Miracle-dz/UniFAR-FTUs huggingface dataset:
MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast

Abstract The first nucleosomes in the downstream of transcription starting sites are called +1 nucleosomes, which are expected to be readily unwrapped for DNA transcription. To investigate DNA accessibility in +1 nucleosomes, MNase-seq experiments were carried out with 20 reconstituted +1 nucleosomes of budding yeast. Although MNase has been known for its sequence preference in DNA digestions, we confirmed that this sequence preference is overwhelmed by DNA accessibility by identifying the sequence-driven and accessibility-driven cleavages. Specifically, we find that sequences favoured by MNase at the end regions such as TA dinucleotide are prohibited from cleavage at the internal sites in the early stage of digestion. Nevertheless, sequences less favoured by MNase at the end regions such as AA/TT dinucleotide are predominantly cleaved at the internal sites in the early stage of digestion. Since AA/TT is known as a rigid dinucleotide step resistant to DNA bending, these internal cleavages reflect the local site exposures induced by DNA mechanics. As the DNA entry site of +1 nucleosomes in yeast is found AA/TT-rich, this sequence element may play a role in gene activation by reducing DNA–histone affinities along the direction of DNA transcription.
Continuous and orientation-preserving correspondences via functional maps

We propose a method for efficiently computing orientation-preserving and approximately continuous correspondences between non-rigid shapes, using the functional maps framework. We first show how orientation preservation can be formulated directly in the functional (spectral) domain without using landmark or region correspondences and without relying on external symmetry information. This allows us to obtain functional maps that promote orientation preservation, even when using descriptors, that are invariant to orientation changes. We then show how higher quality, approximately continuous and bijective pointwise correspondences can be obtained from initial functional maps by introducing a novel refinement technique that aims to simultaneously improve the maps both in the spectral and spatial domains. This leads to a general pipeline for computing correspondences between shapes that results in high-quality maps, while admitting an efficient optimization scheme. We show through extensive evaluation that our approach improves upon state-of-the-art results on challenging isometric and non-isometric correspondence benchmarks according to both measures of continuity and coverage as well as producing semantically meaningful correspondences as measured by the distance to ground truth maps.
Cerebellar synapse properties and cerebellum-dependent motor and non-motor performance in Dp71-null mice

ABSTRACT Recent emphasis has been placed on the role that cerebellar dysfunctions could have in the genesis of cognitive deficits in Duchenne muscular dystrophy (DMD). However, relevant genotype-phenotype analyses are missing to define whether cerebellar defects underlie the severe cases of intellectual deficiency that have been associated with genetic loss of the smallest product of the dmd gene, the Dp71 dystrophin. To determine for the first time whether Dp71 loss could affect cerebellar physiology and functions, we have used patch-clamp electrophysiological recordings in acute cerebellar slices and a cerebellum-dependent behavioral test battery addressing cerebellum-dependent motor and non-motor functions in Dp71-null transgenic mice. We found that Dp71 deficiency selectively enhances excitatory transmission at glutamatergic synapses formed by climbing fibers (CFs) on Purkinje neurons, but not at those formed by parallel fibers. Altered basal neurotransmission at CFs was associated with impairments in synaptic plasticity and clustering of the scaffolding postsynaptic density protein PSD-95. At the behavioral level, Dp71-null mice showed some improvements in motor coordination and were unimpaired for muscle force, static and dynamic equilibrium, motivation in high-motor demand and synchronization learning. Dp71-null mice displayed altered strategies in goal-oriented navigation tasks, however, suggesting a deficit in the cerebellum-dependent processing of the procedural components of spatial learning, which could contribute to the visuospatial deficits identified in this model. In all, the observed deficits suggest that Dp71 loss alters cerebellar synapse function and cerebellum-dependent navigation strategies without being detrimental for motor functions. Summary: Dp71 is the most prominent dystrophin gene product in the adult brain. Here, multiple approaches including behavioral tests and electrophysiology are adopted to explore the role of Dp71 in the cerebellum.
Motor Control Changes in Low Back Pain: Divergence in Presentations and Mechanisms.

