Miracle-dz/UniFAR-FTUs huggingface dataset:
Variability in phytoplankton community structure in response to the North Atlantic Oscillation and implications for organic carbon flux

The North Atlantic Oscillation (NAO) is a major mode of variability in the North Atlantic, dominating atmospheric and oceanic conditions. Here, we examine the phytoplankton community‐structure response to the NAO using the Continuous Plankton Recorder data set. In the Northeast Atlantic, in the transition region between the gyres, variability in the relative influence of subpolar or subtropical‐like conditions is reflected in the physical environment. During positive NAO periods, the region experiences subpolar‐like conditions, with strong wind stress and deep mixed layers. In contrast, during negative NAO periods, the region shifts toward more subtropical‐like conditions. Diatoms dominate the phytoplankton community in positive NAO periods, whereas in negative NAO periods, dinoflagellates outcompete diatoms. The implications for interannual variability in deep ocean carbon flux are examined using data from the Porcupine Abyssal Plain time‐series station. Contrary to expectations, carbon flux to 3000 m is enhanced when diatoms are outcompeted by other phytoplankton functional types. Additionally, highest carbon fluxes were not associated with an increase in biomineral content, which implies that ballasting is not playing a dominant role in controlling the flux of material to the deep ocean in this region. In transition zones between gyre systems, phytoplankton populations can change in response to forcing induced by opposing NAO phases.
Automatic Identification of Architecture Smell Discussions from Stack Overflow

—Architecture Smells (ASs), as one source of technical debt, indicate underlying problems at a high level of systems and negatively impact various system qualities, such as maintainability and evolvability. Detecting and refactoring ASs requires the relevant architectural knowledge and experience. Therefore, gathering the knowledge of ASs from various sources can facilitate ASs detecting and refactoring. However, manually identifying AS knowledge is time-consuming. Automatically and correctly identifying AS-related posts from Stack Overflow is a step toward utilizing the AS knowledge to help developers better maintain their systems. In this work, we propose an approach to automatically identify AS-related posts from Stack Overflow (SoF) by using machine learning algorithms. We evaluate the performance of 12 classifiers based on 3 feature extraction techniques and 4 classification algorithms with a created dataset of SoF posts (including 208 AS-related posts and 187 AS-unrelated posts). The results demonstrate that the SVM algorithm with Word2Vec achieved the best overall performance with an accuracy of 0.650, a precision of 0.613, a recall of 0.905, and an F1-score of 0.731. These results imply that the obtained model of the AS-related posts identification can be used to aid developers and researchers in collecting AS discussions from SoF.
The Need for a National Accreditation Programme for Professionals Working in the Field of Animal Training and Behavioural Modification in New Zealand

Simple Summary Companion animals play an important role in the lives of New Zealanders. Animals’ guardians often engage professional behaviour and training support to ensure their companion animal’s behaviour is compatible with their lifestyle and expectations. The methods these professionals use vary substantially and potentially subject animals to psychological (and physical) harm where outdated, incorrect or aversive methods of training or equipment are used. The national regulation of training methods or techniques would safeguard the welfare of the animal benefactors of these services. In the absence of such regulation, the development of a national accreditation body may act to protect animal welfare by certifying the experience, qualifications and training methods of the professionals offering these services. We investigated industry opinion and readiness for the establishment of an accreditation body via an online survey and found that accreditation, promoting the use of reward-based training and behavioural modification techniques, was generally supported. We conclude that the establishment of a national accreditation body would ensure that those seeking services source professionals who use best practice when it comes to training and behavioural modification, resulting in lasting benefits to animal welfare. Abstract Companion animals are at risk of psychological (and physical) harm if outdated, incorrect or aversive methods of training or equipment are used during training and behavioural modification. Companion animal guardians often engage professional animal behaviour and training services, yet this industry is not regulated in New Zealand. A voluntary national accreditation and registration programme could act to protect the welfare of animals by robustly evaluating the experience, qualifications and training methods of industry professionals. To investigate industry readiness for a national accreditation programme, we conducted an online survey and analysed the responses of 262 animal trainers, behavioural consultants, dog safety educators, veterinarians and veterinary nurses. A national accreditation programme, promoting the use of reward-based training and behavioural modification techniques, was generally supported, especially by individuals holding qualifications and membership of professional organisations. The implementation of such a programme would ensure that those seeking these services are able to source professionals that use best practice when it comes to training and behavioural modification, with lasting benefits to animal welfare.
Adult Urology Oncology: Adrenal/Renal/Upper Tract/Bladder Impact of Time to Surgery and Surgical Delay on Oncologic Outcomes for Renal Cell Carcinoma

