Miracle-dz/UniFAR-FTUs huggingface dataset:
Development of a Novel Antibacterial Peptide, PAM-5, via Combination of Phage Display Selection and Computer-Assisted Modification

Antibacterial peptides (ABPs) have been proposed as potential candidates for alternative antibacterial agents due to the extensive dissemination of antibiotic resistance. However, ABP isolation from natural resources can be tedious without consistent yield. Moreover, many natural ABPs are not developed for clinical application due to potential toxicity to mammalian cells. Therefore, the objective of this study was to develop a potent ABP with minimal toxicity via phage display selection followed by computer-assisted modification. Briefly, a 12-mer phage-displayed peptide library was used to isolate peptides that bound to the cell surface of Pseudomonas aeruginosa with high affinity. The affinity-selected peptide with the highest selection frequency was modified to PAM-5 (KWKWRPLKRKLVLRM) with enhanced antibacterial features by using an online peptide database. Using in vitro microbroth dilution assay, PAM-5 was shown to be active against a panel of Gram-negative bacteria and selected Gram-positive bacteria. Interestingly, the peptide was stable in human plasma by exhibiting a similar bactericidal effect via ex vivo assay. Scanning electron microscopy and SYTOX Green uptake assay revealed that PAM-5 was able to cause membrane disruption and permeabilization of the bacteria. Additionally, the peptide was also able to bind to bacterial DNA as demonstrated by gel retardation assay. In the time-kill assay, PAM-5 was shown to kill the bacteria rapidly in 10 min. More importantly, PAM-5 was non-cytotoxic to Vero cells and non-haemolytic to human erythrocytes at all concentrations tested for the antibacterial assays. Thus, this study showed that the combination of phage display screening and computer-assisted modification could be used to develop potent novel ABPs, and PAM-5 derived from these approaches is worth to be further elucidated for its potential clinical use.
Population relaxation induced by the Boson peak mode observed in optical hyperfine spectroscopy of 167 Er 3+ ions doped in a silicate glass fiber

We demonstrate transient saturation spectroscopy for 167Er3+ ions doped in a silicate glass fiber cooled at 2.5–30 K to measure the population relaxation time t1 of the hyperfine sublevels. The observed t1 value is 3.1 ms at 4 K and we observe anomalous temperature dependence whereby t1 becomes rather longer with heating from 4 to 30 K. We can regard the population relaxation as a result of the Raman scattering of the Boson peak mode (BPM) peculiar to a silicate glass by the 4f-electrons of the 167Er3+ ions. We can attribute the anomalous temperature dependence to the suppression of the Raman scattering by thermal hopping of the localized BPM.
Project Optimus, an FDA initiative: Considerations for cancer drug development internationally, from an academic perspective

Modern cancer therapeutics are increasingly targeted, bringing the promise of new and improved activity, alongside better tolerability. However, while many are indeed resulting in dramatic improvements in disease control and patient survival, short- and long-term tolerability has not always accompanied it. The choice of dose and schedule is often in the upper range of the therapeutic window, driven by the maximum tolerated dose (MTD) model of previous cytotoxic agents. There is increasing recognition that this needs to change, by taking a more holistic approach to determine the optimal dose for desired biological effects and tolerability early in clinical development. In the US, the FDA’s Oncology Centre of Excellence is addressing this via the Project Optimus initiative: aiming to reform dose optimisation studies so that they can demonstrate the most appropriate dose selection. Early clinical development will need to demonstrate the dose-exposure, -pharmacodynamic, -toxicity and -activity relationships, including randomised evaluations for dose selection. Regulatory agencies outside the US are similarly exploring this. Along with Australia, Brazil, Canada, Israel, Singapore and Switzerland, the UK participates in Project Orbis, a collaborative program with the FDA to accelerate patient access to new cancer medicines through coordinated regulatory review. Close alignment with Project Optimus will be important internationally and will require changes across industry, including for academic units and small biotech. We discuss our perspective on the implications, and opportunities, for early phase oncology trials as a uniquely charity-funded drug development facility, the Centre for Drug Development within the Cancer Research UK charity.
Conserved microRNAs and Flipons Shape Gene Expression during Development by Altering Promoter Conformations

