Miracle-dz/UniFAR-FTUs huggingface dataset:
The neural basis of perceived intensity in natural and artificial touch

Electrical connections between nerves and a prosthetic device enable amputees to discern precise, graded sensory intensity ranging from light touch to intense pressure. Perceived intensity: A touchy subject for neuroprostheses Without tactile sensory input, amputees discern a firm handshake from a bone-crushing grip by visual cues and learned behavior. Next-generation prostheses aim to lend a more natural feel to artificial touch by transmitting nuanced sensory feedback. Graczyk et al. looked at direct stimulation of the radial, ulnar, and median nerves via implanted electrodes in two amputees to understand how levels of intensity are perceived and how tactile sensory feedback is transmitted. By modulating the number of nerve fibers stimulated and the frequency of stimulation, sensory information could be transmitted such that the amputees could distinguish distinct levels of tactile intensity, that is, the difference between a 7 and a 10 on a scale of intensity. Electrical stimulation of sensory nerves is a powerful tool for studying neural coding because it can activate neural populations in ways that natural stimulation cannot. Electrical stimulation of the nerve has also been used to restore sensation to patients who have suffered the loss of a limb. We have used long-term implanted electrical interfaces to elucidate the neural basis of perceived intensity in the sense of touch. To this end, we assessed the sensory correlates of neural firing rate and neuronal population recruitment independently by varying two parameters of nerve stimulation: pulse frequency and pulse width. Specifically, two amputees, chronically implanted with peripheral nerve electrodes, performed each of three psychophysical tasks—intensity discrimination, magnitude scaling, and intensity matching—in response to electrical stimulation of their somatosensory nerves. We found that stimulation pulse width and pulse frequency had systematic, cooperative effects on perceived tactile intensity and that the artificial tactile sensations could be reliably matched to skin indentations on the intact limb. We identified a quantity we termed the activation charge rate (ACR), derived from stimulation parameters, that predicted the magnitude of artificial tactile percepts across all testing conditions. On the basis of principles of nerve fiber recruitment, the ACR represents the total population spike count in the activated neural population. Our findings support the hypothesis that population spike count drives the magnitude of tactile percepts and indicate that sensory magnitude can be manipulated systematically by varying a single stimulation quantity.
Dynamix: dynamic visualization by automatic selection of informative tracks from hundreds of genomic datasets

Motivation: Visualization of genomic data is fundamental for gaining insights into genome function. Yet, co‐visualization of a large number of datasets remains a challenge in all popular genome browsers and the development of new visualization methods is needed to improve the usability and user experience of genome browsers. Results: We present Dynamix, a JBrowse plugin that enables the parallel inspection of hundreds of genomic datasets. Dynamix takes advantage of a priori knowledge to automatically display data tracks with signal within a genomic region of interest. As the user navigates through the genome, Dynamix automatically updates data tracks and limits all manual operations otherwise needed to adjust the data visible on screen. Dynamix also introduces a new carousel view that optimizes screen utilization by enabling users to independently scroll through groups of tracks. Availability and Implementation: Dynamix is hosted at http://furlonglab.embl.de/Dynamix. Contact: charles.girardot@embl.de Supplementary information: Supplementary data are available at Bioinformatics online.
Finding Trends in Software Research

Text mining methods can find large scale trends within research communities. For example, using stable Latent Dirichlet Allocation (a topic modeling algorithm) this study found 10 major topics in 35,391 SE research papers from 34 leading SE venues over the last 25 years (divided, evenly, between conferences and journals). Out study also shows how those topics have changed over recent years. Also, we note that (in the historical record) mono-focusing on a single topic can lead to fewer citations than otherwise. Further, while we find no overall gender bias in SE authorship, we note that women are under-represented in the top-most cited papers in our field. Lastly, we show a previously unreported dichotomy between software conferences and journals (so research topics that succeed at conferences might not succeed at journals, and vice versa). An important aspect of this work is that it is automatic and quickly repeatable (unlike prior SE bibliometric studies that used tediously slow and labor intensive methods). Automation is important since, like any data mining study, its conclusions are skewed by the data used in the analysis. The automatic methods of this paper make it far easier for other researchers to re-apply the analysis to new data, or if they want to use different modeling assumptions.
Differences in Multidisciplinary and Interdisciplinary Treatment Programs for Fibromyalgia: A Mapping Review

Fibromyalgia is a multifaceted chronic pain syndrome and the integration of different health disciplines is strongly recommended for its care. The interventions based on this principle are very heterogeneous and the difference across their structures has not been extensively studied, leading to incorrect conclusions when their outcomes are pooled. The objective of this mapping review was to summarize the characteristics of these programs, with particular focus on the integration of their components. We performed a search of the literature about treatments for fibromyalgia involving multiple disciplines on PubMed and Scopus. Starting from 560 articles, we included 22 noncontrolled studies, 10 controlled studies, and 17 RCTs evaluating the effects of 38 multidisciplinary or interdisciplinary interventions. The average quality of the studies was low. Their outcomes were usually pain intensity, quality of life, and psychological variables. We created a map of the programs based on the degree of integration of the included disciplines, which ranged from a juxtaposition of few components to a complex harmonization of different perspectives obtained through teamwork strategies. The rehabilitation programs were then thoroughly described with regard to the duration, setting, therapeutic components, and professionals included. The implications for future quantitative reviews are discussed.
The Potential Impact of Venobasillar System Morphology and Applied Technique on Epidural Cement Leakage with Percutaneous Vertebroplasty.

