julilili42/papers huggingface dataset:
Protocol for a systematic review of outcomes from microsurgical free-tissue transfer performed on short-term collaborative surgical trips in low-income and middle-income countries
2021-09-08

Abstract Background In many units around the world, microsurgical free-tissue transfer represents the gold standard for reconstruction of significant soft tissue defects following cancer, trauma or infection. However, many reconstructive units in low-income and middle-income countries (LMICs) do not yet have access to the resources, infrastructure or training required to perform any microsurgical procedures. Long-term international collaborations have been formed with annual short-term reconstructive missions conducting microsurgery. In the first instance, these provide reconstructive surgery to those who need it. In the longer-term, they offer an opportunity for teaching and the development of sustainable local services. Methods A PRISMA-compliant systematic review and meta-analysis will be performed. A comprehensive, predetermined search strategy will be applied to the MEDLINE and Embase electronic databases from inception to August 2021. All clinical studies presenting sufficient data on free-tissue transfer performed on short-term collaborative surgical trips (STCSTs) in LMICs will be eligible for inclusion. The primary outcomes are rate of free flap failure, rate of emergency return to theatre for free flap salvage and successful salvage rate. The secondary outcomes include postoperative complications, cost effectiveness, impact on training, burden of disease, legacy and any functional or patient reported outcome measures. Screening of studies, data extraction and assessments of study quality and bias will be conducted by two authors. Individual study quality will be assessed according to the Oxford Evidence-based Medicine Scales of Evidence 2, and risk of bias using either the ‘Revised Cochrane risk of bias tool for randomized trials’ (Rob2), the ‘Risk of bias in non-randomized studies of interventions’ (ROBINS-I) tool, or the National Institute for Health Quality Assessment tool for Case Series. Overall strength of evidence will be assessed according to the Grading of Recommendations, Assessment, Development and Evaluations (GRADE) approach. Discussion To-date the outcomes of microsurgical procedures performed on STCSTs to LMICs are largely unknown. Improved education, funding and allocation of resources are needed to support surgeons in LMICs to perform free-tissue transfer. STCSTs provide a vehicle for sustainable collaboration and training. Disseminating microsurgical skills could improve the care received by patients living with reconstructive pathology in LMICs, but this is poorly established. This study sets out a robust protocol for a systematic review designed to critically analyse outcomes. Systematic review registration PROSPERO 225613
Modeling Bioavailability Limitations of Atrazine Degradation in Soils
2021-09-08

Pesticide persistence in soils is a widespread environmental concern in agro-ecosystems. One particularly persistent pesticide is atrazine, which continues to be found in soils and groundwater in the EU despite having been banned since 2004. A range of physical and biological barriers, such as sorption and mass-transfer into bacterial cells, might limit atrazine degradation in soils. These effects have been observed in experiments and models working with simplified systems. We build on that work by developing a biogeochemical model of the degradation process. We extended existing engineered system models by including refined representations of mass-transfer processes across the cell membrane as well as thermodynamic growth constraints. We estimated model parameters by calibration with data on atrazine degradation, metabolite (hydroxyatrazine) formation, biomass, and isotope fractionation from a set of controlled retentostat/chemostat experiments. We then produced site-specific model predictions for arable topsoil and compared them with field observations of residual atrazine concentrations. We found that the model overestimated long-term atrazine biodegradation in soils, indicating that this process is likely not limited by bioavailability or energetic constraints of microbial growth. However, sorption-limited bioavailability, could explain the long-term fate and persistence of the main degradation metabolite hydroxyatrazine. Future studies should seek alternative controls that drive the observed atrazine persistence in soil. This work helps to bridge the gap between engineered and natural systems, allowing us to use laboratory setups to gain insight into real environmental systems.
Roundtable studying the Anthropocene in Central Asia: the challenge of sources and scales in human–environment relations
2021-09-08