The classical view of gene regulation draws from prokaryotic models, where responses to environmental changes involve operons regulated by sequence-specific protein interactions with DNA, although it is now known that operons are also modulated by small RNAs. In eukaryotes, pathways based on microRNAs (miR) regulate the readout of genomic information from transcripts, while alternative nucleic acid structures encoded by flipons influence the readout of genetic programs from DNA. Here, we provide evidence that miR- and flipon-based mechanisms are deeply connected. We analyze the connection between flipon conformation and the 211 highly conserved human miR that are shared with other placental and other bilateral species. The direct interaction between conserved miR (c-miR) and flipons is supported by sequence alignments and the engagement of argonaute proteins by experimentally validated flipons as well as their enrichment in promoters of coding transcripts important in multicellular development, cell surface glycosylation and glutamatergic synapse specification with significant enrichments at false discovery rates as low as 10−116. We also identify a second subset of c-miR that targets flipons essential for retrotransposon replication, exploiting that vulnerability to limit their spread. We propose that miR can act in a combinatorial manner to regulate the readout of genetic information by specifying when and where flipons form non-B DNA (NoB) conformations, providing the interactions of the conserved hsa-miR-324-3p with RELA and the conserved hsa-miR-744 with ARHGAP5 genes as examples.
Enhanced Approach for Agglomerative Clustering Using Topological Relations

Spatial data clustering has long been used to facilitate the knowledge discovery process. Several approaches have been proposed in the literature for detecting and understanding hidden patterns. These approaches are based on different perspectives and can be roughly categorized into several main categories, including centroid-based, density-based, grid-based, and hierarchy-based clustering. In spite of being a very mature research area, existing spatial clustering techniques usually depend on user parameters and continue to utilize distances between objects as their similarity measure. In turn, clustering approaches are generally suffering from performance and scalability issues. To address this problem, we propose ACUTE, an efficient and scalable approach that detects both synthetic and real-world spatial clusters. ACUTE ascertains both the intra-cluster compactness (similarities) and inter-cluster connectedness (dissimilarities) of spatial objects by assessing the topological relations of their corresponding spatial points. While conventional methods conduct clustering according to pairwise comparisons of the distances between objects, our approach focuses on leveraging topological relations that reduce the distances required to be calculated. This in turn minimizes the number of comparisons required, thus enhancing the efficiency and increasing the scalability. To evaluate the accuracy of ACUTE, it has been extensively tested against twelve (12) synthetic datasets and five (5) actual datasets including one location-based (network) dataset. Results show that ACUTE has great performance when compared with state-of-the-art clustering techniques in terms of several evaluation metrics, including precision, recall, and error rates.
Machine-Learning Aided Multiobjective Optimization of Electric Machines— Geometric-Feasibility and Enhanced Regression Models

This article deals with the optimization of electrical machines by means of artificial neural network (ANN)-based classification and regression models. Geometrically (or otherwise) unfeasible designs are detected with high accuracy during the optimization process by means of an ad hoc classification model, whereas continuous targets are predicted through regression models. Training samples are generated with an expensive finite-element (FE) model, resulting in small training sets. Moreover, the design optimization normally involves multiple but correlated subobjectives. The correlation can be leveraged using chained regression or a multioutput ANN; it is shown that both methods can achieve higher predictive performance than predicting the targets separately. The developed methods are successfully applied to a permanent-magnet synchronous machine (PMSM) with 12 geometric parameters and four subobjectives, and considering both no-load and load operation. The results show very good predictive performance of the ANN models and a significant reduction of the computational effort. The optimization can thus be run several times, with, e.g., modified weighting of the subobjectives, with little extra cost.
Disparity profiles in 3DV applications: overcoming the issue of heterogeneous viewing conditions in stereoscopic delivery

