Miracle-dz/UniFAR-FTUs huggingface dataset:
An In Silico Study for Expanding the Utility of Cannabidiol in Alzheimer’s Disease Therapeutic Development

Cannabidiol (CBD), a major non-psychoactive component of the cannabis plant, has shown therapeutic potential in Alzheimer’s disease (AD). In this study, we identified potential CBD targets associated with AD using a drug-target binding affinity prediction model and generated CBD analogs using a genetic algorithm combined with a molecular docking system. As a result, we identified six targets associated with AD: Endothelial NOS (ENOS), Myeloperoxidase (MPO), Apolipoprotein E (APOE), Amyloid-beta precursor protein (APP), Disintegrin and metalloproteinase domain-containing protein 10 (ADAM10), and Presenilin-1 (PSEN1). Furthermore, we generated CBD analogs for each target that optimize for all desired drug-likeness properties and physicochemical property filters, resulting in improved pIC50 values and docking scores compared to CBD. Molecular dynamics (MD) simulations were applied to analyze each target’s CBD and highest-scoring CBD analogs. The MD simulations revealed that the complexes of ENOS, MPO, and ADAM10 with CBD exhibited high conformational stability, and the APP and PSEN1 complexes with CBD analogs demonstrated even higher conformational stability and lower interaction energy compared to APP and PSEN1 complexes with CBD. These findings demonstrated the capable binding of the six identified targets with CBD and the enhanced binding stability achieved with the developed CBD analogs for each target.
Tibial nerve compression due to osteochondroma of the fibular head: A case report

Rationale: Osteochondroma is one of the most common primary benign bone tumors. In most cases, this disease is asymptomatic. However, it may become symptomatic owing to nerve and vascular compression when it affects the knee joint. Isolated tibial nerve palsy caused by proximal fibular osteochondroma is rare. Patients concerns: A 60-year-old male, was treated for degenerative arthritis of the right knee, referred to the right great toe flexion limitation that occurred 3 weeks prior. Diagnoses: Magnetic resonance imaging revealed compression of the tibial nerve and surrounding muscles due to an osseous lesion in the fibular head. A nerve conduction test confirmed tibial neuropathy in the right lower leg. Interventions: Exploratory surgery was performed to decompress the tibial nerve and remove the bony lesion histopathologically diagnosed as an osteochondroma. Outcomes: Fifty-five months postoperatively, toe flexion recovered to normal. No recurrence of osteochondroma was observed. Lessons: As in our case, if a bony lesion is diagnosed on radiographs with neurological symptoms, early decompression surgery is necessary. Moreover, since it can be misdiagnosed as a simple bony spur, magnetic resonance imaging and tissue biopsy are also indicated.
Taxifolin as a novel therapeutic agent for epileptic seizures induced by caffeine-induced oxidative stress in rats.

BACKGROUND Epilepsy is a severe neurological disease that results from excessive and/or synchronized neuronal activity in the brain, and oxidative stress plays a role in its pathogenesis. Taxifolin is a flavonoid that exhibits antioxidant activity. OBJECTIVES To investigate the effects of taxifolin on caffeine-induced epileptic seizures in rats and reveal the role of antioxidant activity in antiepileptic therapy. MATERIAL AND METHODS Forty rats were divided into 4 groups (n = 6/group): caffeine 300 mg/kg group (CG), taxifolin 50 mg/kg + caffeine 300 mg/kg group (TCG), 2 mg/kg diazepam + 300 mg/kg caffeine group (DCG), and a healthy group (HG). Taxifolin was given to the TCG, and diazepam was given to the DCG orally. One hour later, caffeine was injected intraperitoneally into the CG, TCG and DCG rats. The time between the caffeine injection and the contractions (the latency period) was determined. Animals were euthanized 1 h after caffeine injection, and brain tissues were biochemically examined for oxidants and antioxidants. RESULTS Taxifolin and diazepam prolonged the latency period to a similar extent (p = 0.549), while taxifolin was more successful in preventing mortality. Taxifolin suppressed the caffeine-induced increase in myeloperoxidase, total oxidant status and oxidative stress index, and decreased total glutathione, superoxide dismutase and total antioxidant status more effectively than diazepam (p < 0.05). CONCLUSIONS We showed the relationship between antioxidant activity and epilepsy treatment, and demonstrated that taxifolin may be useful for treating epilepsy.
Using multiscale texture information from ALOS PALSAR to map tropical forest

