julilili42/papers huggingface dataset:
Training the next generation of researchers in the Organ-on-Chip field
2022-08-05

Organ-on-chip (OoC) technology bridges the principles of biology and engineering to create a new generation of in vitro models and involves highly interdisciplinary collaboration across STEM disciplines. Training the next generation of scientists, technicians and policy makers is a challenge that requires a tailored effort. To promote the qualification, usability, uptake and long-term development of OoC technology, we designed a questionnaire to evaluate the key aspects for training, identify the major stakeholders to be trained, their professional level and specific skillset. The 151 respondents unanimously agreed on the need to train the next generation of OoC researchers and that the training should be provided early, in interdisciplinary subjects and throughout the researchers’ career. We identified two key training priorities: (i) training scientists with a biology background in microfabrication and microfluidics principles and (ii) training OoC developers in pharmacology/toxicology. This makes training in OoC a transdisciplinary challenge rather than an interdisciplinary one. The data acquired and analyzed here serves to guide training initiatives for preparing competent and transdisciplinary researchers, capable of assuring the successful development and application of OoC technologies in academic research, pharmaceutical/chemical/cosmetic industries, personalized medicine and clinical trials on chip.
Combining Clearing and Fluorescence Microscopy for Visualising Changes in Gene Expression and Physiological Responses to <em>Plasmodiophora brassicae</em>
2022-08-05

Infection of Brassica crops by the soilborne protist Plasmodiophora brassicae leads to gall formation on the underground organs. The formation of galls requires cellular reprogramming and changes in the metabolism of the infected plant. This is necessary to establish a pathogen-oriented physiological sink toward which the host nutrients are redirected. For a complete understanding of this particular plant-pathogen interaction and the mechanisms by which host growth and development are subverted and repatterned, it is essential to track and observe the internal changes accompanying gall formation with cellular resolution. Methods combining fluorescent stains and fluorescent proteins are often employed to study anatomical and physiological responses in plants. Unfortunately, the large size of galls and their low transparency act as major hurdles in performing whole-mount observations under the microscope. Moreover, low transparency limits the employment of fluorescence microscopy to study clubroot disease progression and gall formation. This article presents an optimized method for fixing and clearing galls to facilitate epifluorescence and confocal microscopy for inspecting P. brassicae-infected galls. A tissue-clearing protocol for rapid optical clearing was used followed by vibratome sectioning to detect anatomical changes and localize gene expression with promoter fusions and reporter lines tagged with fluorescent proteins. This method will prove useful for studying cellular and physiological responses in other pathogen-triggered structures in plants, such as nematode-induced syncytia and root knots, as well as leaf galls and deformations caused by insects.
An optimal investor-state dispute settlement mechanism
2022-08-06

Abstract Many investment treaties include investor-state dispute settlement (ISDS) provisions which are supposed to protect a foreign investor against opportunistic behavior of a host country. This paper scrutinizes the optimal design of ISDS provisions that solve the holdup problem. It shows that an efficient investor protection mechanism requires an arbitrator as established in investment treaties. However, this arbitrator does neither have to learn nor to evaluate the circumstances of the dispute. Furthermore, any ISDS compensation from the government to the investor should not be based on reductions in investor profits but on the host country’s welfare effects.
Probabilistic solvers enable a straight-forward exploration of numerical uncertainty in neuroscience models
2022-08-06

Abstract Understanding neural computation on the mechanistic level requires models of neurons and neuronal networks. To analyze such models one typically has to solve coupled ordinary differential equations (ODEs), which describe the dynamics of the underlying neural system. These ODEs are solved numerically with deterministic ODE solvers that yield single solutions with either no, or only a global scalar error indicator on precision. It can therefore be challenging to estimate the effect of numerical uncertainty on quantities of interest, such as spike-times and the number of spikes. To overcome this problem, we propose to use recently developed sampling-based probabilistic solvers, which are able to quantify such numerical uncertainties. They neither require detailed insights into the kinetics of the models, nor are they difficult to implement. We show that numerical uncertainty can affect the outcome of typical neuroscience simulations, e.g. jittering spikes by milliseconds or even adding or removing individual spikes from simulations altogether, and demonstrate that probabilistic solvers reveal these numerical uncertainties with only moderate computational overhead.
A Universal Language for Finding Mass Spectrometry Data Patterns
2022-08-07

Abstract Even though raw mass spectrometry data is information rich, the vast majority of the data is underutilized. The ability to interrogate these rich datasets is handicapped by the limited capability and flexibility of existing software. We introduce the Mass Spec Query Language (MassQL) that addresses these issues by enabling an expressive set of mass spectrometry patterns to be queried directly from raw data. MassQL is an open-source mass spectrometry query language for flexible and mass spectrometer manufacturer-independent mining of MS data. We envision the flexibility, scalability, and ease of use of MassQL will empower the mass spectrometry community to take fuller advantage of their mass spectrometry data and accelerate discoveries.
Individual and Situational Factors Influencing Active Behavior in Professional Video Conferences With Strangers
2022-08-07