BACKGROUND Bone cement leakage during vertebroplasty is a frequently reported complication with the potential for neural injury. OBJECTIVE To assess risk factors for epidural cement leakage during vertebroplasty. SETTING Neurosurgical department of a scientific research institute. STUDY DESIGN This is a prospective cross-sectional randomized trial. METHODS Seventy-five patients with intractable pain due to low energy vertebral compression fractures between T11 and L5 were treated with vertebroplasty at 150 vertebral levels. Preoperative computed tomography (CT) scans were utilized to characterize vertebral parameters including the type of nutrient foramina in the posterior vertebral cortex. Following vertebroplasty, distance from the needle tracts to the midline and the presence and type of any epidural cement leakage were determined. Using logistic regression analysis, significant risk factors for cement leakage were determined. RESULTS A smaller distance between the tip of the needle and the midline and a magistral type of venobasillar system were found to be significant risk factors for epidural cement leakage (P < 0.0001). Use of a bipedicular vs. monopedicular technique did not significantly affect the rate of epidural cement leakage (P = 0.3869). LIMITATIONS This study is limited because of the relatively small number of patients and the lack of any patients who had clinical consequences as a result of extensive epidural cement leakage. CONCLUSION The type of venobasillar system should be taken into account when planning a vertebroplasty procedure as a magistral type of venobasillar system is associated with the increased rate of epidural cement leakage. It is important to try and achieve a large distance between the needle tip and the midline, especially when a magistral type of venobasillar system is present, to reduce the risk of epidural cement leakage.
A qualitative study of pain experiences in patients requiring hip and knee arthroplasty

The aim of this study was to conduct an in-depth investigation of experiences with pain before knee and hip replacement surgery. A total of 20 patients were interviewed, and interpretative phenomenological analysis was used to identify themes. These were as follows: living with pain, pain conceptualised, pain treatments and healthcare system. Pre-surgical pain is very disabling and is viewed as biological. There was an associated loss of independence. Pharmaceutical management is used by all but not entirely effective, psychological therapies are underutilised. Patients were frustrated, angry, and confused about qualifying for surgery. Many areas of care could be improved to help these pre-surgical patients.
The OncoPPi Portal: an integrative resource to explore and prioritize protein–protein interactions for cancer target discovery

Motivation As cancer genomics initiatives move toward comprehensive identification of genetic alterations in cancer, attention is now turning to understanding how interactions among these genes lead to the acquisition of tumor hallmarks. Emerging pharmacological and clinical data suggest a highly promising role of cancer-specific protein-protein interactions (PPIs) as druggable cancer targets. However, large-scale experimental identification of cancer-related PPIs remains challenging, and currently available resources to explore oncogenic PPI networks are limited. Results Recently, we have developed a PPI high-throughput screening platform to detect PPIs between cancer-associated proteins in the context of cancer cells. Here, we present the OncoPPi Portal, an interactive web resource that allows investigators to access, manipulate and interpret a high-quality cancer-focused network of PPIs experimentally detected in cancer cell lines. To facilitate prioritization of PPIs for further biological studies, this resource combines network connectivity analysis, mutual exclusivity analysis of genomic alterations, cellular co-localization of interacting proteins and domain-domain interactions. Estimates of PPI essentiality allow users to evaluate the functional impact of PPI disruption on cancer cell proliferation. Furthermore, connecting the OncoPPi network with the approved drugs and compounds in clinical trials enables discovery of new tumor dependencies to inform strategies to interrogate undruggable targets like tumor suppressors. The OncoPPi Portal serves as a resource for the cancer research community to facilitate discovery of cancer targets and therapeutic development. Availability and implementation The OncoPPi Portal is available at http://oncoppi.emory.edu. Contact andrey.ivanov@emory.edu or hfu@emory.edu.
Glycosphingolipid metabolic reprogramming drives neural differentiation