The emerging and vibrant field of environmental humanities to date has not received considerable attention in Central Asia. In light of the Anthropocene crises, there is a real urgency for maturing this field and investigating the methodological and epistemological challenges that environmental topics demand, often working across disciplinary habits and time scales. This roundtable brings together Central Asianists from a range of backgrounds to discuss the sources and scales of their investigation, their challenges and potential. The contributors discuss how particular kinds of sources such as climate models, archival manuscripts, ethnographic fieldwork and media analyses have been used to understand environmental changes in the region. In what ways do the traditions of scholars' disciplinary training guide the scale of analysis? Looking toward the future of environmental humanities in Central Asia, this roundtable suggests paths for developing this vital field of enquiry.
Firewall-as-a-Service for Campus Networks Based on P4-SFC
2021-09-08

Taking care of security is a crucial task for every operator of a campus network. One of the most fundamental security-related network functions that can be found in most networks for this purpose are stateful firewalls. However, deploying firewalls in large campus networks, e.g., at a university, can be challenging. Hardware appliances that can cope with today's high data rates at the border of a campus network are not cost-effective enough for most deployments. Shifting the responsibility to run firewalls to single departments at a university is not feasible because the expertise to manage these devices is not available there. For this reason, we propose a cloud-like infrastructure based on service function chaining (SFC) and network function virtualization (NFV) that allows users to deploy network functions like firewalls at a central place while hiding most technical details from the users.
Inflammatory and regenerative processes in bioresorbable synthetic pulmonary valves up to two years in sheep–Spatiotemporal insights augmented by Raman microspectroscopy
2021-09-09

In situ heart valve tissue engineering is an emerging approach in which resorbable, off-the-shelf available scaffolds are used to induce endogenous heart valve restoration. Such scaffolds are designed to recruit endogenous cells in vivo, which subsequently resorb polymer and produce and remodel new valvular tissue in situ. Recently, preclinical studies using electrospun supramolecular elastomeric valvular grafts have shown that this approach enables in situ regeneration of pulmonary valves with long-term functionality in vivo. However, the evolution and mechanisms of inflammation, polymer absorption and tissue regeneration are largely unknown, and adverse valve remodeling and intra- and inter-valvular variability have been reported. Therefore, the goal of the present study was to gain a mechanistic understanding of the in vivo regenerative processes by combining routine histology and immunohistochemistry, using a comprehensive sheep-specific antibody panel, with Raman microspectroscopy for the spatiotemporal analysis of in situ tissue-engineered pulmonary valves with follow-up to 24 months from a previous preclinical study in sheep. The analyses revealed a strong spatial heterogeneity in the influx of inflammatory cells, graft resorption, and foreign body giant cells. Collagen maturation occurred predominantly between 6 and 12 months after implantation, which was accompanied by a progressive switch to a more quiescent phenotype of infiltrating cells with properties of valvular interstitial cells. Variability among specimens in the extent of tissue remodeling was observed for follow-up times after 6 months. Taken together, these findings advance the understanding of key events and mechanisms in material-driven in situ heart valve tissue engineering. STATEMENT OF SIGNIFICANCE: This study describes for the first time the long-term in vivo inflammatory and regenerative processes that underly in situ heart valve tissue engineering using resorbable synthetic scaffolds. Using a unique combinatorial analysis of immunohistochemistry and Raman microspectroscopy, important spatiotemporal variability in graft resorption and tissue formation was pinpointed in in situ tissue-engineered heart valves, with a follow-up time of up to 24 months in sheep. This variability was correlated to heterogenous regional cellular repopulation, most likely instigated by region-specific differences in surrounding tissue and hemodynamics. The findings of this research contribute to the mechanistic understanding of in situ tissue engineering using resorbable synthetics, which is necessary to enable rational design of improved grafts, and ensure safe and robust clinical translation.
Assessment of single-vessel cerebral blood velocity by phase contrast fMRI
2021-09-09

Current approaches to high-field functional MRI (fMRI) provide 2 means to map hemodynamics at the level of single vessels in the brain. One is through changes in deoxyhemoglobin in venules, i.e., blood oxygenation level–dependent (BOLD) fMRI, while the second is through changes in arteriole diameter, i.e., cerebral blood volume (CBV) fMRI. Here, we introduce cerebral blood flow–related velocity-based fMRI, denoted CBFv-fMRI, which uses high-resolution phase contrast (PC) MRI to form velocity measurements of flow. We use CBFv-fMRI in measure changes in blood velocity in single penetrating microvessels across rat parietal cortex. In contrast to the venule-dominated BOLD and arteriole-dominated CBV fMRI signals, CBFv-fMRI is comparable from both arterioles and venules. A single fMRI platform is used to map changes in blood pO 2 (BOLD), volume (CBV), and velocity (CBFv). This combined high-resolution single-vessel fMRI mapping scheme enables vessel-specific hemodynamic mapping in animal models of normal and diseased states and further has translational potential to map vascular dementia in diseased or injured human brains with ultra–high-field fMRI.
Therapeutic Potential of Sodium Channel Blockers as a Targeted Therapy Approach in KCNA1-Associated Episodic Ataxia and a Comprehensive Review of the Literature
2021-09-09

