Analysis showed no significant differences in TTR between the three time periods (p=0.520), the three groups (p=0.460) or the groups over time (p=0.263). Comparison of e-learning and group training showed no significant differences in TTR between the time periods (p=0.614), the groups (p=0.460) or the groups over time (p=0.263). No association was found between GSES and TTR (p=0.717) or education level and TTR (p=0.107). No significant difference was found between the self-management groups in usage of the platform (0–6 months p=0.571; 6–12 months p=0.866; 12–18 months p=0.260). The percentage of complications was low in all groups (3.2%; 1.4%; 0%). Conclusions No differences were found between OAT patients trained by e-learning or by a group course regarding therapeutic control (TTR) and usage of a supporting eHealth platform. The TTR was similar in self-management and regular care patients. With adequate e-learning or group training, self-management seems safe and reliable for a selected proportion of motivated vitamin K antagonist patients. Trial registration number NTR3947.
Multimode Control Attacks on Elections

In 1992, Bartholdi, Tovey, and Trick [1992] opened the study of control attacks on elections--attempts to improve the election outcome by such actions as adding/deleting candidates or voters. That work has led to many results on how algorithms can be used to find attacks on elections and how complexity-theoretic hardness results can be used as shields against attacks. However, all the work in this line has assumed that the attacker employs just a single type of attack. In this paper, we model and study the case in which the attacker launches a multipronged (i.e., multimode) attack. We do so to more realistically capture the richness of reallife settings. For example, an attacker might simultaneously try to suppress some voters, attract new voters into the election, and introduce a spoiler candidate. Our model provides a unified framework for such varied attacks, and by constructing polynomial-time multiprong attack algorithms we prove that for various election systems even such concerted, flexible attacks can be perfectly planned in deterministic polynomial time.
Control of contractile properties within adaptive ranges by patterns of impulse activity in the rat

These experiments explore the relationship between patterned impulse activity and contractile properties of skeletal muscles. Soleus (SOL) and extensor digitorum longus (EDL) muscles of adult rats were denervated and stimulated directly from 4 to 15 weeks with the same number of pulse trains at different intratrain pulse frequencies (1–500 Hz), with different numbers of pulse trains (864–4,320,000 pulses/d) at the same intratrain pulse frequencies, or with different combinations of pulse trains at 10 and 100 Hz. Chronic stimulation of the denervated SOL resulted in twitch times-to-peak and half-relaxation times that varied in a graded manner between values longer than those in the normal SOL to values as fast as those in the normal EDL, depending upon the pattern used. Increasing pulse frequencies (constant number) resulted in faster twitches, lower twitch/tetanus ratios, increasing post-tetanic potentiations, and larger tetanic tensions. Increasing pulse numbers (constant frequencies) resulted in slower twitches, lower twitch/tetanus ratios, post-tetanic depressions, and higher fatigue indices. The effect of varying the pulse number on twitch parameters was greater at low frequencies (10–20 Hz) than at high frequencies (100 Hz). SOL muscles receiving pulse trains at both 10 and 100 Hz became much faster than muscles receiving pulse trains at 10 Hz only, even in the experiments where the stimulation pattern contained 9 times as many pulses at 10 as at 100 Hz. Chronic stimulation of both the denervated and the innervated EDL with large numbers of pulses at 10 or 15 Hz resulted in twitches that were only half as slow as those induced in the SOL by the same “slow” patterns. In addition, these patterns led to a marked decrease in maximum tetanic tension and a marked increase in twitch/tetanus ratio. During stimulation with a small number of pulses at 150 Hz, on the other hand, twitch speed, twitch/tetanus ratio, and maximum tetanic tension remained normal or almost normal. We conclude that the isometric twitch and related properties of the rat SOL muscle can be graded within wide “adaptive ranges” by varying either the number or the frequency of pulses. In the EDL, the corresponding adaptive ranges appear much narrower, suggesting that the EDL and the SOL contain intrinsically different muscle fibers.
Magnetic Domain State Diagnosis in Soils, Loess, and Marine Sediments From Multiple First‐Order Reversal Curve‐Type Diagrams

First‐order reversal curve (FORC) diagrams provide information about domain states and magnetostatic interactions that underpin paleomagnetic interpretations. FORC diagrams are a complex representation of remanent, induced, and transient magnetizations that can be assessed individually using additional FORC‐type measurements along with conventional measurements. We provide the first extensive assessment of the information provided by remanent, transient, and induced FORC diagrams for a diverse range of soil, loess/paleosol, and marine sediment samples. These new diagrams provide substantial information in addition to that provided by conventional FORC diagrams that aids comprehensive domain state diagnosis for mixed magnetic particle assemblages. In particular, we demonstrate from transient FORC diagrams that particles occur routinely in the magnetic vortex state. Likewise, remanent FORC diagrams provide information about the remanence‐bearing magnetic particles that are of greatest interest in paleomagnetic studies.
Waveguide power combiner with adjustable amplitude and phase response

Maximum gain from combining multiple high-power signals is achieved by equalising both the amplitude and phase of the combination. Achieving in-phase and equal amplitude power combining with amplifiers of unequal gain and group delay requires compensation by means of delay lines and external gain adjustment. This paper proposes an improved X-band waveguide H-plane cross-guide combiner which allows for post-production adjustment of the combining power ratio, as well as equalization of the phase responses. This adjustment capability allows for mass-production of the combiner, irrespective of the exact phase and gain characteristics of individual amplifiers. The nominally equal amplitude combining ratio is shown to be adjustable by ±0.4 dB over 400 MHz bandwidth at X-band, whilst the phase difference may be altered, independently from the amplitude response, from -2.52° to +2.52°. Good agreement is found between simulated and measured results.
Efficient Code Construction for Certain Two-Dimensional Constraints

Efficient encoding algorithms are presented for two types of constraints on two-dimensional binary arrays. The first constraint considered is that of t-conservative arrays, where each row and each column has at least t transitions of the form '0'/spl rarr/'1' or '1'/spl rarr/'0. ' The second constraint is that of two-dimensional DC-free arrays, where in each row and each column the number of '0's equals the number of '1's.