From the Section of Urology (BS, PP, DD), University of Manitoba, Winnipeg, Manitoba, Canada, Division of Urology (RHB, LL), University of Ottawa, Ottawa, Ontario, Canada, Ottawa Hospital Research Institute (RMa), Ottawa, Ontario, Canada, Division of Urology (ST), McGill University, Montreal, Quebec, Canada, Department of Urologic Sciences (AS), University of British Columbia, Vancouver, British Columbia, Canada, Division of Urology (RMo), University of Alberta, Edmonton, Alberta, Canada, Department of Urology (RR), Dalhousie University, Halifax, Nova Scotia, Canada, Division of Urology (AK), McMaster University, Hamilton, Ontario, Canada, Division of Urology (FP), Universit e Laval, Quebec City, Quebec, Canada, Division of Urology (AF), University of Toronto, Toronto, Ontario, Canada, Section of Urology (BB), University of Calgary, Calgary, Alberta, Canada, Section of Urology (JBL), Universit e de Montreal, Montreal, Quebec, Canada, Department of Oncology (NB), University of Alberta, Edmonton, Alberta, Canada, Division of Medical Oncology (LW), Dalhousie University, Halifax, Nova Scotia, Canada, Department of Oncology (DH), University of Calgary, Calgary, Alberta, Canada, and Department of Oncology (GB), University of Toronto, Toronto, Ontario, Canada
Elimination of Senescent Neutrophils by TNF-Related Apoptosis-Inducing Ligand1

Neutrophils are phagocytic effectors which are produced in the bone marrow and released into the circulation. Thereafter, they are either recruited to sites of inflammation or rapidly become senescent, return to the bone marrow, and undergo apoptosis. Stromal cell-derived factor 1 (SDF-1) coordinates the return of senescent neutrophils to the bone marrow by interacting with CXCR4 that is preferentially expressed on senescent neutrophils. We demonstrate that CXCR4 ligation by SDF-1 or other CXCR4 agonists significantly increases the expression of both TNF-related apoptosis-inducing ligand (TRAIL) and of the death-inducing TRAIL receptors on neutrophils, which confers an acquired sensitivity to TRAIL-mediated death and results in TRAIL-dependent apoptosis. In vivo administration of TRAIL antagonists results in neutrophilic accumulation within the bone marrow and a reduction in neutrophil apoptosis; conversely recombinant TRAIL administration reduced neutrophil number within bone marrow. Thus, SDF-1 ligation of CXCR4 causes the parallel processes of chemotaxis and enhanced TRAIL and TRAIL death receptor expression, resulting in apoptosis of senescent neutrophils upon their return to the bone marrow.
Green Coffea arabica Extract Ameliorates Testicular Injury in High-Fat Diet/Streptozotocin-Induced Diabetes in Rats