Introduction: Among genetic paroxysmal movement disorders, variants in ion channel coding genes constitute a major subgroup. Loss-of-function (LOF) variants in KCNA1 , the gene coding for K V 1.1 channels, are associated with episodic ataxia type 1 (EA1), characterized by seconds to minutes-lasting attacks including gait incoordination, limb ataxia, truncal instability, dysarthria, nystagmus, tremor, and occasionally seizures, but also persistent neuromuscular symptoms like myokymia or neuromyotonia. Standard treatment has not yet been developed, and different treatment efforts need to be systematically evaluated. Objective and Methods: Personalized therapeutic regimens tailored to disease-causing pathophysiological mechanisms may offer the specificity required to overcome limitations in therapy. Toward this aim, we (i) reviewed all available clinical reports on treatment response and functional consequences of KCNA1 variants causing EA1, (ii) examined the potential effects on neuronal excitability of all variants using a single compartment conductance-based model and set out to assess the potential of two sodium channel blockers (SCBs: carbamazepine and riluzole) to restore the identified underlying pathophysiological effects of K V 1.1 channels, and (iii) provide a comprehensive review of the literature considering all types of episodic ataxia. Results: Reviewing the treatment efforts of EA1 patients revealed moderate response to acetazolamide and exhibited the strength of SCBs, especially carbamazepine, in the treatment of EA1 patients. Biophysical dysfunction of K V 1.1 channels is typically based on depolarizing shifts of steady-state activation, leading to an LOF of KCNA1 variant channels. Our model predicts a lowered rheobase and an increase of the firing rate on a neuronal level. The estimated concentration dependent effects of carbamazepine and riluzole could partially restore the altered gating properties of dysfunctional variant channels. Conclusion: These data strengthen the potential of SCBs to contribute to functional compensation of dysfunctional K V 1.1 channels. We propose riluzole as a new drug repurposing candidate and highlight the role of personalized approaches to develop standard care for EA1 patients. These results could have implications for clinical practice in future and highlight the need for the development of individualized and targeted therapies for episodic ataxia and genetic paroxysmal disorders in general.
Vertical sonar beam width and scanning behavior of wild belugas (Delphinapterus leucas) in West Greenland
2021-09-09

Echolocation signals of wild beluga whales ( Delphinapterus leucas ) were recorded in 2013 using a vertical, linear 16-hydrophone array at two locations in the pack ice of Baffin Bay, West Greenland. Individual whales were localized for 4:42 minutes of 1:04 hours of recordings. Clicks centered on the recording equipment (i.e. on-axis clicks) were isolated to calculate sonar parameters. We report the first sonar beam estimate of in situ recordings of wild belugas with an average -3 dB asymmetrical vertical beam width of 5.4°, showing a wider ventral beam. This narrow beam width is consistent with estimates from captive belugas; however, our results indicate that beluga sonar beams may not be symmetrical and may differ in wild and captive contexts. The mean apparent source level for on-axis clicks was 212 dB pp re 1 μPa and whales were shown to vertically scan the array from 120 meters distance. Our findings support the hypothesis that highly directional sonar beams and high source levels are an evolutionary adaptation for Arctic odontocetes to reduce unwanted surface echoes from sea ice (i.e., acoustic clutter) and effectively navigate through leads in the pack ice (e.g., find breathing holes). These results provide the first baseline beluga sonar metrics from free-ranging animals using a hydrophone array and are important for acoustic programs throughout the Arctic, particularly for acoustic classification between belugas and narwhals ( Monodon monoceros ).
Immunomonitoring of Human Breast Milk Cells During HCMV-Reactivation
2021-09-09

