jimnoneill/paper-to-field-training huggingface dataset:
Resources and datasets for automated high-throughput droplet screening by iSort

Field: Engineering (Physical Sciences)

Contains the design files and source data linked to the following publication in Cell Reports Methods (2023, https://doi.org/10.1016/j.crmeth.2023.100478) iSort enables automated complex microfluidic droplet sorting in an effort to democratize technology. Abstract:
Fluorescence activated droplet sorting (FADS) is a widely used microfluidic technique for high throughput screening. However, it requires highly trained specialists to determine optimal sorting parameters, resulting in a large combinatorial space that is challenging to optimize systematically. Additionally, there is currently no way to track every single droplet within a screen, leading to compromised sorting and “hidden” false positive events. To overcome all these limitations, we have developed a setup in which the droplet frequency, spacing and trajectory at the sorting junction are monitored in real time using impedance analysis. The resulting data is used to continuously optimize all parameters automatically and to counteract perturbations, resulting in higher throughput, higher reproducibility, increased robustness and a beginner-friendly character. We believe this provides a missing piece for the spreading of phenotypic single-cell analysis methods, similar to what we have seen for single-cell genomics platforms. To cite: https://doi.org/10.1016/j.crmeth.2023.100478
GIPC and GAIP Form a Complex with TrkA: A Putative Link between G Protein and Receptor Tyrosine Kinase Pathways

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

NGF initiates the majority of its neurotrophic effects by promoting the activation of the tyrosine kinase receptor TrkA. Here we describe a novel interaction between TrkA and GIPC, a PDZ domain protein. GIPC binds to the juxtamembrane region of TrkA through its PDZ domain. The PDZ domain of GIPC also interacts with GAIP, an RGS (regulators of G protein signaling) protein. GIPC and GAIP are components of a G protein-coupled signaling complex thought to be involved in vesicular trafficking. In transfected HEK 293T cells GIPC, GAIP, and TrkA form a coprecipitable protein complex. Both TrkA and GAIP bind to the PDZ domain of GIPC, but their binding sites within the PDZ domain are different. The association of endogenous GIPC with the TrkA receptor was confirmed by coimmunoprecipitation in PC12 (615) cells stably expressing TrkA. By immunofluorescence GIPC colocalizes with phosphorylated TrkA receptors in retrograde transport vesicles located in the neurites and cell bodies of differentiated PC12 (615) cells. These results suggest that GIPC, like other PDZ domain proteins, serves to cluster transmembrane receptors with signaling molecules. When GIPC is overexpressed in PC12 (615) cells, NGF-induced phosphorylation of mitogen-activated protein (MAP) kinase (Erk1/2) decreases; however, there is no effect on phosphorylation of Akt, phospholipase C-γ1, or Shc. The association of TrkA receptors with GIPC and GAIP plus the inhibition of MAP kinase by GIPC suggests that GIPC may provide a link between TrkA and G protein signaling pathways.
Periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis syndrome: Clinical characteristics and treatment outcomes – a single center study in Japan

Field: Medicine (Health Sciences)

Abstract Background Periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome is an autoinflammatory disease occurring in children. Although PFAPA is the most common periodic fever syndrome found in children, there are only a few studies defining the clinical characteristics and the efficacy of treatment strategies among Japanese children. This study aimed to clarify the demographic characteristics and clinical features of patients with PFAPA syndrome and to evaluate treatment efficacy. Methods We retrospectively reviewed the clinical features of children with PFAPA who visited Saitama Children's Medical Center between January and December 2019. We also evaluated treatment strategies and their efficacy; abortive treatment with corticosteroids, prophylaxis with cimetidine or colchicine, and surgical management with tonsillectomy. Results A total of 100 Japanese children (61% male) with PFAPA were included. Median age of onset was 3 years, median duration of fever episodes was 5 days, and median interval between episodes was 4 weeks. The symptoms (frequencies) were pharyngitis (89%), exudate on tonsils (71%), cervical adenitis (50%), and aphthous stomatitis (49%). Approximately 37% of patients took prednisolone for aborting fever attacks, showing a 100% response; 93% were treated with cimetidine, showing an 79.6% response, and 18% were treated with colchicine, showing a 66.7% response. Only one patient underwent tonsillectomy. Conclusions Among Japanese children with PFAPA, 28% of them were ≥5 years with a male predominance. Pharyngitis is the most frequent symptom associated with fever. Cimetidine is suitable for initial therapy because of its safety and efficacy.
Electrochemical Synthesis of Urea: Co‐Reduction of Nitrite and Carbon Dioxide on Binuclear Cobalt Phthalocyanine