This research investigated the ability of the Advanced Land Observing Satellite (ALOS) Phased Array type L-band Synthetic Aperture Radar (PALSAR) to map tropical forest in central Sumatra, Indonesia. The study used PALSAR 50 m resolution orthorectified HH and HV data. As land-cover discrimination is difficult with only two bands (HH and HV), we added textures as additional information for classification. We calculated both first- and second-order texture features and studied the effects of texture window size, quantization scale and displacement length on discrimination capability. We found that rescaling to a lower number of grey levels (8 or 16) improved discrimination capability and that equal probability quantization was more effective than uniform quantization. Increasing displacement tended to reduce the discrimination capability. Low spatial resolution increased the discrimination capability because low spatial resolution features reduce the effects of noise. A larger number of features also improved discrimination capability. However, the amount of improvement depended on the window size. We used the optimum combination of backscatter amplitude and textures as input data into a supervised multi-resolution maximum likelihood classification. We found that including texture information improved the overall classification accuracy by 10%. However, there was significant confusion between natural forest and acacia plantations, as well as between oil palm and clear cuts, presumably because the backscatter and texture of these class pairs are very similar.
Sixty Years of Frequency-Domain Monaural Speech Enhancement: From Traditional to Deep Learning Methods

Frequency-domain monaural speech enhancement has been extensively studied for over 60 years, and a great number of methods have been proposed and applied to many devices. In the last decade, monaural speech enhancement has made tremendous progress with the advent and development of deep learning, and performance using such methods has been greatly improved relative to traditional methods. This survey paper first provides a comprehensive overview of traditional and deep-learning methods for monaural speech enhancement in the frequency domain. The fundamental assumptions of each approach are then summarized and analyzed to clarify their limitations and advantages. A comprehensive evaluation of some typical methods was conducted using the WSJ + Deep Noise Suppression (DNS) challenge and Voice Bank + DEMAND datasets to give an intuitive and unified comparison. The benefits of monaural speech enhancement methods using objective metrics relevant for normal-hearing and hearing-impaired listeners were evaluated. The objective test results showed that compression of the input features was important for simulated normal-hearing listeners but not for simulated hearing-impaired listeners. Potential future research and development topics in monaural speech enhancement are suggested.
Vagusnervstimulation (VNS) als Behandlungsoption für Depressionen

Zusammenfassung Einführung Depressionen sind häufig und zeigen bei einem Drittel der Fälle einen therapieresistenten und chronifizierten Verlauf. Die invasive Vagusnervstimulation (VNS) ist eine langfristige Zusatzbehandlungsoption, die in den letzten Jahren zunehmend häufig angewandt wird. Eine CE-Zertifizierung für die Behandlung der chronischen und therapierefraktären Depression besteht seit 2001. Methoden Basierend auf einer systematischen Literaturrecherche geben wir in diesem narrativen Review einen Überblick mit klinischem Schwerpunkt über die invasive VNS als Behandlungsoption bei der Depressionen. Ergebnisse Nach psychiatrischer Indikationsstellung und Aufklärung wird in einem kurzen operativen Eingriff der Impulsgeber im Bereich der linken Brust implantiert. Die Einstellung der Stimulationsparameter erfolgt ambulant-psychiatrisch in den ersten Wochen nach der OP. Das VNS-System wird zunächst in 3-, später in 6-monatigen Intervallen kontrolliert. Die Stimulation erfolgt für 30 Sekunden zwischen 5-minütigen Intervallen. Stimulationssynchrone Heiserkeit ist die häufigste Nebenwirkung. Steigerung noradrenerger und serotonerger Transmission im Gehirn und anti-inflammatorische Effekte werden als Wirkmechanismen diskutiert. Der Behandlungseffekt tritt verzögert nach 6–12 Monaten ein. Die kumulative Responserate nach 5 Jahren liegt für die VNS plus Standardbehandlung bei ca. 67,6% im Vergleich zu 40.9% bei Standardbehandlung ohne VNS. Langfristige positive Effekte auf Lebensqualität, Kognition, Morbidität und Mortalität wurden beschrieben. Schlussfolgerung Die VNS ist eine langfristige, sichere Behandlungsoption bei schwer betroffenen Depressionspatienten mit positivem Effekt auf Symptomschwere, Lebensqualität und kognitive Funktion.
Topoisomerase 1 facilitates nucleosome reassembly at stress genes during recovery