Diabetes mellitus (DM) is a chronic endocrine disease characterized by persistent hyperglycemia. Oxidative damage, inflammatory cytokines, and apoptotic cell death play a major role in the induction and progression of male testicular damage. Plant-derived phytochemicals such as green coffee (Coffea arabica) can possess antidiabetic effects with little toxicity. The current study is aimed at investigating the therapeutic roles of green coffee in diabetic testicular injury stimulated by high-fat diet/streptozotocin administration. Diabetes mellitus was induced by a high-fat diet and a single dose of streptozotocin (STZ) (35 mg kg−1) in male albino rats. Diabetic animals were orally given two different concentrations of green coffee (50 mg kg−1 and 100 mg kg−1) for 28 days. The levels of testosterone, luteinizing hormone, and follicle-stimulating hormone and parameters of oxidative stress, inflammation, and apoptosis were measured. mRNAs and protein levels were detected quantitatively by real-time PCR and ELISA, respectively. In the diabetic group, the levels of testosterone, luteinizing hormone, and follicle-stimulating hormone showed a significant reduction while they increased significantly after green coffee treatment. A significant increase of antioxidant markers glutathione, superoxide dismutase, catalase, glutathione peroxidase, and glutathione reductase along with decreased levels of lipid peroxides and nitric oxide was observed after green coffee treatment in the diabetic group. Finally, the levels of IL-1β, TNF-α, Bax, and caspase-3 were also decreased in both treated groups (metformin and green coffee) when compared to the diabetic group. We conclude that testicular oxidative impairment induced by a high-fat diet (HFD) and STZ can be reversed by green coffee. Administration of green coffee could represent a promising therapeutic agent which can help the treatment of type 2 DM-induced testicular dysfunction.
Novel In Situ Hybridization and Multiplex Immunofluorescence Technology Combined With Whole-slide Digital Image Analysis in Kidney Transplantation

The elusive nature of assessing immunological processes in situ in organ transplantation is one of the major impediments to improve diagnostics and treatment. Here, we present a proof-of-concept study using multiplexed in situ hybridization (ISH) (RNAscope) to detect low-abundance cytokines in formalin-fixed paraffin-embedded (FFPE) human transplant kidney biopsies in combination with immunofluorescence (IF) for cell phenotyping. We show that a multiplex IF and ISH (mIFISH) assay is feasible to identify the cellular source of cytokines and chemokines (tumor necrosis factor-α, interferon-γ, and CXCL9) in FFPE transplant kidney biopsies and that quantification of the mRNA and protein signal is also possible at single-cell resolution in the context of tissue complexity. Furthermore, the mIFISH assay allows precise quantitative assessment of tubulitis, one of the key morphological correlates of alloimmune injury. Simultaneous in situ identification and quantification of multiple cellular phenotypes and mRNA expression of proinflammatory cytokines in FFPE tissues offer a novel insight into the biology of alloimmune injury in kidney transplantation and may contribute to improved diagnostic accuracy and patient care.
Dry Electrodes for Human Bioelectrical Signal Monitoring

Bioelectrical or electrophysiological signals generated by living cells or tissues during daily physiological activities are closely related to the state of the body and organ functions, and therefore are widely used in clinical diagnosis, health monitoring, intelligent control and human-computer interaction. Ag/AgCl electrodes with wet conductive gels are widely used to pick up these bioelectrical signals using electrodes and record them in the form of electroencephalograms, electrocardiograms, electromyography, electrooculograms, etc. However, the inconvenience, instability and infection problems resulting from the use of gel with Ag/AgCl wet electrodes can’t meet the needs of long-term signal acquisition, especially in wearable applications. Hence, focus has shifted toward the study of dry electrodes that can work without gels or adhesives. In this paper, a retrospective overview of the development of dry electrodes used for monitoring bioelectrical signals is provided, including the sensing principles, material selection, device preparation, and measurement performance. In addition, the challenges regarding the limitations of materials, fabrication technologies and wearable performance of dry electrodes are discussed. Finally, the development obstacles and application advantages of different dry electrodes are analyzed to make a comparison and reveal research directions for future studies.
Micropropagation of Alocasia longiloba Miq and Comparative Antioxidant Properties of Ethanolic Extracts of the Field-Grown Plant, In Vitro Propagated and In Vitro-Derived Callus