Since the outbreak of the Covid-19 pandemic, the use of video conferences in professional settings increased rapidly. Here, we examine how individual and situational characteristics jointly predict active behavior in video conferences (i.e., activating one’s webcam, small talk, contacting other attendees) between strangers. We focus on external networking as well as proactive and reactive online networking and social anxiety as individual characteristics and investigate how these interact with social norms (operationalized as proportion of other attendees using the webcam), in predicting our outcome variable active video conference behavior. An online vignette experiment with three conditions (social norms: 25 vs. 75% of other attendees using the webcam vs. offline) was conducted to analyze the self-reported likelihood of active video conference versus active offline behavior. Regression analysis was used to test the hypotheses. Results indicate that external networking is a positive and social anxiety a negative predictor of self-reported active video conference behavior. Furthermore, the likelihood of engaging in active (video conference) behavior differed between the three scenarios, with highest values in the offline scenario and lowest in the online scenario with only 25% of other attendees using the webcam. However, no interaction effects of social norms with social anxiety were found. Overall, the findings suggest that individual differences in networking tendencies and social anxiety and social norms influence active behavior in video conferences independently.
The Successful Incorporation of Nd Into Ba Site of Y0.9Ho0.1Ba2-yNdyCu3O7-δ Bulk Superconductors
2022-08-07

Abstract: This inclusive study reports the effect of the Nd atoms on the mechanical, microstructural, electrical and superconducting characteristics of Y0.9Ho0.1Ba2-yNdyCu3O7-δ superconductors with the aid of standard characterization methods, including X-ray diffraction, scanning electron microscopy, the bulk density, dc resistivity, and transport critical current density. The experimental results such as the degree of granularity, hole localization effect, room temperature resistivity, critical transition temperature, degree of the broadening, thermodynamic fluctuations, crystallinity, crystal plane alignments, crystal structure, grain size, phase purity and lattice parameters, the appearance of flux pinning centers, grain boundary weak-links, surface morphologies elemental compositions and distributions belonging to Y-site Ho and Ba-site Nd substituted Y-123 superconducting samples are discussed in detail for the first time. All the experimental findings show that the microstructural, electrical, mechanical and superconducting properties regularly improve with the increment in the HcN (Ho constant+Nd changeble) until a certain value of y=0.100, beyond which the characteristics tend to retrograde rapidly. This is attributed to the fact that excess penetration of the Nd damages the crucial properties given above.
Abstracts for Free Communications, Thematic Sessions, Round Tables, Posters
2022-08-07

Collected here are the abstracts of the speeches delivered by the participants at the 24th International Congress of Byzantine Studies in the different sessions divided into Free Communications, Thematic Sessions, Round Tables, and Posters. Please refer to the Congress website for an overview of the programme: https://byzcongress2022.org/programme/.
Rewiring Cortico-Muscular Control in the Healthy and Poststroke Human Brain with Proprioceptive β-Band Neurofeedback
2022-08-08

In severely affected stroke survivors, cortico-muscular control is disturbed and volitional upper limb movements often absent. Mental rehearsal of the impaired movement in conjunction with sensory feedback provision are suggested as promising rehabilitation exercises. Knowledge about the underlying neural processes, however, remains vague. In male and female chronic stroke patients with hand paralysis, a brain-computer interface controlled a robotic orthosis and turned sensorimotor β-band desynchronization during motor imagery (MI) of finger extension into contingent hand opening. Healthy control subjects performed the same task and received the same proprioceptive feedback with a robotic orthosis or visual feedback only. Only when proprioceptive feedback was provided, cortico-muscular coherence (CMC) increased with a predominant information flow from the sensorimotor cortex to the finger extensors. This effect (1) was specific to the β frequency band, (2) transferred to a motor task (MT), (3) was proportional to subsequent corticospinal excitability (CSE) and correlated with behavioral changes in the (4) healthy and (5) poststroke condition; notably, MI-related enhancement of β-band CMC in the ipsilesional premotor cortex correlated with motor improvements after the intervention. In the healthy and injured human nervous system, synchronized activation of motor-related cortical and spinal neural pools facilitates, in accordance with the communication-through-coherence hypothesis, cortico-spinal communication and may, thereby, be therapeutically relevant for functional restoration after stroke, when voluntary movements are no longer possible.<b>SIGNIFICANCE STATEMENT</b> This study provides insights into the neural processes that transfer effects of brain-computer interface neurofeedback to subsequent motor behavior. Specifically, volitional control of cortical oscillations and proprioceptive feedback enhances both cortical activity and behaviorally relevant connectivity to the periphery in a topographically circumscribed and frequency-specific way. This enhanced cortico-muscular control can be induced in the healthy and poststroke brain. Thereby, activating the motor cortex with mental rehearsal of the impaired movement and closing the loop by robot-assisted feedback synchronizes ipsilesional premotor cortex and spinal neural pools in the β frequency band. This facilitates, in accordance with the communication-through-coherence hypothesis, cortico-spinal communication and may, thereby, be therapeutically relevant for functional restoration after stroke, when voluntary movements are no longer possible.
A brain atlas of the carrion crow (Corvus corone)
2022-08-08