Abstract Chromatin remodeling is essential to allow full development of alternative gene expression programs in response to environmental changes. In fission yeast, oxidative stress triggers massive transcriptional changes including the activation of hundreds of genes, with the participation of histone modifying complexes and chromatin remodelers. DNA transcription is associated to alterations in DNA topology, and DNA topoisomerases facilitate elongation along gene bodies. Here, we test whether the DNA topoisomerase Top1 participates in the RNA polymerase II-dependent activation of the cellular response to oxidative stress. Cells lacking Top1 are resistant to H2O2 stress. The transcriptome of Δtop1 strain was not greatly affected in the absence of stress, but activation of the anti-stress gene expression program was more sustained than in wild-type cells. Top1 associated to stress open reading frames. While the nucleosomes of stress genes are partially and transiently evicted during stress, the chromatin configuration remains open for longer times in cells lacking Top1, facilitating RNA polymerase II progression. We propose that, by removing DNA tension arising from transcription, Top1 facilitates nucleosome reassembly and works in synergy with the chromatin remodeler Hrp1 as opposing forces to transcription and to Snf22 / Hrp3 opening remodelers.
In Vitro Antioxidant Activity, Bioaccessibility, and Thermal Stability of Encapsulated Strawberry Fruit (Fragaria × ananassa) Polyphenols

Bioactive compounds in red fruits, such as strawberries, are vulnerable to digestion, and encapsulation has become an alternative for their protection. This study aims at encapsulating strawberry juice (SJ) by freeze-drying with pea protein and okra mucilage (SJPO), pea protein and psyllium mucilage (SJPP), and pea protein, psyllium mucilage, and okra mucilage (SJPPO) and investigating the in vitro release. The highest encapsulation efficiency was observed in capsule SJPPO (95.38%) and the lowest efficiency in SJPO (82.45%). Scanning electron microscopy revealed an amorphous glassy structure for the structure of the strawberry microcapsules, and X-ray diffraction confirmed that observation. However, X-ray diffraction further showed that SJPPO was crystalline, indicating a tighter crosslinking density than the other microcapsules. Fourier transform infrared spectroscopy showed peaks at 3390 and 1650 cm−1, confirming the presence of polyphenols and polysaccharides in the strawberry microcapsules. Thermal stability was higher for SJPPO, and the observed thermal transitions were due to the bonds formed between the polymers and polyphenols. Pelargonidin 3-glucoside, cyanidin 3-glucoside, cyanidin, delphinidin, malvidin 3-glucoside, ellagic acid, chlorogenic acid, catechin, and kaempferol were identified in the strawberry microcapsules. Digestion affected the compounds’ content; the bioaccessibility for SJ was 39.26% and 45.43% for TPC and TAC, respectively. However, encapsulation improved the bioaccessibility of both TPC (SJPP, 51.54%; SJPO, 48.52%; and SJPPO, 54.39%) and TAC (SJPP, 61.08%; SJPO, 55.03%; and SJPPO, 71.93%). Thus, encapsulating pea protein isolate, psyllium mucilage, and okra mucilage is an effective method to facilitate targeted release and preserve the biological activities of fruits.
EcoTroph (ET): a trophic level based software for assessing the impacts of fishing on aquatic ecosystems.