Neural development is accomplished by differentiation events leading to metabolic reprogramming. Glycosphingolipid metabolism is reprogrammed during neural development with a switch from globo‐ to ganglio‐series glycosphingolipid production. Failure to execute this glycosphingolipid switch leads to neurodevelopmental disorders in humans, indicating that glycosphingolipids are key players in this process. Nevertheless, both the molecular mechanisms that control the glycosphingolipid switch and its function in neurodevelopment are poorly understood. Here, we describe a self‐contained circuit that controls glycosphingolipid reprogramming and neural differentiation. We find that globo‐series glycosphingolipids repress the epigenetic regulator of neuronal gene expression AUTS2. AUTS2 in turn binds and activates the promoter of the first and rate‐limiting ganglioside‐producing enzyme GM3 synthase, thus fostering the synthesis of gangliosides. By this mechanism, the globo–AUTS2 axis controls glycosphingolipid reprogramming and neural gene expression during neural differentiation, which involves this circuit in neurodevelopment and its defects in neuropathology.
Growth of microorganisms on HVAC filters under controlled temperature and humidity conditions

A recirculating duct system was used to challenge a glass fiber media filter, a polymer fiber media filter, and a two-stage electrostatic precipitator (electronic air cleaner) with generated Cladosporium fungal spores and Flavobacterium bacteria. Over a period of a year, the continuous airflow in the ducts was maintained at 70 F (21 C) and 90% relative humidity (RH), but ambient loading was minimal. Filtration efficiency measurements were made, as well as microbial sampling on the surfaces of the filters, to determine filter removal and potential growth of the generated bioaerosols. The electrostatic precipitator demonstrated greater than 90% effectiveness on the fungal and bacterial bioaerosols. The media filters demonstrated initially lower efficiencies, which rose to more than 90% as the filters loaded. At the end of the first year, observable microbial growth took place only on the upstream side of the glass fiber filter. With subsequent nutrient loading and wetting, however, significant microbial growth was found on the downstream side as well as the upstream side of the fiber media filters.
Modifiable parenting factors associated with adolescent alcohol misuse: a systematic review and meta‐analysis of longitudinal studies

BACKGROUND AND AIMS Adolescent alcohol misuse is a growing global health concern. Substantial research suggests that parents have an important role in reducing young people's risk for early initiation of alcohol and alcohol-related harms. To facilitate research translation, we conducted a systematic review and meta-analyses of longitudinal studies examining the range of modifiable parenting factors that are associated with adolescent alcohol initiation and levels of later use/misuse. METHODS A systematic literature search was conducted in PubMed, PsycINFO and Embase. Studies were included if they (i) used a longitudinal design; (ii) were published in English; (iii) measured any modifiable parenting factors in adolescence as predictors; (iv) assessed any alcohol-related outcome variables in adolescence and/or alcohol-related problems in adulthood; and (v) had a follow-up interval of at least 1 year. Parental behaviours were categorized into 12 parenting factors. Stouffer's P analyses were used to determine whether the associations between variables were reliable; when there were sufficient studies available, meta-analyses were also conducted to estimate mean effect sizes. RESULTS Based on 131 studies, three risk factors (parental provision of alcohol, favourable parental attitudes towards alcohol use and parental drinking) and four protective factors (parental monitoring, parent-child relationship quality, parental support and parental involvement) were identified as longitudinal predictors of both alcohol initiation and levels of later alcohol use/misuse, based on their significant results in both Stouffer's P analyses and meta-analyses. The mean effect sizes were mainly small (rs = -0.224 to 0.263). CONCLUSIONS Risk of adolescent alcohol misuse is positively associated with parental provision of alcohol, favourable parental attitudes towards alcohol use and parental drinking. It is negatively associated with parental monitoring, parent-child relationship quality, parental support and parental involvement.
Temporal more than spatial regulation of sway is important for posture in response to an ultra-compliant surface

Abstract Background and aim: Many people use balance training as a rehabilitation or habilitation modality. Although the time course of changes to temporal and spatial aspects of postural sway over the initial weeks of such training is as yet unclear. Particularly, we sought to explore the effects of training on sway during a dynamic task of stance on an ultra-compliant surface. Such a task provides different mechanical, and thus sensorimotor, constraints compared to stance on a solid surface. Methods: Center of pressure (COP) was measured on an ultra-compliant surface atop a force plate at the start of each of 18 days of a 6-week balance training program. Range and standard deviation quantified amount of sway while velocity and Lyapunov exponent (LyE) quantify speed and rhythmicity of sway, respectively. Results: Trend analysis indicated quadratic changes in COP range and standard deviation, with initial reductions followed by returns to initial values by the end of training. Linear reduction of movement velocity and LyE continued through the duration of the program. Reduced LyE indicates regular (self-similar) structure of the COP path. Conclusions: These results provide insight to the developing postural strategy necessary for maintaining upright stance within the dynamics created by interactions with an ultra-compliant surface. Participants showed sensitivity to surface properties, moving both more slowly and with a more regular movement pattern; suggesting that they were able to develop a more feed-forward approach to the maintenance of balance by exploiting task constraints.
Inhibitory Gi/O-coupled receptors in somatosensory neurons: Potential therapeutic targets for novel analgesics