Field: Chemistry (Physical Sciences)

Abstract Exploration of molecular catalysts with the atomic‐level tunability of molecular structures offers promising avenues for developing high‐performance catalysts for the electrochemical co‐reduction reaction of carbon dioxide (CO 2 ) and nitrite (NO 2 − ) into value‐added urea. In this work, a binuclear cobalt phthalocyanine (biCoPc) catalyst is prepared through chemical synthesis and applied as a C─N coupling catalyst toward urea. Achieving a remarkable Faradaic efficiency of 47.4% for urea production at –0.5 V versus reversible hydrogen electrode (RHE), this biCoPc outperforms many known molecular catalysts in this specific application. Its unique planar macromolecular structure and the increased valence state of cobalt promote the adsorption of nitrogenous and carbonaceous species, a critical factor in facilitating the multi‐electron C─N coupling. Combining highly sensitive in situ attenuated total reflection surface‐enhanced infrared absorption spectroscopy (ATR‐SEIRAS) with density functional theory (DFT) calculations, the linear adsorbed CO (CO L ) and bridge adsorbed CO (CO B ) is captured on biCoPc catalyst during the co‐reduction reaction. CO B , a pivotal intermediate in the co‐reduction from CO 2 and nitrite to urea, is evidenced to be labile and may be attacked by nitrite, promoting urea production. This work demonstrates the importance of designing molecular catalysts for efficient co‐reduction of CO 2 and nitrite to urea.
Towards a rapid identification and a novel proteomic analysis for dermatophytes from human and animal dermatophytosis

Field: Immunology and Microbiology (Life Sciences)

Summary Background Since accurate identification of dermatophyte species is essential for epidemiological studies and implementing antifungal treatment, overcoming limitations of conventional diagnostics is a fruitful subject. Objectives and methods In this study, we investigated real‐time polymerase chain reaction(q‐PCR), matrix‐assisted laser desorption/ionisation time of flight mass spectrometry (MALDI‐TOF MS) and nano‐electrospray ionisation mass spectrometry (nano‐ESI‐MS) to detect and identify the most frequently isolated dermatophytes from human and animal dermatophytosis in comparison with conventional methods. Results Among 200 samples, the identified species were Microsporum canis (78.22%), Trichophyton verrucosum (10.89%) and T. mentagrophytes (5.94%). Q‐PCR assay displayed great execution attributes for dermatophytes detection and identification. Using MALDI‐TOF MS, M. canis , but none of T. violacium, T. verrucosum or T. mentagrophytes , could be identified. Nano‐ESI‐MS accurately identified all species. The potential virulence attributes of secreted proteases were anticipated and compared between species. Secreted endoproteases belonging to families/subfamilies of metalloproteases, subtilisins and aspartic protease were detected. The analysed exoproteases are aminopeptidases, dipeptidyl peptidases and carboxypeptidases. Microsporum canis have three immunogenic proteins, siderophore iron transporter mirB, protease inhibitors, plasma membrane proteolipid 3 and annexin. Conclusion In essence, q‐PCR, MALDI‐TOF MS and nano‐ESI‐MS assays are very nearly defeating difficulties of dermatophytes detection and identification, thereby, supplement or supplant conventional diagnosis of dermatophytosis.
Impulse: An Adaptable Memory System