SYNOPSIS Compared to healthy individuals, patients with low back pain demonstrate differences in all aspects of trunk motor control that are most often studied as differences in muscle activity and kinematics. However, differences in these aspects of motor control are largely inconsistent. We propose that this may reflect the existence of 2 phenotypes or possibly the ends of a spectrum, with "tight control" over trunk movement at one end and "loose control" at the other. Both may have beneficial effects, with tight control protecting against large tissue strains from uncontrolled movement and loose control protecting against high muscle forces and resulting spinal compression. Both may also have long-term negative consequences. For example, whereas tight control may cause high compressive loading on the spine and sustained muscle activity, loose control may cause excessive tensile strains of tissues. Moreover, both phenotypes could be the result of either an adaptation process aimed at protecting the low back or direct interference of low back pain and related changes with trunk motor control. The existence of such phenotypes would suggest different motor control exercise interventions. Although some promising data supporting these phenotypes have been reported, it remains to be shown whether these phenotypes are valid, how treatment can be targeted to these phenotypes, and whether this targeting yields superior clinical outcomes. J Orthop Sports Phys Ther 2019;49(6):370-379. Epub 12 Jun 2018. doi:10.2519/jospt.2019. 7917.
Scene categorization based on heterogeneous features

In this paper we present a complete framework for scene categorization that builds upon and extends several recent ideas including spatial pyramid representation and a variety of base local descriptors which have different discriminative power and invariance from task to task. Furthermore, we propose two strategies: sum-max and max-max, used to effectively combine diverse source of data in a unified setting way. Our approach shows significantly improved performance on a large, challenging data set of fifteen natural scene categories. Owing to combination of complementary information cues, our approach is expected to equally applicable to a range of tasks.
Speech Dereverberation in the Time-Frequency Domain

In this thesis, we address the problem of dereverberation of speech signals, acquired in an enclosed space by a single microphone. We spectrally estimate and suppress the dereverberation in the time-frequency domain, using two representations: The short-time Fourier transform (STFT), and the Single-Side-Band transform (SSB). In the first part of this thesis, the problems of system identification and dereverberation are addressed in the SSB domain. We derive an analytical relation between the input and output signals in the SSB domain, and formulate a system identification routine for a band-to-band approximation of that relation. The dereverberation problem is addressed using a statistical model for the acoustic impulse response (AIR) function. We present exact and approximate representations of the AIR and the reverberant signal in the SSB domain. The performance of the dereverberation algorithm is evaluated as a function of the representation complexity. The SSB and the STFT representations are compared; it is found that the STFT representation is more suitable for the dereverberation application. In the second part of the thesis, we propose a new algorithm for the estimation of the reverberant component, which is a critical part of dereverberation in the spectral domain. In order to address the frequency variation of the reflection coefficients in the room, we formulate the problem directly in the STFT domain. First, a system identification stage is performed. A white noise signal is played in the reverberant environment, and a filter is extracted relating the recorded output signal to its reverberant component. In order to reduce the complexity of the computation, we propose approximate representations of the filter, that use only some or none of the crossband filters. The latter case is referred to as a ”band-to-band filter”. The performance of the system identification stage is analysed in terms of the meansquare error (MSE) between the actual reverberant component and its estimate by the
TOPK Promotes Microglia/Macrophage Polarization towards M2 Phenotype via Inhibition of HDAC1 and HDAC2 Activity after Transient Cerebral Ischemia