Abstract Corvidae, passerine songbirds such as jays, crows, and ravens known as corvids, have become model systems for the study of avian cognition. The superior cognitive capabilities of corvids mainly emerge from a disproportionally large telencephalon found in these species. However, a systematic mapping of the neuroanatomy of the corvid brain, and the telencephalon in particular, is lacking so far. Here, we present a brain atlas of the carrion crow, Corvus corone , with special emphasis on the telencephalic pallium. We applied four staining techniques to brain slices (Nissl, myelin, combination of Nissl and myelin, and tyrosine hydroxylase targeting catecholaminergic neurons). This allowed us to identify brain nuclei throughout the brain and delineate the known pallial subdivisions termed hyperpallium, entopallium, mesopallium, nidopallium, arcopallium, and hippocampal complex. The extent of these subdivisions and brain nuclei are described according to stereotaxic coordinates. In addition, 3D depictions of pallial regions were reconstructed from these slices. While the overall organization of the carrion crow's brain matches other songbird brains, the relative proportions and expansions of associative pallial areas differ considerably in agreement with enhanced cognitive skills found in corvids. The presented global organization of the crow brain in stereotaxic coordinates will help to guide future neurobiological studies in corvids.
A Novel and Cross-Species Active Mammalian INDY (NaCT) Inhibitor Ameliorates Hepatic Steatosis in Mice with Diet-Induced Obesity
2022-08-08

Mammalian INDY (mINDY, NaCT, gene symbol SLC13A5) is a potential target for the treatment of metabolically associated fatty liver disease (MAFLD). This study evaluated the effects of a selective, cross-species active, non-competitive, non-substrate-like inhibitor of NaCT. First, the small molecule inhibitor ETG-5773 was evaluated for citrate and succinate uptake and fatty acid synthesis in cell lines expressing both human NaCT and mouse Nact. Once its suitability was established, the inhibitor was evaluated in a diet-induced obesity (DIO) mouse model. DIO mice treated with 15 mg/kg compound ETG-5773 twice daily for 28 days had reduced body weight, fasting blood glucose, and insulin, and improved glucose tolerance. Liver triglycerides were significantly reduced, and body composition was improved by reducing fat mass, supported by a significant reduction in the expression of genes for lipogenesis such as SREBF1 and SCD1. Most of these effects were also evident after a seven-day treatment with the same dose. Further mechanistic investigation in the seven-day study showed increased plasma β-hydroxybutyrate and activated hepatic adenosine monophosphate-activated protein kinase (AMPK), reflecting findings from Indy (−/−) knockout mice. These results suggest that the inhibitor ETG-5773 blocked citrate uptake mediated by mouse and human NaCT to reduce liver steatosis and body fat and improve glucose regulation, proving the concept of NaCT inhibition as a future liver treatment for MAFLD.
Pitfalls in Determining the Electrical Bandwidth of Nonideal Nanomaterials for Photodetection
2022-08-08

The electrical 3 dB bandwidth is regularly used as a measure for the response speed of a photodetector and is estimated via various approaches in literature, ranging from direct measurements to gauged values via approximations. Great care must be taken when comparing these 3 dB bandwidths, since approximations are only strictly valid for ideal circuits. This paper demonstrates that for typical photodetectors based on new emerging nanostructured materials, namely, quantum dots and transition metal dichalcogenides, the bandwidth can deviate up to 103 depending on the chosen approach for the bandwidth specification.
Instrumental swallowing assessment in adults in residential aged care homes: Practice patterns and opportunities
2022-08-08

