Active Bird2Vec: Towards End-to-End Bird Sound Monitoring with Transformers

We propose a shift towards end-to-end learning in bird sound monitoring by combining self-supervised (SSL) and deep active learning (DAL). Leveraging transformer models, we aim to bypass traditional spectrogram conversions, enabling direct raw audio processing. ActiveBird2Vec is set to generate high-quality bird sound representations through SSL, potentially accelerating the assessment of environmental changes and decision-making processes for wind farms. Additionally, we seek to utilize the wide variety of bird vocalizations through DAL, reducing the reliance on extensively labeled datasets by human experts. We plan to curate a comprehensive set of tasks through Huggingface Datasets, enhancing future comparability and reproducibility of bioacoustic research. A comparative analysis between various transformer models will be conducted to evaluate their proficiency in bird sound recognition tasks. We aim to accelerate the progression of avian bioacoustic research and contribute to more effective conservation strategies.Comment: Accepted @AI4S ECAI2023. This is the author's version of the wor

ActiveGLAE: A Benchmark for Deep Active Learning with Transformers

Deep active learning (DAL) seeks to reduce annotation costs by enabling the model to actively query instance annotations from which it expects to learn the most. Despite extensive research, there is currently no standardized evaluation protocol for transformer-based language models in the field of DAL. Diverse experimental settings lead to difficulties in comparing research and deriving recommendations for practitioners. To tackle this challenge, we propose the ActiveGLAE benchmark, a comprehensive collection of data sets and evaluation guidelines for assessing DAL. Our benchmark aims to facilitate and streamline the evaluation process of novel DAL strategies. Additionally, we provide an extensive overview of current practice in DAL with transformer-based language models. We identify three key challenges - data set selection, model training, and DAL settings - that pose difficulties in comparing query strategies. We establish baseline results through an extensive set of experiments as a reference point for evaluating future work. Based on our findings, we provide guidelines for researchers and practitioners.Comment: Accepted @ ECML PKDD 2023. This is the author's version of the work. The definitive Version of Record will be published in the Proceedings of ECML PKDD 202

The Ursinus Weekly, June 8, 1964

Dr. Sturgis retires from faculty after 40 years; Honored by alumni, Saturday • 222 seniors receive degrees at Commencement today; Dr. John Ciardi addresses class and guests • Dr. Roger Staiger given US patent • Whitians select officers • Placement Office report • UC chapter APO chosen to participate in Denver convention • Alumni seek student writers • Editorial: Contemplation • UC hosts Summer assembly: Four denominations represented • Awards presented at WAA banquet • Wagner to attend conference • Paul I. Guest, recipient of 1964 Alumni Award • Student government heads comment on year\u27s activities • Graduation 50 years ago • Permanent class officers announced by seniors • Commencement awards and prizes • New soph rulers plan Fall customs program • Dr. D. Fortnum receives Summer chemistry grant • Greeks name IFS officers • Greek gleanings • Marsteller gets science grant at Colorado State • Library plans Summer changes: Collections expanded • Campus project underway: Bond and Miller design $1,580,000 student activities building • Chest drive totals$1,700https://digitalcommons.ursinus.edu/weekly/1275/thumbnail.jp

Interactive Effects of Biochar, Nitrogen, and Phosphorous on the Symbiotic Performance, Growth, and Nutrient Uptake of Soybean (Glycine max L.)

Numerous studies reported the positive effect of soil amendment with biochar on plant development. However, little is known about biochar and its interrelation with nitrogen (N) and phosphorous (P) additions and their impact on plant growth. We carried out greenhouse experiments to understand the interactive effects of nitrogen and phosphorus supply, as well as biochar amendment, on the symbiotic performance of soybean (Glycine max L.) with Bradyrhizobium japonicum, and plant growth and nutrient uptake. The biochar was produced from maize by heating at 600 °C for 30 min and used for pot experiments at an application rate of 2%. Plants were fertilized with two different concentrations of P (KH2PO4) and N (NH4NO3). Biochar application significantly increased the dry weight of soybean root and shoot biomass, by 34% and 42%, under low nitrogen and low phosphorus supply, respectively. Bradyrhizobium japonicum inoculation enhanced the dry weight of shoot biomass significantly, by 41% and 67%, in soil without biochar and with biochar addition, respectively. The nodule number was 19% higher in plants grown under low N combined with low or high P, than in high N combinations, while biochar application increased nodule number in roots. Moreover, biochar application increased N uptake of plants in all soil treatments with N or P supply, compared with B. japonicum-inoculated and uninoculated plants. A statistical difference in P uptake of plants between biochar and nutrient levels was observed with low N and high P supply in the soil. Our results show that the interactions between nitrogen, phosphorus, and biochar affect soybean growth by improving the symbiotic performance of B. japonicum and the growth and nutrition of soybean. We observed strong positive correlations between plant shoot biomass, root biomass, and N and P uptake. These data indicated that the combined use of biochar and low N, P application can be an effective approach in improving soybean growth with minimum nutrient input.Peer Reviewe

The Effect of Biochars and Endophytic Bacteria on Growth and Root Rot Disease Incidence of Fusarium Infested Narrow-Leafed Lupin (Lupinus angustifolius L.)