More and more numerous 3D movies are released each year. Thanks to the current spread of 3D-TV displays, these 3D Video (3DV) contents are about to enter massively the homes. Yet viewing conditions determine the stereoscopic features achievable for 3DV material. Because the conditions at home - screen size and distance to screen - differ significantly from a theater, 3D Cinema movies need to be repurposed before broadcast and replication on 3D Blu-ray Discs for being fully enjoyed at home. In that paper we tackle that particular issue of how to handle the variety of viewing conditions in stereoscopic contents delivery. To that extend we first investigate what is basically at stake for granting stereoscopic viewers' comfort, through the well-known - and sometimes dispraised - vergence-accommodation conflict. Thereby we define a set of basic rules that can serve as guidelines for 3DV creation. We propose disparity profiles as new requirements for 3DV production and repurposing. Meeting proposed background and foreground constraints prevents from visual fatigue, and occupying the whole depth budget available grants optimal 3D effects. We present an efficient algorithm for automatic disparity-based 3DV retargeting depending on the viewing conditions. Variants are proposed depending on the input format (stereoscopic binocular content or depth-based format) and the level of complexity achievable.
Transport, radiative, and dynamical effects of the antarctic ozone hole: A GFDL SKYHI' model experiment

Abstract The GFDL “SKYHI” general circulation model has been used to simulate the effect of the Antarctic “ozone hole” phenomenon on the radiative and dynamical environment of the lower stratosphere. Both the polar ozone destruction and photochemical restoration chemistries are calculated by parameterized simplifications of the still somewhat uncertain chemical processes. The modeled total column ozone depletions are near 25% in spring over Antarctica, with 1% depletion reaching equatorial latitudes by the end of the 4½–year model experiment. In the lower stratosphere, ozone reductions of 5% reach to the equator. Large coolings of about 8 K are simulated in the lower stratosphere over Antarctica in late spring, while a general cooling of about 1–1.5 K is present throughout the Southern Hemisphere lower stratosphere. The model atmosphere experiences a long-term positive temperature-chemical feedback because significant ozone reductions carry over into the next winter. The overall temperature response to th.
Cloud Identification and Properties Retrieval of the Fengyun-4A Satellite Using a ResUnet Model

The Advanced Geostationary Radiation Imager (AGRI) onboard the Fengyun-4A (FY4A) satellite has good cloud observation ability, but it still absents all-weather and high-precision official cloud products. This study develops a deep-learning ResUnet model for all-weather retrieval of cloud phase (CLP) and cloud properties using the brightness temperature from water vapor and longwave infrared channels of AGRI. The ResUnet model is trained with the Himawari-8 satellite Level-2 (H8-L2) cloud products as true targets and adopts image-by-image way to learn the spatial structure information of clouds, which compensates for the difficulty of retrieving thick clouds by thermal infrared radiation at night to some extent. On an independent testing dataset, the model has an overall accuracy of 90.64% for CLP identification and performs well at retrieving cloud top height (CTH). Even without using visible and near-infrared radiation, the root-mean-square error of cloud effective radius (CER) and cloud optical thickness (COT) estimations still reaches $7.14 \mu \text{m}$ and 9.01 in the range of 0–60. To further illustrate the reliability and applicability, CLP and cloud properties provided by the Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) and Moderate Resolution Imaging Spectroradiometer (MODIS) are used as benchmarks to assess the quality of cloud products from FY4A satellite Level-2 (FY4A-L2), H8-L2, and ResUnet model retrieval. The ResUnet model provides a significant improvement over FY4A-L2 for the accuracy of cloud identification and in the quality of CTH products. In the range of 0– $40 \mu \text{m}$ (0–60), the CER (COT) product of ResUnet model retrieval has a reliable and higher precision that is comparable with H8-L2.
Effects of speech coding on speaker verification

The impact of speech coding on automatic speaker verification is investigated. Two different coders, classifiers and parametric representations of speech are considered. It is found that coding degrades mean speaker verification accuracy. Classifications of speech frames, for a given speaker, fluctuate by up to 30% relative to the uncoded case.
Research hotspots and frotiers of stem cells in stroke: A bibliometric analysis from 2004 to 2022