Abstract Objective To describe practice patterns in the use of instrumental swallowing assessment (ISA) for older adults in residential aged care homes (RACHs). Methods A retrospective audit of medical records of residents living in RACHs in Melbourne, Australia to extract data on speech‐language pathologist (SLP) involvement, indications for ISA and ISA practice patterns. Results Medical files of 323 residents across four Melbourne facilities were reviewed. 36% ( n = 115) of residents were referred to SLP for swallowing assessment. Referral to SLP was related to length of stay ( U = 7393.00, p &lt; 0.001), dementia status ( χ 2 [1] = 7.06, p = 0.008), texture modification ( χ 2 [1] = 93.34, p &lt; 0.001) and an existing dysphagia diagnosis ( χ 2 [1] = 112.89, p &lt; 0.001). There were no referrals for ISA and no instances of ISA being used. Among 115 residents who were referred to SLP for swallowing assessment, there were 33 instances where ISA might be clinically relevant according to ISA indicators. Conclusions Instrumental swallowing assessment is not being used for the management of swallowing in RACHs in Australia despite a clinical need for ISA and a potential role for ISA to improve swallowing care quality. Lack of timely ISA may fail to meet the complex health‐care needs of older adults living with dysphagia in RACHs, increasing their vulnerability to complications of dysphagia and its management.
Xenobiotic responses of Drosophila melanogaster to insecticides with different modes of action and entry
2022-08-08

Abstract Depending on their chemical structure, insecticides enter the insect body either through the cuticle or by ingestion (mode of entry [MoE]), and, naturally, harm or even kill insects through different mechanisms (modes of action). In parallel, they trigger a systemic detoxification response, especially by activation of detoxification gene expression. We monitored the acute genetic alterations of known xenobiotic response target genes against five different insecticides with two most common MoEs (contact toxicity and stomach toxicity), found that: 1. only a few genes were detected responding to acute exposure to insecticides (LD 90 ); 2. The expression of cyp12d1 was upregulated in all experiments, except for dichlorodiphenyltrichloroethane exposure, suggesting that cyp12d1 is a general first response gene of the xenobiotic response; 3. The contact and stomach entries did not show any notable difference, both MoEs induced the response of JNK signaling pathway, possibly serving as the driver of the response of cyp12d1 and a few other genes. In conclusion, the changes in gene expression levels were relatively modest and no significant differences were found between the two MoEs, so the insecticide entry route does not seem to have an impact on the detoxification response. However, the two MoEs of the same insecticide showed different efficiencies in our test. Thus, the study of these two MoEs will help to develop more efficient release and management methods for the use of such insecticides.
Triathletes are experts in self-regulating physical activity – But what about self-regulating neural activity?
2022-08-08

Regular exercise improves cognitive control abilities and successful self-regulation of physical activity. However, it is not clear whether exercising also improves the ability to self-regulate one's own brain activity. We investigated this in 26 triathletes and 25 control participants who did not exercise regularly. Within each group half of the participants performed one session of sensorimotor rhythm (SMR, 12-15 Hz) upregulation neurofeedback training, the other half received a sham neurofeedback training. The neurofeedback training session took about 45 min. In a separate session, participants underwent structural magnetic resonance imaging (MRI) to investigate possible differences in brain structure between triathletes and controls. Triathletes and controls were able to voluntarily upregulate their SMR activity during neurofeedback when receiving real feedback. Triathletes showed a stronger increase in SMR activity in the second half of the training compared to controls, suggesting that triathletes are able to self-regulate their own brain activity over a longer period of time. Further, triathletes and controls showed differences in brain structure as reflected by larger gray and white matter volumes in the inferior frontal gyrus and insula compared to controls. These brain areas are generally involved in cognitive control mechanisms. Our results provide new evidence regarding self-regulation abilities of people who exercise regularly and might impact the practical application of neurofeedback.
How do Teachers Collaborate in Informal Professional Learning Activities? An Epistemic Network Analysis
2022-08-08

Teachers turn to many sources for support and professional learning, including social media-based communities that have shown promise to help teachers access resources and facilitate productive exchanges. Although such online communities show promise, questions about their quality for providing a suitable learning environment remain insufficiently answered. This study examines how teachers’ engagement on Twitter may adhere to characteristics of high-quality professional development activities. In that, we employ advanced conversational analysis techniques that extend the primarily descriptive methods used in prior research. Specifically, we collected data from three Twitter communities related to Advanced Placement Biology (N = 2,040 tweets, N = 93 teachers). Qualitive two-cycle content analyses derived both tweet content and sentiment. Using epistemic network analyses, we examined the collaborative structures to examine how participation patterns can identify characteristics of high-quality teacher professional development. Results indicate that some teachers use Twitter with a content focus and coherent to their individual contexts and prior knowledge. Notably, differences in collaboration and participation patterns by teachers’ overall activity level hint at the existence of an online community of practice. More active teachers communicated more about how their individual contexts relate to instruction, whereas less active teachers exhibited more targeted engagement, for instance, related to sharing teaching resources and organizing learning opportunities. Overall, this study illustrates how Twitter may provide a meaningful learning