The effects of biochar on plant growth vary depending on the applied biochar type, study site environmental conditions, microbial species, and plant–microbial interactions. The objectives of the present study were therefore to assess 1) the response of growth parameters of lupin and root disease incidence to the application of three biochar types in a loamy sandy soil, and 2) the role of endophytic bacteria in biological control of root rot disease incidence in lupin after the amendment of soil with different biochar types. As biochar types we tested (i) hydrochar (HTC) from maize silage, (ii) pyrolysis char from maize (MBC), and (iii) pyrolysis char from wood (WBC) at three different concentrations (1%, 2%, and 3% of char as soil amendments). There were no significant effects in lupin shoot and root growth in soils amended with WBC at any of the concentrations. MBC did not affect plant growth except for root dry weight at 2% MBC. HTC char at 2% concentration, significantly increased the root dry weight of lupin by 54–75%, and shoot dry weight by 21–25%. Lupin plants grown in soil amended with 2% and 3% WBC and MBC chars showed 40–50% and 10–20% disease symptoms, respectively. Plants grown in soil without biochar and with HTC char were healthy, and no disease incidence occurred. Pseudomonas putida L2 and Stenotrophomonas pavanii L8 isolates demonstrated a disease reduction compared to un-inoculated plants under MBC and WBC amended soil that was infested with Fusarium solani.Chinese Academy of SciencesPeer Reviewe

Endoscopic vacuum therapy for in- and outpatient treatment of colorectal defects

Background. Evidence for endoscopic vacuum therapy (EVT) for colorectal defects is still based on small patient series from various institutions, employing different treatment algorithms and methods. As EVT was invented at our institution 20 years ago, the aim was to report the efficacy and safety of EVT for colorectal defects as well as to analyze factors associated with efficacy, therapy duration, and outpatient treatment. Methods. Cohort study with analysis of prospectively collected data of patients receiving EVT for colorectal defects at a tertiary referral center in Germany (n=281). Results. The majority of patients had malignant disease (83%) and an American Society of Anesthesiologists classification of III/IV (81%). Most frequent indications for EVT were anastomotic leakage after sigmoid or rectal resection (67%) followed by rectal stump leakage (20%). EVT was successful in 256 out of 281 patients (91%). EVT following multi-visceral resection (P = 0.037) and recent surgical revision after primary surgery (P = 0.009) were risk factors for EVT failure. EVT-associated adverse events occurred in 27 patients (10%). Median treatment duration was 25 days. Previous chemo-radiation (P = 0.006) was associated with a significant longer duration of EVT. Outpatient treatment was conducted in 49% of patients with a median hospital stay reduction of 15 days and 98% treatment success. Younger patient age (P = 0.044) was associated with the possibility of outpatient treatment. Restoration of intestinal continuity was achieved in 60% of patients where technically possible with a 12-month rate of 52%. Conclusions. In patients with colorectal defects, EVT appears to be a safe and effective, minimally invasive option for in- and outpatient treatment

Infections after kidney transplantation: A comparison of mTOR‐Is and CNIs as basic immunosuppressants. A systematic review and meta‐analysis

Background Side effects of the immunosuppressive therapy after solid organ transplantation are well known. Recently, significant benefits were shown for mTOR‐Is with respect to certain viral infections in comparison with CNIs. However, reported total incidences of infections under mTOR‐Is vs CNIs are usually not different. This raises the question to additional differences between these immunosuppressants regarding development and incidence of infections. Methods The current literature was searched for prospective randomized controlled trials in renal transplantation. There were 954 trials screened of which 19 could be included (9861 pts.). The 1‐year incidence of infections, patient and graft survival were assessed in meta‐analyses. Results Meta‐analysis on 1‐year incidence of infections showed a significant benefit of an mTOR‐I based therapy when combined with a CNI vs CNI‐based therapy alone (OR 0.76). There was no difference between mTOR‐I w/o CNI and CNI therapy (OR 0.97). For pneumonia, a significant disadvantage was seen only for mTOR‐I monotherapy compared to CNI's (OR 2.09). The incidence of CMV infections was significantly reduced under mTOR‐I therapy (combination with CNI: OR 0.30; mTOR w/o CNI: OR: 0.46). There was no significant difference between mTOR‐I and CNI therapy with respect to patient survival (mTOR‐I w/o CNI vs CNI: OR 1.22; mTOR‐I with CNI vs CNI: OR 0.86). Graft survival was negatively affected by mTOR‐I monotherapy (OR 1.52) but not when combined with a CNI (OR 0.97). Conclusion Following renal transplantation the incidence of infections is lower when mTOR‐Is are combined with a CNI compared to a standard CNI therapy. Pneumonia occurs more often under mTOR‐I w/o CNI