2 Introduction . 3 PART I – The trophic level based model: theoretical approach . 5 1. Building the model: principles, assumptions and equations . 5 1.1. Origin of the model . 5 1.2. EcoTroph: general principles . 6 1.3. EcoTroph: biomass and flow equations . 10 1.4. EcoTroph and Ecopath: first comparison . 12 1.5. Flow kinetic equation . 14 1.6. Top-down control and biomass input control . 17 1.7. Catch equation and accessibility. 20 1.8. From steady-state to timedynamic modelling . 22 2. Learning from the model: some generic rules of the ecosystem functioning . 24 2.1. Simulation of a virtual ecosystem: method . 24 2.2. Impact of transfer efficiency and flow kinetics on unexploited biomass . 26 2.3. Impact of fishing on biomass . 27 2.4. Catch simulations . 30 2.5. Dynamic model: impact of fishing on ecosystem stability . 33 2.6. Concluding remarks on the theoretical approach . 35 3. The Catch Trophic Spectrum Analysis (CTSA) . 37 3.1. From EcoTroph to the CTSA . 37 3.2. Testing the method on simulated data . 38 3.3. Application to real case studies . 41 4. Conclusion: the trophic level based approach . 42 PART II ECOTROPH: A new tool in the EwE family . 43 1. General information . 43 1.1. Structure of the EcoTroph routines: . 43 1.2. Installation of the plug-in . 44 1.3. Additional information . 45 2. ET-Transpose: looking at an Ecopath model using EcoTroph . 45 2.1. What is it used for? 45 2.2. How it works. 45 2.3. How to use it . 49 2.4. Example of application . 52 3. ET-CTSA: estimating input parameters of EcoTroph . 53 3.1. What is it used for? 53 3.2. How it works . 54 3.3. How to use . 55 3.4. Example of application . 60 4. ET-Diagnosis: using EcoTroph for simulation and global diagnosis . 60 4.1. What is it used for? 60 4.2. How it works . 61 4.3. How to use it . 61 4.4. Example of application: . 64 5. ET-Dynamic: using EcoTroph with time series . 65 5.1. What is it used for? 65 5.2. How it works . 66 5.3. How to use it . 66 5.4. Example of application . 71 Acknowledgments . 73 References . 73 Appendix I – A Non-continuous simulation of EcoTroph . 77 Appendix II – Estimating transfer efficiency from catch data . 80 (1) Université Européenne de Bretagne, Agrocampus Ouest Pôle Halieutique / Aquatic and fisheries sciences centre, UMR Ecologie et Santé des Ecosystèmes, 65 Route de Saint Brieuc, CS 84215, 35042 Rennes, France – Didier.Gascuel@agrocampus-ouest.fr (2) University of British Columbia, Fisheries Centre, AERL, 2202 Main Mall, Vancouver BC, V6T 1Z4, Canada l.boyer@fisheries.ubc. ca; d.pauly@fisheries.ubc. ca A Research Report from the Fisheries Centre at UBC, with support provided by The EU project TrophMod MOIF-CT-2006-38767, and The Pew Charitable Trusts (Philadephia, USA) through the Sea Around Us Project. 82 pages © Fisheries Centre, University of British Columbia, 2009 Fisheries Centre Research Reports are abstracted in the FAO Aquatic Sciences and Fisheries Abstracts (ASFA) ISSN 1198-6727
Sprite observations above the U.S. High Plains in relation to their parent thunderstorm systems

Transient luminous events (sprites, blue jets, elves) above large mesoscale convective systems (MCSs) over the U.S. High Plains have been routinely monitored from the Yucca Ridge Field Station near Fort Collins, Colorado using ground-based low-light video systems. We analyzed 36 sprites above the Nebraska MCS of August 6, 1994. The results lend further support to the hypothesis that sprites are almost uniquely associated with positive cloud-to-ground (+CG) lightning flashes. Sprite-associated +CGs also averaged substantially larger peak currents than the remaining +CG population (81 kA versus 30 kA in this storm system). There is some evidence that sprite-associated +CGs also have higher stroke multiplicity. This study yields no evidence of sprites associated with negative CG events. In the central United States an additional requirement appears to be that the parent MCS has a contiguous radar reflectivity area exceeding 20-25,000 km 2 . The majority of the sprites occur above the large stratiform precipitation region and not the high-reflectivity convective core of the MCS. Triangulation of a limited number of paired images (from September 7, 1994) suggests that the sprite is generally centered within 50 km of the parent +CG. Assuming the +CG provides the range, single-image photogrammetric analyses provide estimates of the maximum vertical extent of the sprites. For this storm the sprite tops averaged 77 km with a maximum of 88 km. The bases averaged 50 km but with a few sprite tendrils extending as low as 31 km.
Chat-UniVi: Unified Visual Representation Empowers Large Language Models with Image and Video Understanding

Large language models have demonstrated impressive universal capabilities across a wide range of open-ended tasks and have extended their utility to encompass multimodal conversations. However, existing methods encounter challenges in effectively handling both image and video understanding, particularly with limited visual tokens. In this work, we introduce Chat-UniVi, a Unified Vision-language model capable of comprehending and engaging in conversations involving images and videos through a unified visual representation. Specifically, we employ a set of dynamic visual tokens to uniformly represent images and videos. This representation framework empowers the model to efficiently utilize a limited number of visual tokens to simultaneously capture the spatial details necessary for images and the comprehensive temporal relationship required for videos. Moreover, we leverage a multi-scale representation, enabling the model to perceive both high-level semantic concepts and low-level visual details. Notably, Chat-UniVi is trained on a mixed dataset containing both images and videos, allowing direct application to tasks involving both mediums without requiring any modifications. Extensive experimental results demonstrate that Chat-UniVi consistently outperforms even existing methods exclusively designed for either images or videos. Code is available at https://github.com/PKU-YuanGroup/Chat-UniVi.
Memory-efficient Stochastic methods for Memory-based Transformers