Background Breast milk leukocytes may play a role in protecting the infant from pathogens. The dynamics and the role of lymphocytes in human cytomegalovirus (HCMV)-seropositive mothers shedding HCMV into breast milk during the first months postpartum (p.p.) are mostly unclear. Methods Breast milk cells were analyzed by Pappenheim panoptic and alpha-naphthyl acetate esterase staining as well as by imaging and polychromatic flow cytometry to simultaneously establish their morphological and phenotypic properties. The latter were characterized in HCMV-seropositive and seronegative mothers ́ breast milk cells at different time points p.p. Results Panoptic staining of breast milk cells revealed the presence of monocytes/macrophages, granulocytes and lymphocytes. Imaging flow cytometry data combining phenotypic and morphological analysis identified NKT-like cells, NK cells, epithelial cells, T cells and monocytes/macrophages. HCMV-seropositive but not -seronegative mothers had significantly higher T cell frequencies in mature milk. Conclusions The presence of lymphocyte subsets in breast milk may be more influenced by the HCMV-seropositivity of the mother than previously recognized.
Identification of the Natural Transformation Genes in Riemerella anatipestifer by Random Transposon Mutagenesis
2021-09-09

In our previous study, it was shown that Riemerella anatipestifer , a Gram-negative bacterium, is naturally competent, but the genes involved in the process of natural transformation remain largely unknown. In this study, a random transposon mutant library was constructed using the R. anatipestifer ATCC11845 strain to screen for the genes involved in natural transformation. Among the 3000 insertion mutants, nine mutants had completely lost the ability of natural transformation, and 14 mutants showed a significant decrease in natural transformation frequency. We found that the genes RA0C_RS04920 , RA0C_RS04915 , RA0C_RS02645 , RA0C_RS04895 , RA0C_RS05130 , RA0C_RS05105 , RA0C_RS09020 , and RA0C_RS04870 are essential for the occurrence of natural transformation in R. anatipestifer ATCC11845. In particular, RA0C_RS04895 , RA0C_RS05130 , RA0C_RS05105 , and RA0C_RS04870 were putatively annotated as ComEC, DprA, ComF, and RecA proteins, respectively, in the NCBI database. However, RA0C_RS02645, RA0C_RS04920, RA0C_RS04915, and RA0C_RS09020 were annotated as proteins with unknown function, with no homology to any well-characterized natural transformation machinery proteins. The homologs of these proteins are mainly distributed in the members of Flavobacteriaceae . Taken together, our results suggest that R. anatipestifer encodes a unique natural transformation machinery.
Development and Evaluation of a Data Privacy Concept for a Frustration-Aware In-Vehicle System
2021-09-09

To realize frustration-aware in-vehicle systems based on real-time user monitoring, personal data have to be recorded, analyzed and&#13;\\n(potentially) stored raising data privacy concerns that may reduce the user acceptance and hence the spread of such systems. Complementing the development of a frustration-aware system with voice interface in the project F-RELACS, a data privacy concept&#13;\\nwas created based on the principles privacy by design and privacy by default recommended in the European General Data Protection&#13;\\nRegulation. Nine criteria were formulated and 23 concrete measures to satisfy the criteria were derived. The measures were evaluated in an online study with 96 participants between 18 and 74 years. On average, the measures were rated as rather sufficient to sufficient. Participants evaluated the use of commercial third-party software for speech processing as most critical. All results are discussed and proposals to further increase the acceptance of frustration-aware systems are outlined.
Geopositioned 3D Areas of Interest for Gaze Analysis
2021-09-09

To understand driver's gaze behavior, the gaze is usually matched to surrounding objects or static areas of interest (AOI) at fixed positions around the car. Full surround object tracking allows for an understanding of the traffic situation. However, because it requires an extensive sensor set and a lot of processing power, it's not yet broadly available in production cars. The use of static AOIs only requires the addition of eye tracking sensors. They are at fixed positions around the car and can't adapt to the environment, therefore their usefulness is limited. We propose geopositioned 3D AOIs. With adaptability and the use of a small sensor set, they combine the strengths of both methods. To test 3D AOIs' capabilities for gaze analysis, a driving simulator study with 74 participants was conducted. We show that 3D AOIs are suitable for driver's gaze analysis and a promising tool for driver intention prediction.
Analysis of a Deep Learning-Based Superresolution Algorithm Tailored to Partial Fourier Gradient Echo Sequences of the Abdomen at 1.5 T
2021-09-10