T-LAK-cell-originated protein kinase (TOPK) is a newly identified member of the mitogen-activated protein kinase family. Our previous study has showed that TOPK has neuroprotective effects against cerebral ischemia-reperfusion injury. Here, we investigated the involvement of TOPK in microglia/ macrophage M1/M2 polarization and the underlying epigenetic mechanism. The expression profiles, co-localization and in vivo interaction of TOPK, M1/M2 surface markers, and HDAC1/HDAC2 were detected after middle cerebral artery occlusion models (MCAO). We demonstrated that TOPK, the M2 surface markers CD206 and Arg1, p-HDAC1, and p-HDAC2 showed a similar pattern of in vivo expression over time after MCAO. TOPK co-localized with CD206, p-HDAC1, and p-HDAC2 positive cells, and was shown to bind to HDAC1 and HDAC2. In vitro study showed that TOPK overexpression in BV2 cells up-regulated CD206 and Arg1, and promoted the phosphorylation of HDAC1 and HDAC2. In addition, TOPK overexpression also prevented LPS plus IFN-γ-induced M1 transformation through reducing release of inflammatory factor of M1 phenotype TNF-α, IL-6 and IL-1β, and increasing TGF-β release and the mRNA levels of TGF-β and SOCS3, cytokine of M2 phenotype and its regulator. Moreover, the increased TNF-α induced by TOPK siRNA could be reversed by HDAC1/HDAC2 inhibitor, FK228. TOPK overexpression increased M2 marker expression in vivo concomitant with the amelioration of cerebral injury, neurological functions deficits, whereas TOPK silencing had the opposite effects, which were completely reversed by the FK228 and partially by the SAHA. These findings suggest that TOPK positively regulates microglia/macrophage M2 polarization by inhibiting HDAC1/HDAC2 activity, which may contribute to its neuroprotective effects against cerebral ischemia-reperfusion injury.
Effect of Sterilization Process and Storage on the Antioxidative Properties of Runner Bean

In this study, we investigated the effect of standard preservation of bean seeds on changes in contents and activity of their selected components: dry matter, ash, different forms of nitrogen, composition of protein fractions; total phenolics and condensed tannins; ability to chelate iron(II) ions; antiradical activity against ABTS•+ and DPPH•; and capability for inhibiting autoxidation and enzymatic oxidation of linoleic acid. The conducted technological process caused various changes in contents of nitrogen forms and partial loss of phenolic compounds. The antiradical and antioxidative activity of the extracts decreased significantly, while an increase was observed in their ability to chelate Fe(II). These changes were due to the migration of active compounds to the brine, and to their structural transformations and degradation. Longer storage of the sterilized product caused restoration of part of the antiradical activity of the seeds.
Continuous-Time Flows for Efficient Inference and Density Estimation

Two fundamental problems in unsupervised learning are efficient inference for latent-variable models and robust density estimation based on large amounts of unlabeled data. Algorithms for the two tasks, such as normalizing flows and generative adversarial networks (GANs), are often developed independently. In this paper, we propose the concept of {\em continuous-time flows} (CTFs), a family of diffusion-based methods that are able to asymptotically approach a target distribution. Distinct from normalizing flows and GANs, CTFs can be adopted to achieve the above two goals in one framework, with theoretical guarantees. Our framework includes distilling knowledge from a CTF for efficient inference, and learning an explicit energy-based distribution with CTFs for density estimation. Both tasks rely on a new technique for distribution matching within amortized learning. Experiments on various tasks demonstrate promising performance of the proposed CTF framework, compared to related techniques.
Financially Unstable Households

Abstract: One of Hyman Minsky’s most important contributions is the Financial Instability Hypothesis (FIH), which explains why capitalist economies experience periods of optimism (booms) and pessimism (bust). At the beginning of a cycle, businesses take on more debt, but they are conservative, and the principal is easily paid back (a hedge position). As optimism grows, so does risk-taking and businesses take on more debt. At some point they can only afford to pay interest on that debt (speculative position). In the most extreme case, businesses take on so much debt that they can neither pay the principal nor make interest payments (Ponzi position). Minsky wrote about financial instability (e.g., 1975, 1982) before U.S. households had taken on large levels of debt. Minsky focused on businesses since they were the debt drivers. Today household debt is at record levels, so it makes sense to understand how financially unstable U.S. households are and what this means for the economy. We begin the article by arguing that Minsky’s categories should be applied to households; then we operationalize them using the Federal Reserve’s Survey of Consumer Finances. This enables us to measure changes in household financial instability using a Minsky-inspired framework and draw some conclusions.
Pengaruh kepemimpinan kepala sekolah dan biaya pendidikan terhadap kualitas proses belajar mengajar dan dampaknya dengan kompetensi lulusan SMK di Kabupaten Gunungkidul