Training Memory-based transformers can require a large amount of memory and can be quite inefficient. We propose a novel two-phase training mechanism and a novel regularization technique to improve the training efficiency of memory-based transformers, which are often used for long-range context problems. For our experiments, we consider transformer-XL as our baseline model which is one of memorybased transformer models. We show that our resultant model, Skip Cross-head TransformerXL, outperforms the baseline on character level language modeling task with similar parameters and outperforms the baseline on word level language modelling task with almost 20% fewer parameters. Our proposed methods do not require any additional memory. We also demonstrate the effectiveness of our regularization mechanism on BERT which shows similar performance with reduction in standard deviation of scores of around 30% on multiple GLUE tasks.
Noise-Resilient Group Testing with Order-Optimal Tests and Fast-and-Reliable Decoding

Group testing (GT) is the Boolean counterpart of compressed sensing and the marketplace of new ideas for related problems such as cognitive radio and heavy hitter. A GT scheme is considered good if it is nonadaptive, uses $O(k \log n)$ tests, resists noise, can be decoded in $O(k \operatorname{poly}(\log n))$ time, and makes nearly no mistakes. In this paper, we propose"Gacha GT", an elementary, self-contained, and unified randomized scheme that, for the first time, satisfies all criteria for a fairly large region of parameters, namely when $\log k<\log(n)^{1-1/O(1)}$. Outside this parameter region, Gacha can be specialized to outperform the state-of-the-art partial-recovery GTs, exact-recovery GTs, and worst-case GTs. The new idea that runs through this paper, using an analogy, is to ask every person to break her $9$-digit"phone number"into three $3$-digit numbers $x$, $y$, and $z$ and write $(b, x)$, $(b, y)$, and $(b, z)$ on three pieces of sticky notes, where $b$ is her"birthday". This way, one can sort the sticky notes by birthday to reassemble the phone numbers. This birthday--number code and other coded constructions can be stacked like a multipartite graph pyramid. Gacha's encoder will synthesize the test results from the bottom up; and Gacha's decoder will reassemble the phone numbers from the top down.
Approximate Bregman Proximal Gradient Algorithm for Relatively Smooth Nonconvex Optimization

In this paper, we propose the approximate Bregman proximal gradient algorithm (ABPG) for solving composite nonconvex optimization problems. ABPG employs a new distance that approximates the Bregman distance, making the subproblem of ABPG simpler to solve compared to existing Bregman-type algorithms. The subproblem of ABPG is often expressed in a closed form. Similarly to existing Bregman-type algorithms, ABPG does not require the global Lipschitz continuity for the gradient of the smooth part. Instead, assuming the smooth adaptable property, we establish the global subsequential convergence under standard assumptions. Additionally, assuming that the Kurdyka--{\L}ojasiewicz property holds, we prove the global convergence for a special case. Our numerical experiments on the $\ell_p$ regularized least squares problem, the $\ell_p$ loss problem, and the nonnegative linear system show that ABPG outperforms existing algorithms especially when the gradient of the smooth part is not globally Lipschitz or even local Lipschitz continuous.
Dynamical friction in dark matter superfluids: The evolution of black hole binaries

The theory of superfluid dark matter is characterized by self-interacting sub-eV particles that thermalize and condense to form a superfluid core in galaxies. Massive black holes at the center of galaxies, however, modify the dark matter distribution and result in a density enhancement in their vicinity known as dark matter spikes. The presence of these spikes affects the evolution of binary systems by modifying their gravitational wave emission and inducing dynamical friction effects on the orbiting bodies. In this work, we assess the role of dynamical friction for bodies moving through a superfluid core enhanced by a central massive black hole. As a first step, we compute the dynamical friction force experienced by bodies moving in a circular orbit. Then, we estimate the gravitational wave dephasing of the binary, showing that the effect of the superfluid drag force is beyond the reach of space-based experiments like LISA, contrarily to collisionless dark matter, therefore providing an opportunity to distinguish these dark matter models.