Primary sensory neurons in the dorsal root ganglia and trigeminal ganglia are responsible for sensing mechanical and thermal stimuli, as well as detecting tissue damage. These neurons express ion channels that respond to thermal, mechanical, or chemical cues, conduct action potentials, and mediate transmitter release. These neurons also express a large number of G-protein coupled receptors, which are major transducers for extracellular signaling molecules, and their activation usually modulates the primary transduction pathways. Receptors that couple to phospholipase C via heterotrimeric Gq/11 proteins and those that activate adenylate cyclase via Gs are considered excitatory; they positively regulate somatosensory transduction and they play roles in inflammatory sensitization and pain, and in some cases also in inducing itch. On the other hand, receptors that couple to Gi/o proteins, such as opioid or GABAB receptors, are generally inhibitory. Their activation counteracts the effect of Gs-stimulation by inhibiting adenylate cyclase, as well as exerts effects on ion channels, usually resulting in decreased excitability. This review will summarize knowledge on Gi-coupled receptors in sensory neurons, focusing on their roles in ion channel regulation and discuss their potential as targets for analgesic and antipruritic medications.
Edge Effects Are Important in Supporting Beetle Biodiversity in a Gravel-Bed River Floodplain

Understanding complex, dynamic, and diverse ecosystems is essential for developing sound management and conservation strategies. Gravel-bed river floodplains are composed of an interlinked mosaic of aquatic and terrestrial habitats hosting a diverse, specialized, and endangered fauna. Therefore, they serve as excellent models to investigate the biodiversity of multiple ecotones and related edge effects. In this study, we investigated the abundance, composition, richness, and conservation status of beetle assemblages at varying sediment depth (0, 0.1, 0.6 and 1.1 m), distance from the channel (1, 5, 20, and 60–100 m, and 5 m within the riparian forest), and time of the year (February–November) across a 200 m-wide gravel bar at the near-natural Tagliamento River (Italy), to detect edge effects in four floodplain ecotones: aquatic-terrestrial, forest-active floodplain, sediment-air, and sediment-groundwater. We used conventional pitfall traps and novel tube traps to sample beetles comparably on the sediment surface and within the unsaturated sediments. We found a total of 308 beetle species (including 87 of conservation concern) that showed multiple, significant positive edge effects across the floodplain ecotones, mainly driven by spatial heterogeneity: Total and red list beetle abundance and richness peaked on the sediment surface, at channel margins, and at the edge of the riparian forest. All ecotones possessed edge/habitat specialists. Most red list species occurred on the sediment surface, including five species previously considered extinct – yet two of these species occurred in higher densities in the unsaturated sediments. Conservation and management efforts along gravel-bed rivers must therefore promote a dynamic flow and sediment regime to create and maintain habitat heterogeneity and ecotone diversity, which support a unique and high biodiversity.
Redox Activities and ROS, NO and Phenylpropanoids Production by Axenically Cultured Intact Olive Seedling Roots after Interaction with a Mycorrhizal or a Pathogenic Fungus

Roots of intact olive seedlings, axenically cultured, were alternatively placed in contact with Rhizophagus irregularis (mycorrhizal) or Verticillim dahliae (pathogenic) fungi. MeJA treatments were also included. In vivo redox activities in the apoplast of the intact roots (anion superoxide generation, superoxide dismutase and peroxidase activities) were measured. All our results showed that apoplastic redox activities of intact seedling roots in contact with the compatible mycorrhizal fungus were clearly attenuated in comparison with the pathogenic fungus or treated with MeJA, even at the early stages of treatment used. Total phenolics, flavonoids and phenylpropanoid glycosides were also quantified. Roots in contact with the mycorrhizal fungus did not enhance the biosynthesis of phenolic compounds with respect to controls, while those in contact with the pathogenic one significantly enhanced the biosynthesis of all phenolic fractions measured. Reactive oxygen species and nitric oxid accumulation in roots were examined by fluorescence microscopy. All of them presented much higher accumulation in roots in contact with the pathogenic than with the mycorrhizal fungus. Altogether these results indicate that intact olive seedling roots clearly differentiated between mycorrhizal and pathogenic fungi, attenuating defense reactions against the first to facilitate its establishment, while inducing a strong and sustained defense reaction against the second. Both reactive oxygen and nitrogen species seemed to be involved in these responses from the first moments of contact. However, further investigations are required to clarify the proposed crosstalk between them and their respective roles in these responses since fluorescence images of roots revealed that reactive oxygen species were mainly accumulated in the apoplast (congruently with the measured redox activities in this compartment) while nitric oxid was mainly stored in the cytosol.