Background: Stroke is one of the leading causes of mortality and permanent disability worldwide. However, the current stroke treatment has a limited effect. Therefore, a new treatment is urgently needed. Stem cell therapy is a cutting-edge treatment for stroke patients. This study aimed to gain better understanding of global stem cell trends in stroke via a bibliometric analysis. Methods: We used the Web of Science Core Collection to search pertinent articles about stem cells in stroke published between 2004 and 2022. Analysis was conducted using CiteSpace, VOSviewer, and the R package “bibliometrix” to identify publication outputs, countries/regions, institutions, authors/co-cited authors, journals/co-cited journals, co-cited references, and keywords. Results: A total of 6,703 publications were included in the bibliometric analysis. The total number of citations significantly and rapidly increased between 2004 and 2022, with the most pronounced growth pattern observed in the period of 2008–2009. In terms of authoritarian countries, the USA had the most publications among the countries. As for institutions and authors, the most prolific institution was the University of South Florida, followed by Oakland University and then Shanghai Jiao Tong University, and Chopp, M. and Borlongan, Cesario V, had the most output among the authors. Regarding the journals, Cell Transplantation had the highest publication, followed by Brain Research. As for references, “Mesenchymal stem cells as trophic mediators” was the most frequently cited (2,082), and the article entitled Neuronal replacement from endogenous precursors in the adult brain after stroke had the strongest burstiness (strength = 81.35). Emerging hot words in the past decade included “adhesion molecule,” “mesenchymal stromal cell,” “extracellular vesicle,” “pluripotent stem cells,” “signaling pathway,” “plasticity,” and “exosomes. ” Conclusion: Between 2004 and 2022, the terms “neurogenesis,” “angiogenesis,” “mesenchymal stem cells,” “extracellular vesicle,” “exosomes,” “inflammation,” and “oxidative stress” have emerged as the hot research areas for research on stem cells in stroke. Although stem cells exert a number of positive effects, the main mechanisms for mitigating the damage caused by stroke are still unknown. Clinical challenges may include complicating factors that can affect the efficacy of stem cell therapy, which are worth a deep exploration.
Potential space, dialectics, reflective function, mindfulness and mentalization

The therapeutic encounter becomes transformational through the creation of potential space, dialectics, reflective function, mindfulness or mentalization. This paper dialogues these concepts as employed by different therapeutic modalities within New Zealand, namely; Object-relations (Thomas Ogden and Donald Winnicott), the Conversational Model (Russell Meares), Dialectical Behaviour Therapy (Marsha Linehan) and Mentalization (Anthony Bateman and Peter Fonagy). It suggests that there is sufficient common ground to view them as one concept in different therapeutic bottles.
Immunization and Host Responses to MB-1, a Live Hatchery Vaccine against Infectious Bursal Disease

MB-1 is an attenuated infectious bursal disease virus vaccine. Previously, we observed a temporal delay of vaccine virus replication in the bursae of chicks due to maternally derived antibodies (MDAs). The mechanism that allowed its survival despite MDA neutralization remained unclear. We hypothesized that after vaccination at 1 day of age (DOA), the MB-1 virus penetrates and resides in local macrophages that are then distributed to lymphoid organs. Furthermore, MB-1’s ability to survive within macrophages ensures its survival during effective MDA protection. PCR analysis of lymphoid organs from chicks with MDA, vaccinated on 1 DOA, demonstrated that the MB-1 virus was identified at low levels solely in the spleen pre-14 days of age. Fourteen days after vaccination, the virus was identified using PCR in the bursa, with viral levels increasing with time. The possible delay in viral colonization of the bursa was attributed to the presence of anti-IBDV capsid VP2 maternal IgA and IgY in the bursa interstitium. These indicate that during the period of high MDA levels, a small but viable MB-1 viral reservoir was maintained in the spleen, which might have served to colonize the bursa after MDA levels declined. Thereafter, individual immunization of chicks against Gumboro disease was achieved.
Flow Diverter Device-Assisted Coiling Treatment for Cerebral Blister Aneurysm: A Single-Center Study