Field: Computer Science (Physical Sciences)

This paper presents the Impulse adaptable memory system, which allows applications to make efficient use of cache space and bus bandwidth. Impulse has a configurable memory controller that allows applications to remap data in the memory system. As a result, applications can control how their data is accessed, organized, and cached. We describe the current design of the Impulse architecture, describe the software transformations that will be necessary to make full use of Impulse, and examine in detail the optimizations that Impulse enables: scatter/gather access to sparse data, no-copy page coloring, and no-copy tile remapping. Results of a simulation study show that Impulse can improve the performance of conjugate gradient by 30%. 1 Introduction Since 1985, microprocessor performance has improved at a rate of 60% per year. In contrast, DRAM latencies have improved by only 7% per year, and DRAM bandwidths by only 15-20% per year. In addition, as the issue rates of processors increase, ...
Micro/nano-scale Manipulation of Material Properties

Field: Materials Science (Physical Sciences)

Femtosecond laser interaction with dielectrics has unique characteristics for micromachining, notably non-thermal interaction with materials, precision and flexibility. The nature of this interaction is highly nonlinear due to multiphoton ionization, so the laser energy can be nonlinearly absorbed by the material, leading to permanent change in the material properties in a localized region of Mu-m3. This dissertation demonstrated the potential of these nonlinear interactions induced changes (index modification and ablation for machining) in the dielectrics and explored several practical applications. We studied femtosecond laser ablation of Poly-methayl methacrylate (PMMA) under single and multiple pulse irradiation regimes. We demonstrated that the onset of surface ablation in dielectric surface is associated with surface swelling, followed by material removal. Also, the shape of the ablation craters becomes polarization dependent with increasing fluence, except for circular polarization. The morphology of the damaged/ablated material was examined by optical and scanning electron microscopy. The dynamics of laser ablation of PMMA was simulated using a 2 dimensional Molecular Dynamics model and a 3 dimensional Finite Difference Time Domain model. The results from numerical simulations agreed well with experimental results presented in this thesis. We also demonstrated the formation of nano-pillar within the ablation crater when the surface of bulk-PMMA was irradiated by two femtosecond pulses at a certain delay with energies below single shot ablation threshold. With increasing fluence, the nano-pillar vanished and the structure within the ablation crater resembled volcanic eruption. At higher fluences we demonstrated nanoscale porosity in PMMA. For application, a novel in-line fiber micro-cantilever was fabricated in bend insensitive fiber, that provides details of in-line measurement of frequency and amplitude of vibration, and can be further extended to be used as chemical/bio and temperature sensors. By modifying the refractive index at random spacing within the single mode fiber core, a unique quasi-random micro-cavities fiber laser was fabricated, which exhibits comparable characteristics with a commercial fiber laser in terms of narrow linewidth and frequency stability.
DETERMINAN UTILISASI LAYANAN WISATA KEBUGARAN (WELLNESS TOURISM) DI RSUP DR. SARDJITO, YOGYAKARTA

Field: Health Professions (Health Sciences)

Wellness tourism have become a new trend for Indonesian people in maintaining their physical and spiritual health. Dr. Sardjito General Central Hospital is one of the hospital institutions that develops medical & wellness tourism services by utilizing Javanese culture and using traditional materials. This study aims to determine the factors that influence patients using wellness tourism. Qualitative research with a phenomenological approach and sample selection using purposive sampling with specified criteria. The total informants were 10 patients, and 5 from service providers such as management, administration and therapists at the Kalimosodo polyclinic. Data collection was carried out through in-depth interviews and thematic analysis. The characteristics of patients using medical and wellness tourism services are women with a high educational background. The determinants of using fitness services at Dr. Sardjito Hospital are that the patient knows the function of the fitness service, the facilities are considered clean and adequate, the service costs are affordable, and the patient also has family support. This study showed that predisposing factors or the patient's personal condition are the dominant factors in utilizing fitness services. The use of Dr. Sardjito Hospital fitness services is influenced by individual characteristics, knowledge and positive perceptions of facilities and quality services. Thus, hospital management needs to increase literacy regarding the benefits of fitness services for patients so that this service becomes increasingly popular and becomes an attractive service option for patients and the public to stay healthy and productive.
Специфіка відображення теми спорту в творах античного мистецтва