The Role of Gut-Derived Lipopolysaccharides and the Intestinal Barrier in Fatty Liver Diseases

BACKGROUND Hepatosteatosis is the earliest stage in the pathogenesis of nonalcoholic fatty (NAFLD) and alcoholic liver disease (ALD). As NAFLD is affecting 10-24% of the general population and approximately 70% of obese patients, it carries a large economic burden and is becoming a major reason for liver transplantation worldwide. ALD is a major cause of morbidity and mortality causing 50% of liver cirrhosis and 10% of liver cancer related death. Increasing evidence has accumulated that gut-derived factors play a crucial role in the development and progression of chronic liver diseases. METHODS A selective literature search was conducted in Medline and PubMed, using the terms \textquotedblnonalcoholic fatty liver disease,\textquotedbl \textquotedblalcoholic liver disease,\textquotedbl \textquotedbllipopolysaccharide,\textquotedbl \textquotedblgut barrier,\textquotedbl and \textquotedblmicrobiome.\textquotedbl RESULTS Gut dysbiosis and gut barrier dysfunction both contribute to chronic liver disease by abnormal regulation of the gut-liver axis. Thereby, gut-derived lipopolysaccharides (LPS) are a key factor in inducing the inflammatory response of liver tissue. The review further underlines that endotoxemia is observed in both NAFLD and ALD patients. LPS plays an important role in conducting liver damage through the LPS-TLR4 signaling pathway. Treatments targeting the gut microbiome and the gut barrier such as fecal microbiota transplantation (FMT), probiotics, prebiotics, synbiotics, and intestinal alkaline phosphatase (IAP) represent potential treatment modalities for NAFLD and ALD. CONCLUSIONS The gut-liver axis plays an important role in the development of liver disease. Treatments targeting the gut microbiome and the gut barrier have shown beneficial effects in attenuating liver inflammation and need to be further investigated

Detection of pre-existing SARS-CoV-2-reactive T cells in unexposed renal transplant patients

Background: Recent data demonstrate potentially protective pre-existing T cells reactive against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in samples of healthy blood donors, collected before the SARS-CoV-2 pandemic. Whether pre-existing immunity is also detectable in immunosuppressed patients is currently not known. Methods: Fifty-seven patients were included in this case-control study. We compared the frequency of SARS-CoV-2-reactive T cells in the samples of 20 renal transplant (RTx) patients to 20 age/gender matched non-immunosuppressed/immune competent healthy individuals collected before the onset of the SARS-CoV-2 pandemic. Seventeen coronavirus disease 2019 (COVID-19) patients were used as positive controls. T cell reactivity against Spike-, Nucleocapsid-, and Membrane-SARS-CoV-2 proteins were analyzed by multi-parameter flow cytometry. Antibodies were analyzed by neutralization assay. Results: Pre-existing SARS-CoV-2-reactive T cells were detected in the majority of unexposed patients and healthy individuals. In RTx patients, 13/20 showed CD4(+) T cells reactive against at least one SARS-CoV-2 protein. CD8(+) T cells reactive against at least one SARS-CoV-2 protein were demonstrated in 12/20 of RTx patients. The frequency and Th1 cytokine expression pattern of pre-formed SARS-CoV-2 reactive T cells did not differ between RTx and non-immunosuppressed healthy individuals. Conclusions: This study shows that the magnitude and functionality of pre-existing SARS-CoV-2 reactive T cell in transplant patients is non-inferior compared to the immune competent cohort. Although several pro-inflammatory cytokines were produced by the detected T cells, further studies are required to prove their antiviral protection

An integrated genetic-demographic model to unravel the origin of genetic structure in European eel (Anguilla anguilla L.)

The evolutionary enlightened management of species with complex life cycles often requires the development of mathematical models integrating demographic and genetic data. The genetic structure of the endangered European eel (Anguilla anguilla L.) has been thoroughly analyzed in several studies in the past years. However, the interpretation of the key demographic and biologic processes that determine the observed spatio-temporal genetic structure has been very challenging owing to the complex life cycle of this catadromous species. Here, we present the first integrated demographic-genetic model applied to the European eel that explicitly accounts for different levels of larval and adult mixing during oceanic migrations and allows us to explore alternative hypotheses on genetic differentiation. Our analyses show that (i) very low levels of mixing occurring during larval dispersal or adult migration are sufficient to erase entirely any genetic differences among sub-populations; (ii) small-scale temporal differentiation in recruitment can arise if the spawning stock is subdivided in distinct reproductive groups; and (iii) the geographic differentiation component might be overestimated if a limited number of temporal recruits are analyzed. Our study can inspire the scientific debate on the interpretation of genetic structure in other species characterized by complex life cycle and long-range migrations