Tujuan penelitian ini untuk mengetahui pengaruh kepemimpinan kepala sekolah dan biaya pendidikan terhadap kualitas proses belajar mengajar dan dampaknya dengan kompetensi lulusan SMK. Penelitian ini merupakan penelitian Ex Post Facto dengan menggunakan pendekatan kuantitatif. Penelitian dilaksanakan di sembilan SMK di Gunungkidul, dengan responden 210 guru. Pengumpulan data dalam penelitian ini menggunakan kuesioner. Analisis data dalam penelitian ini menggunakan analisis regresi dan analisis jalur (Path Analysis). Hasil penelitian menunjukkan bahwa: (1) struktur pengaruh yang mempengaruhi kompetensi lulusan tidak terbukti secara empiris; (2) Tidak terdapat pengaruh langsung kepemimpinan kepala sekolah dengan kompetensi lulusan dan terdapat pengaruh tidak langsung kepemimpinan kepala sekolah dengan kompetensi lulusan melalui kualitas proses belajar mengajar yaitu sebesar 0,059; (3) Terdapat pengaruh langsung sebesar 0,221 dan tidak langsung sebesar 0,096 biaya pendidikan dengan kompetensi lulusan; (4) pengaruh kepemimpinan kepala sekolah, biaya pendidikan dan kualitas proses belajar mengajar terhadap kompetensi lulusan masing-masing sebesar 2,6%, 10,6%, 13,0%; (5) pengaruh kepemimpinan kepala sekolah dan biaya pendidikan terhadap kualitas proses belajar mengajar sebesar 21% dan pengaruh setiap variabel sebesar 8,7%, 16,8%. dan 5,9%. The effect of principal leadership and education costs on the quality of the teaching and learning process and the subsequent impact on competence of vocational school graduates in Gunungkidul RegencyAbstractThe purpose of this study was to determine the effect of principals' leadership and education costs on the quality of teaching and learning processes and their impact on the competence of vocational school graduates. This study is an Ex Post Facto study using a quantitative approach. The study was conducted in 9 Vocational Schools in Gunungkidul, with 210 teachers as respondents. Data collection in this study uses a questionnaire. Testing the hypothesis with Path Analysis. The results of the study show that: (1) the structure of influence that influences graduate competency is not empirically proven; (2) There is no direct influence of the principal's leadership with graduate competency and there is an indirect influence of the principal's leadership with graduate competence through the quality of the teaching and learning process which is equal to 0.059; (3) There is a direct effect of 0.221 and indirectly by 0.096 costs of education with graduate competencies; (4) the influence of principals' leadership, education costs and the quality of the teaching and learning process on graduate competencies of 2.6%, 10.6%, 13.0% respectively; (5) the influence of principals' leadership and education costs on the quality of teaching and learning processes is 21% and the effect of each variable is 8.7%, 16.8% and.5. 9%.
Heterologous Expression of Key C and N Metabolic Enzymes Improves Re-assimilation of Photorespired CO2 and NH3, and Growth1[OPEN]