In this study, an efficient micropropagation protocol was developed for A. longiloba and the antioxidant properties of field-grown plant, in vitro-derived greenhouse-grown plant and in vitro-derived callus extracts were compared. The A. longiloba seeds tested using tetrazolium chloride salt exhibited 89% viability. Due to poor germination capacity of A. longiloba seeds, the seeds were treated with gibberellic acid (GA3) or sulfuric acid (H2SO4). The maximum seed germination of 87% was observed at 30% H2SO4 treatment after 19.00 d, whereas GA3 treatment showed maximum germination of 53% after 22 d. In vitro shoot multiplication was carried out using various types of cytokinins alone or in combination with auxin. Among them, 6-benzyl amino purine (BAP) single treatment was found to be the best hormone. The highest shoot-length (7.26 cm) and maximum number of shoots per explant (18) were recorded at 3-mg L−1 BAP. For in vitro rooting, indole-3-acetic acid at 0.5-mg L−1 was found to be the optimum concentration. Callus was induced using various types of auxins alone or in combinations with cytokinins. The highest percentage of callus of 91 and fresh weight of 6 g was obtained with 3-mg L−1 IAA. The plantlets produced in the current study were subjected to acclimatization. The combination of topsoil and peat moss at 1:2 ratio was found to be the best soil media. In this study, in vitro-derived callus extract showed the highest phenolic content (538 mg GAE), followed by extracts of field-grown plant parts, i.e., fruit and petiole (504 and 300 mg GAE) while in vitro plant extract showed the lowest (98 mg GAE). Meanwhile, the highest flavonoids was recorded in petiole extract. Comparative antioxidant activity study shows, in vitro-derived callus exhibited better DPPH-radical-scavenging activity (IC50: 0.113-mg mL−1) whereas the extracts of petiole, fruit and in vitro plant showed 0.126-, 0.137- and 0.173-mg mL−1, respectively. At the same time, the fruit extract showed better (IC50: 0.088-mg mL−1) ABTS radical scavenging activity than all extracts tested. In conclusion, the in vitro-derived callus extract could be favored for high TPC and better DPPH scavenging activity. Hence, the present study was conducted to establish an efficient micropropagation protocol and to compare the antioxidant activity of the field-grown plant, in vitro plant and in vitro derived callus extracts of A. longiloba.
Gut Microbiota Restricts NETosis in Acute Mesenteric Ischemia-Reperfusion Injury

Supplemental Digital Content is available in the text. Objective: Recruitment of neutrophils and formation of neutrophil extracellular traps (NETs) contribute to lethality in acute mesenteric infarction. To study the impact of the gut microbiota in acute mesenteric infarction, we used gnotobiotic mouse models to investigate whether gut commensals prime the reactivity of neutrophils towards formation of neutrophil extracellular traps (NETosis). Approach and Results: We applied a mesenteric ischemia-reperfusion (I/R) injury model to germ-free (GF) and colonized C57BL/6J mice. By intravital imaging, we quantified leukocyte adherence and NET formation in I/R-injured mesenteric venules. Colonization with gut microbiota or monocolonization with Escherichia coli augmented the adhesion of leukocytes, which was dependent on the TLR4 (Toll-like receptor-4)/TRIF (TIR-domain–containing adapter-inducing interferon-β) pathway. Although neutrophil accumulation was decreased in I/R-injured venules of GF mice, NETosis following I/R injury was significantly enhanced compared with conventionally raised mice or mice colonized with the minimal microbial consortium altered Schaedler flora. Also ex vivo, neutrophils from GF and antibiotic-treated mice showed increased LPS (lipopolysaccharide)-induced NETosis. Enhanced TLR4 signaling in GF neutrophils was due to elevated TLR4 expression and augmented IRF3 (interferon regulatory factor-3) phosphorylation. Likewise, neutrophils from antibiotic-treated conventionally raised mice had increased NET formation before and after ischemia. Increased NETosis in I/R injury was abolished in conventionally raised mice deficient in the TLR adaptor TRIF. In support of the desensitizing influence of enteric LPS, treatment of GF mice with LPS via drinking water diminished LPS-induced NETosis in vitro and in the mesenteric I/R injury model. Conclusions: Collectively, our results identified that the gut microbiota suppresses NETing neutrophil hyperreactivity in mesenteric I/R injury, while ensuring immunovigilance by enhancing neutrophil recruitment.
Accelerated aortic stiffness is associated with brain structure, perfusion and cognition in the Whitehall II Imaging Sub-study