Objectives The aim of this study was to investigate the feasibility and impact of a novel deep learning superresolution algorithm tailored to partial Fourier allowing retrospectively theoretical acquisition time reduction in 1.5 T T1-weighted gradient echo imaging of the abdomen. Materials and Methods Fifty consecutive patients who underwent a 1.5 T contrast-enhanced magnetic resonance imaging examination of the abdomen between April and May 2021 were included in this retrospective study. After acquisition of a conventional T1-weighted volumetric interpolated breath-hold examination using Dixon for water-fat separation (VIBE Std ), the acquired data were reprocessed including a superresolution algorithm that was optimized for partial Fourier acquisitions (VIBE SR ). To accelerate theoretically the acquisition process, a more aggressive partial Fourier setting was applied in VIBE SR reconstructions practically corresponding to a shorter acquisition for the data included in the retrospective reconstruction. Precontrast, dynamic contrast-enhanced, and postcontrast data sets were processed. Image analysis was performed by 2 radiologists independently in a blinded random order without access to clinical data regarding the following criteria using a Likert scale ranging from 1 to 4 with 4 being the best: noise levels, sharpness and contrast of vessels, sharpness and contrast of organs and lymph nodes, overall image quality, diagnostic confidence, and lesion conspicuity. Wilcoxon signed rank test for paired data was applied to test for significance. Results Mean patient age was 61 ± 14 years. Mean acquisition time for the conventional VIBE Std sequence was 15 ± 1 seconds versus theoretical 13 ± 1 seconds of acquired data used for the VIBE SR reconstruction. Noise levels were evaluated to be better in VIBE SR with a median of 4 (4–4) versus a median of 3 (3–3) in VIBE Std by both readers ( P &lt; 0.001). Sharpness and contrast of vessels as well as organs and lymph nodes were also evaluated to be superior in VIBE SR compared with VIBE Std with a median of 4 (4–4) versus a median of 3 (3–3) ( P &lt; 0.001). Diagnostic confidence was also rated superior in VIBE SR with a median of 4 (4–4) versus a median of 3.5 (3–4) in VIBE Std by reader 1 and with a median of 4 (4–4) for VIBE SR and a median of 4 (4–4) for VIBE Std by reader 2 (both P &lt; 0.001). Conclusions Image enhancement using deep learning–based superresolution tailored to partial Fourier acquisitions of T1-weighted gradient echo imaging of the abdomen provides improved image quality and diagnostic confidence in combination with more aggressive partial Fourier settings leading to shorter scan time.
Imaging of α-Synuclein Aggregates in a Rat Model of Parkinson’s Disease Using Raman Microspectroscopy
2021-09-10

A hallmark of Parkinson’s disease (PD) is the formation of Lewy bodies in the brain. Lewy bodies are rich in the aggregated form of misfolded α-Synuclein (α-Syn). The brain from PD patients can only be analyzed after postmortem, therefore, limiting the diagnosis of PD to the manifestation of motor symptoms. In PD patients and animal models, phosphorylated α-Syn was detected in the peripheral tissues including the gut, thus, raising the hypothesis that early-stage PD could be diagnosed based on colon tissue biopsies. Non-invasive marker-free technologies represent ideal methods to potentially detect aggregated α-Syn in vivo . Raman microspectroscopy has been established for the detection of molecular changes such as alterations of protein structures. Using Raman imaging and microspectroscopy, we analyzed the olfactory bulb in the brain and the muscularis mucosae of colon tissue sections of a human BAC-SNCA transgenic (TG) rat model. Raman images from TG and WT rats were investigated using principal component analysis (PCA) and true component analysis (TCA). Spectral components indicated protein aggregates (spheroidal oligomers) in the TG rat brain and in the colon tissues even at a young age but not in WT. In summary, we have demonstrated that Raman imaging is capable of detecting α-Syn aggregates in colon tissues of a PD rat model and making it a promising tool for future use in PD pathology.