Heterologous coexpression of phosphoenolpyruvate carboxylase (ZmPepcase), aspartate aminotransferase (GmAspAT) and glutamine synthetase (NtGS) improves the re-assimilation of photorespiratory CO2 and NH3 with concomitant gains in shoot biomass and seed yield in transgenic Arabidopsis. We investigated the effect of the heterologous expression of phosphoenolpyruvate carboxylase (ZmPepcase), aspartate aminotransferase (GmAspAT), and glutamine synthetase (NtGS) on carbon (C) and nitrogen (N) metabolism in Arabidopsis (Arabidopsis thaliana). These transgenes were expressed either separately or in different combinations. The highest gains in shoot dry weight were observed in transgenic lines coexpressing all three genes. Tracer experiments using NaH14CO3 suggested that the coexpression of ZmPepcase, GmAspAT, and NtGS resulted in a higher flux of assimilated CO2 toward sugars and amino acids. Upon feeding the leaf discs with glycine-1-14C, transgenic lines evolved significantly lower 14CO2 levels than the wild type, suggesting that a higher reassimilation of CO2 evolved during photorespiration. Leaves of transgenic plants accumulated significantly lower ammonium without any significant difference in the levels of photorespiratory ammonium relative to the wild type, suggesting a higher reassimilation of photorespired NH3. Transgenic lines also showed improved photosynthetic rates, higher shoot biomass accumulation, and improved seed yield in comparison with wild-type plants under both optimum and limiting N conditions. This work demonstrates that the heterologous coexpression of ZmPepcase, GmAspAT, and NtGS reduced the photorespiratory loss of C and N with concomitant enhancements in shoot biomass and seed yield.
Supporting residents to transition practices in zero energy homes

Residential housing has to become more sustainable to meet global energy goals (Silvester et al., 2017), yet the challenge is to integrate the refurbishments that reduce energy with the way people live. The context of this project is the 2ndSKIN project, which refurbishes houses to become zero energy. Zero energy houses are more airtight as a result of improved insulation, therefore ventilation becomes increasingly important. Yet, residents struggle to integrate the new balanced ventilation system into their practices. Residents use the system different from how it is intended. This does not only impact energy goals (Behar a Chiu, 2013) but can also result in decreased comfort and unhealthy situations. Hence, the aim of the project is to support residents to transition their practices in zero energy homes. The project first described the practice of maintaining indoor air quality to identify points that hinder a transition of the practice. Insights show that the lack of feedback of the ventilation system makes residents insecure and makes it hard to understand the system. Besides, associations that mismatch the new material make residents reluctant to use the balanced ventilation systems. In the concept phase, I generated ideas to improve feedback and foster desirable associations with the ventilation system. Through the iterations, I learned feedback on functioning and on the systems’ activity helps residents. It helps them to trust the system is working, understand what the system is doing and develop appreciation for it. The final concept is the feedback fan. This add-on to ventilation valves spins on the supplied air. In a natural way, it provides residents with feedback. An evaluation proved that with increased feedback, residents are able to incorporate the system in their daily routines and even align their own actions to the systems’ activity. Future steps are to make a solid prototype and develop the service around it. Besides, future design projects can continue on other identified points that hinder the transition of practices. Moreover, insights about feedback of the ventilation system and the practice of maintaining indoor air quality will be valuable, when designing future ventilation systems. In conclusion, both the final design and the insights of the project can contribute to a transition of residents’ practices zero energy homes.
Comparison between Tetrel Bonded Complexes Stabilized by σ and π Hole Interactions

The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH4, TH3F, and TH2F2 (T = Si, Ge, Sn) and the latter by TH2=CH2, THF=CH2, and TF2=CH2, all paired with NH3 as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of the tetrel bond, whether σ or π. The magnitudes of the maxima of the molecular electrostatic potential in the two types of systems are not good indicators of either the interaction energy or even the full Coulombic energy. The geometry of the Lewis acid is significantly distorted by the formation of the dimer, more so in the case of the σ-bonded complexes, and this deformation intensifies the σ and π holes.
Connective tissue representation for detection of microcalcifications in digital mammograms

Microcalcification clusters appear as an early sign of breast cancer and play an important role in interpreting mammograms. Progress is reported towards an automated computer aided detection system for clustered microcalcifications utilizing two image feature parameters: local contrast and shape. The use of a shape parameter is necessary to distinguish thin patches of connective tissue from microcalcifications. Two shape parameter techniques are compared in the segmentation of 15 digital mammogram images. The first technique implements the linear Hough transform, while the second uses image phase information in the Fourier domain. In both cases labeling of the image is performed by a deterministic relaxation scheme, in which both image data dn prior beliefs are weighted simultaneously. Similar segmentation results are obtained for each shape parameter technique however the execution time for the phase method is approximately one quarter that for the Hough method. Both techniques offer an improvement over segmentation results obtained without the shape parameter.