Although endovascular treatment is a promising approach, blood blister-like aneurysms (BBAs) still present treatment challenges. This study aimed to assess the effectiveness and safety of flow diverter device-assisted coiling (FDDAC) for the treatment of BBAs, which are broad based and friable with a high rebleeding risk. Eight patients (five females and three males) who presented with subarachnoid hemorrhages (SAH) due to BBA ruptures between May 2020 and May 2022 were retrospectively enrolled. All patients were treated by flow diverter device (Tubridge) adjunctive coil embolization using a semi-deploying technique. The demographic information, angiographic data, interval between admission and treatment, materials, therapy, clinical outcomes (including periprocedural and intraprocedural mortality and morbidity), and follow-up results of all patients were reviewed. The mean age of the patients with BBAs was 48.5 years (range 31–62 years); aneurysm sizes ranged from 2.2 × 1.7 mm to 4.6 × 3.2 mm, and the median Hunt–Hess score was 3. All aneurysms were completely closed at follow-up, and all 8 patients had excellent clinical outcomes (modified Rankin scores = 0–2) at discharge. Angiograms showed complete aneurysm occlusion after 6 months to 1 year. In addition, there were no cases of re-rupture, re-treatment, or recurrence of the aneurysms. FDDAC is safe to use in patients with BBAs and provides an alternative treatment option for this disease.
Kritik Epistemologi Feminis: Upaya De-Westernisasi Ilmu Pengetahuan dalam Perkembangan Konsep Feminisme di Korea Selatan

Modernisasi dan westerinasi yang terjadi secara masif di pada masa awal Korea menyababkan Korea mengalami kemiskinan reproduksi ilmu pengetahuan serta ilmu pengetahuan yang terkolonisasi, khususnya dalam konteks feminisme. Konsep feminisme, keadilan, dan kesetaraan atas hak-hak perempuan di Korea belum menjadi diskursus aktif hingga tahun 1993. Prinsip Konfusianisme yang menjadi akar dari nilai dan tradisi Korea dianggap mengopresi dan melimitasi ruang gerak perempuan, sehingga aktivisme perempuan di Korea dimulai untuk menuntut hak-hak dasarnya. Menggunakan metode kritik epistemologi feminis, penelitian ini dilakukan untuk menelaah pengaruh pemikiran barat terhadap konseptualisasi dan praktik konsep Feminisme dalam masyarakat Konfusianisme Korea dan juga perkembangannya pada era kontemporer. Didukung dengan teori stand point oleh Sandra Harding, peneliti menemukan bahwa diperlukannya upaya de-westernisasi dalam ilmu pengetahuan agar dapat menemukan “warna asli” dari perempuan Korea itu sendiri. Peneliti juga menemukan bahwa diperlukannya dekonstruksi dan rekonspetualisasi ilmu pengetahuan agar feminisme barat dan nilai Konfusius dapat berjalan beriringan secara harmonis.
Silicon to nickel‐silicide axial nanowire heterostructures for high performance electronics

Silicon to nickel disilicide axial nanowire (NW) heterostructures have been fabricated and investigated extensively. To this end, intrinsic Si‐NWs were grown by chemical vapor deposition using Au as the catalyst. The Si‐NWs were contacted with Ni reservoirs so that upon annealing Ni diffused axially into the NWs. Single‐crystalline NiSi2 NW segments were formed at the diffusion path of Ni as proven by high‐resolution transmission electron microscopy images. Further, the axial NiSi2 to Si interfaces showed a sharpness of a couple of nanometers. Fully silicided NiSi2‐NWs had maximal resistivities of 98 μΩ cm and conducted current densities of up to 205 MA/cm2 before breakdown. Controlled silicidation from both NW ends gave NiSi2/Si/NiSi2 axial NW heterostructures, which were implemented to fabricate Schottky contact field effect transistors (FET). The n++‐substrate was used as a common back gate and the Si to NiSi2 interfaces formed the Schottky source‐ and drain‐(S/D) contacts to the active region. These Si‐NW SB‐FETs exhibited p‐type behavior, and current densities in the on state of up to 0.8 MA/cm2 for 1 V bias, the drain current could be modulated over a range of 107. Moreover, the use of thin gate dielectrics enabled inverse subthreshold slopes as low as 110 mV/dec. These data show an efficient gate control over the devices by only using a back gate, due to an enhanced gate field coupling to the tip‐like S/D‐Schottky contacts. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Can ADCs broaden the treatment landscape of metastatic ER+/HER2− breast cancer resistant to CDK4/6 inhibition?

antibody-drugs conjugates (ADCs) and oral selective ER degraders (SERDs) (11,12). In a recent paper by Rugo et al. published in the Journal of Clinical Oncology the use of one such ADC, sacituzumab-govitecan (SG) in ER+/HER2− disease is explored (11)