Field: Arts and Humanities (Social Sciences)

Aim of work is to identify sport reflection features in ancient art. The paper uses methods of systematization and updating of analytical information about the peculiarities of the reflection of elements related to sports in the styles of the ancient world. The accumulation, systematization and implementation of information is carried out by studying the specialized professional literature and sites depicting the reflection of elements related to sports in ancient art. The main reflections of sports life in ancient art are identified and characterized. There is a description of ancient art that reflects sporting events. A summary analysis of the elements related to sports in the objects of the ancient world. The most interesting in the context of modernity are the elements of joy in Cretan art, the emphasis on dynamism in the first period of Minoan art; didactic orientation of the image of sculptural and pictorial works of sports events. Special attention needs to be paid to objects that are the result of all-Hellenic holidays. The example of creation of art objects on an example of figurines, painting, a vase-painting, minting connected with acrobatic jumps through a bull is considered. The elements of active dynamics, up to the existence of sloping lines in vase-painting and paintings in certain periods, of passive dynamics in the "golden age of Pericles" are shown. Then the visual ideal of athletics was created. The generalization of the classical period does not correspond to the superdynamic modernity. The most interesting emotional facial expression in both sculpture and painting of the period of imperial Rome. Since the II century. B.C. the portrait of the athlete is more and more individualized. The study is based on the study of sport as historically formed in the form of special competitive activities and sports practice socio-cultural phenomenon that promotes the harmonious development of natural and social psychophysiological abilities of motor activity and moral and aesthetic qualities of man, which determines his sports activities. The paper shows the trends in the creation of sculptures, frescoes, reliefs, vase paintings in ancient art, which reflect the sport. Prospects for further research should be related to assessing the impact of various modern processes on the creation of art and design, based on clear characteristics of new materials, a deep understanding of existing and new technological processes, general global trends in society as a whole.
Individual variation in growing-finishing pig feeding patterns

Field: Agricultural and Biological Sciences (Life Sciences)

The feeding patterns of growing-finishing pigs, consisting of intake, duration, frequency and rate, could potentially be used to monitor pig welfare. Feeding patterns, however, contain variation across and within days that appears unrelated to pig welfare and should be considered baseline, such as an increase in intake over time while duration and frequency decrease, and a peak in feeding activity in the afternoon. Although these patterns are clear at group level, many authors have reported large standard deviations around the means, implying that individual pigs may show vastly different patterns. Little is known about the variation in patterns at individual level, nevertheless distinct individual patterns could require different monitoring (e.g. modelling) methods. Our study aimed to gain insight into the feeding patterns of individual pigs, specifically looking into the variation between pigs and within a pig over time. We collected data from electronic feeding stations of 110 pigs (11 pigs/pen) and visualised group and individual patterns. At group level, we saw similar feeding patterns to what was expected from literature. Preliminary results showed distinct feeding strategies at the individual level. Pigs varied, for example, in the time of day during which they fed most and in the balance between feeding frequency and visit size used to obtain daily intake. These individual patterns became clearer with age. We conclude that pigs indeed show individual patterns in feeding behaviour, which develop over time. These individual patterns should be taken into account when developing welfare monitoring systems based on pig feeding patterns.
Cognitive Mechanism of Analogy and its Role in Processes of Primary Metaphor Creation

Field: Arts and Humanities (Social Sciences)