Background: Aortic stiffness is closely linked with cardiovascular diseases, but recent studies suggest that it is also a risk factor for cognitive decline and dementia. However, the brain changes underlying this risk are unclear. We examined whether aortic stiffening in the transition from mid to late-life affects brain structure and cognition. Methods and Findings: Aortic pulse wave velocity was measured in 2007-09 (Phase 9) and at a 4-year follow-up in 2012-13 (Phase 11) in the Whitehall II Imaging Sub-study cohort. Between 2012-2016 (Imaging Phase), participants received a multi-modal 3T brain magnetic resonance imaging (MRI) scans and cognitive tests. Participants were selected if they had no clinical diagnosis of dementia and no gross brain structural abnormalities. Voxel-based analyses were used to assess grey matter volume, white matter microstructure (fractional anisotropy and diffusivity), cerebral blood flow, and white matter lesions. Cognitive outcomes were performance on verbal memory, semantic fluency, working memory and executive function tests. Of 544 participants, 445 (81.8%) were men. The mean (SD) age was 63.9 (5.2) years at the baseline Phase 9 examination, 67.9 (5.3) years at Phase 11 and 69.8 (5.2) years at the Imaging Phase. Voxel-based analysis revealed that accelerated aortic stiffening in mid-to-late life was associated with poor white matter integrity, viz. lower fractional anisotropy in 4.2% of white matter and higher radial diffusivity in 6.7% of white matter, including the corpus callosum, corona radiata, superior longitudinal fasciculus and corticospinal tracts. Accelerated aortic stiffening was also related to lower cerebral perfusion in 1.1% of grey matter including the parietal, frontal, and occipital cortices. No associations with grey matter volume or white matter lesions were observed. Further, higher baseline aortic stiffness was associated with poor semantic fluency (B=-0.48, 95%CI -0.77 to -0.19, p<0.005) and verbal learning outcomes (B=-0.36, 95%CI -0.60 to -0.13, p<0.005). Conclusions: Faster aortic stiffening in mid-to-late life is associated with poor brain white matter microstructural integrity and reduced cerebral perfusion, likely due to increased transmission of pulsatile energy to the delicate cerebral microvasculature. Strategies to prevent arterial stiffening prior to this point may be required to offer cognitive benefit in older age.
Nitrogen inputs into the euphotic zone by vertically migrating Rhizosolenia mats

Rhizosolenia mats conduct extensive vertical migrations in the oligotrophic central North Pacific (cNP) gyre that permit these diatoms to acquire nitrate at depth and return to the surface for photosynthesis. The ultimate fate of this N within the ecosystem is unknown, but may include remineralization by grazing, loss to depth by sinking biomass, or N excretion by Rhizosolenia mats. Direct release of N by mats into the mixed layer would represent an upward biological pump that circumvents the diffusion barriers and nutrient sinks at the base of the oceanic euphotic zone. We examined Rhizosolenia mat N release along a transect (28-31° N) in the summer of 2002 (Hawaii to California) and 2003 (Hawaii to west of Midway Island) using sensitive fluorometric and chemiluminescence methods. Nitrate, NO 2 - and NH 4 + release was determined. Nitrate and NH 4 + release by the mats occurred in both 2002(22.84 ± 6.04 and 3.69 + 1.74 nmol N μg 1 Chl a h -1 , respectively) and 2003 (23.74 ± 3.54 and 3.60 ± 0.74 nmol N μg -1 Chl a h -1 , respectively). Nitrite release only occurred in the 2003 summer period but occurred in both years when Fe chelators were added. Fv/Fm values decreased westward in 2003 suggesting a gradient of increasing physiological stress towards the west. The various physiological measures are consistent with concurrent Fe stress; however, other possibilities exist Nitrate excretion was the dominant form of N release in both years and provided a substantial addition to the ambient nitrate pool in the mixed layer. Rhizosolenia mat nitrate release supplies at least 4-7% of the nitrate pool on daily basis, and possibly as much as 27%. Rhizosolenia mats are part of a large phytoplankton community that appears to migrate, and rates could be significantly higher. Literature reports suggest little or no nitrification in the upper euphotic zone, and thus biological transport and release of nitrate may be a major source to this region. This N release is uncoupled from upward CO 2 transport and, like N 2 fixation, provides a component of the N pool available for net carbon removal.