The article deals with the problem of the cognitive nature of metaphor formed in the medium of mythological consciousness of the primitive human. It is supposed that such the main features of the mythological thinking as sensory concreteness and inability to form abstract notions caused the nature of the primary metaphor which was formed through the cognitive mechanism of analogy the surrounding objects and phenomena, and the inner mental states of the human – this metaphor was not linguistic, but concrete and sensory. It is ascertained that the direction of metaphorization in the primitive consciousness was inverted to modern one, because the modern people mind uses more intelligible concrete concepts to express abstract concepts, but the primitive humans conceiving themselves as a part of the nature and understanding their inner world as the outer one projected their inner states, which are comprehended as abstract now, onto the natural phenomena, which can be perceived through the organs of sense. It is argued that formation of critical abstract thinking is related with the development of the human cognitive abilities, what caused the metaphorization veer and also the transition from the mythological mind to linguistic one. It is analyzed three approaches to solving the problem of the relation between language and myth where an important argument was the metaphoricity both of thinking and language: 1) the linguistic theory of myth by M. Müller according to which the loss initial sense of the linguistic metaphor generated myth; 2) the theory of myth based not on the linguistic metaphor, but on the concrete sensory analogy of the real objects and human perceptions (E. Tylor, A. Potebnya); 3) Neo-Kantian theory by E. Cassirer which postulates the simultaneous development of language and myth which have the common sources. It is proved that metaphoricity is inherent in the human mind of every historical period, because the linguistic metaphor is based on the cognitive one, that is the latter makes it possible to comprehend the world and ourselves in this world and express the obtained knowledge by means of language. At the same time, metaphoricity and abstractness of thinking are harmonious processes which provides the productive cognizing of the world and the creative working its results out through the fixation of them in the linguistic forms.
Impact of Management Strategies on Reducing of Mulching Film Residues Pollution in Arid Regions

Field: Environmental Science (Physical Sciences)

Plastic pollution caused by mulching film residues (MFRs) is escalating in arable lands, which affects the function of agricultural ecosystems, and poses a serious obstacle to agricultural sustainable development in arid regions. Internationally, increasing recycling rate of polyethylene (PE) film and adopting biodegradable films are recommended strategies to mitigate plastic pollution in farmland, aiming to increase agricultural sustainability and food security. However, impacts of the future of these strategies remain underexplored. This study estimated MFRs accumulation over the next 50 years under varying PE and polybutylene adipate terephthalate (PBAT) film recovery scenarios: no recovery, and recovery rates increased to 80%, 85%, 90%, and 95%. Additionally, cumulative ecological effects (CEEs) of MFR pollution were assessed based on historical MFRs accumulations of 75 kg hm−2, 160 kg hm−2, 220 kg hm−2, 300 kg hm−2, and 400 kg hm−2, by evaluating direct and indirect ecological effects. The findings revealed that (1) with no recovery, PE film residues could increase by 480 kg hm−2, whereas achieving a 95% recovery rate could limit residues increasing to below the national threshold of 75 kg hm−2, outperforming the 80%, 85%, and 90% recovery rates. On the other hand, using PBAT film would maintain the increasing MFRs below 75 kg hm−2 regardless of recovery rate. (2) Without PE film recovery, CEEs would intensify significantly, as both the direct and indirect effects increase notably, while the CEEs of MFRs could maintain the current status or decrease under the strategy of 95% recovery rate of PE film and using PBAT film, similar to the variation of direct effects. However, indirect effects would persist due to ongoing microplastics (MPs) and phthalate esters (PAEs) released from residual films. Overall, a 95% PE film recycling rate and PBAT film usage emerged as particularly effective strategies for minimizing MFRs accumulation and mitigating ecological impacts over the next 50 years. Further research should prioritize the indirect ecological effects of MFRs, given their persistence despite reduction efforts. The results could provide a theoretical support for agricultural sustainable development in arid regions.