bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-modal Language Models in Bioacoustics with Zero-shot Transfer: A Case Study
Authors: Miao Zhongqi , Elizalde Benjamin , Deshmukh Soham , Kitzes Justin , Wang Huaming , Dodhia Rahul , Ferres Juan Lavista 
Published: June 2024

Abstract

Automatically detecting sound events with Artificial Intelligence (AI) has become increasingly popular in the field of bioacoustics, particularly for wildlife monitoring and conservation. Conventional methods predominantly employ supervised learning techniques that depend on substantial amounts of manually annotated bioacoustic data. However, manual annotation in bioacoustics is tremendously resource-intensive in terms of both human labor and financial resources, and it requires considerable domain expertise. Moreover, the supervised learning framework limits the application scope to predefined categories within a closed setting. The recent advent of multi-modal language models has markedly enhanced the versatility and possibilities within the realm of AI applications, as this technique addresses many of the challenges that inhibit the deployment of AI in real-world applications. In this paper, we explore the potential of multi-modal language models in the context of bioacoustics through a case study. We aim to showcase the potential and limitations of multi-modal language models in bioacoustic applications.
In our case study, we applied an Audio-Language model--—a type of multi-modal language model that aligns language with audio data—--named CLAP (Contrastive Language–Audio Pretraining) to eight bioacoustic benchmarks covering a wide variety of sounds previously unfamiliar to the model. We demonstrate that CLAP, out-of-the-box, can effectively recognize group-level categories such as birds, frogs, and whales across the benchmarks without the need for specific model fine-tuning or additional training, achieving a zero-shot transfer recognition performance comparable to supervised learning baselines. Moreover, we show that CLAP has the potential to perform tasks previously unattainable with supervised bioacoustic approaches, such as estimating relative distances and discovering unknown animal species. On the other hand, we also identify limitations of CLAP, such as the model's inability to recognize fine-grained species-level categories and the reliance on manually engineered text prompts in real-world applications.
RETRACTED: Characterization of therapeutic effects in Glioblastoma through integrated spatial single-cell multiome profiling of longitudinal samples: unveiling clinically relevant subtypes of pathological changes
Authors: De Smet Frederik , Vanmechelen Maxime , Nazari Pouya , Beckervordersandforth Jan , Leunissen Daphne , Cole Basiel , Decraene Brecht , De Visser Yanti , Shankar Gautam , Verduin Maikel , Pantano Daniele , González-Blas Carmen Bravo , Bevers Sien , Moors Tom , Telang Jayesh , Sebastian Ivey , Messiaen Julie , Herck Yannick Van , Geens Emma , Eekers Danielle , Claeys Annelies , Derweduwe Marleen , Hausen Axel zur , Bosisio Francesca , Weyns Frank , Daenekindt Thomas , Eyken Peter Van , Govers Mieke , Mennens Ferdinand , Hovinga Koos , De Vleeschouwer Steven , Clement Paul , Broen Martijn , Vooijs Marc , Sciot Raf , Antoranz Asier , Pey Jon , Speel Ernst-Jan , Hoeben Ann 
Published: June 2024

Abstract

The authors have requested that this preprint be removed from Research Square.
Feasibility of iodine concentration parameter and extracellular volume fraction derived from dual-energy CT for distinguishing type Ⅰ and type Ⅱ epithelial ovarian carcinoma
Authors: Song Qingling , Li Ye , Wu Tingfan , Hu Wenjun , Liu Yijun , Liu Ailian 
Published: June 2024

Abstract

Objectives: To investigate the feasibility of using the iodine concentration (IC) parameter and extracellular volume (ECV) fraction derived from dual-energy CT for distinguishing between type Ⅰ and type Ⅱ epithelial ovarian carcinoma (EOC).
Methods: This study retrospectively included 140 patients with EOC preoperatively underwent dual-energy CT scans. Patients were grouped as type Ⅰ and type Ⅱ EOC according to postoperatively pathologic results. Normalized IC (NIC, %) values from arterial-phase (AP), venous-phase (VP) and delay-phase (DP) were measured by two observers. ECV fraction (%) was calculated by DP-NIC and hematocrit. Intra-observer correlation coefficient (ICC) was used to assess the agreement between measurements made by two observers. The differences of imaging parameters between the two groups were compared. Logistic regression was used to select independent predictive factors and establish combined parameter. Receiver operating characteristic curve was used to analyze performance of all parameters.
Results: The ICCs for all parameters exceeded 0.75. All parameters in type Ⅱ EOC were all significantly higher than those in type Ⅰ EOC (all P < 0.05). DP-NIC exhibited the highest Area under the curve (AUC) of 0.828, along with 88.51% sensitivity and 62.26% specificity. DP-NIC was identified as the independent factor. The sensitivity and specificity of ECV fraction were 83.91% and 67.92%, respectively. The combined parameter consisting of AP-NIC, VP-NIC, DP-NIC, and ECV fraction yielded an AUC of 0.848, with sensitivity of 82.76% and specificity of 75.47%. The AUC of the combined parameter was significantly higher than that of VP-NIC (P = 0.042).
Conclusion: It is valuable for dual-energy CT IC-based parameters and ECV fraction in preoperatively identifying type Ⅰ and type Ⅱ EOC.
Critical relevance statement
Dual-energy CT-normalized iodine concentration and extracellular volume fraction achieved satisfactory discriminative efficacy, distinguishing between type Ⅰ and type Ⅱ epithelial ovarian carcinoma.
Development of a new EGFR-VHH-CAR T-cell therapy for treatment of esophageal squamous cell carcinoma
Authors: Zhang Chenglin , Liu Yanyan , zhou danya , guo haoran , peng ying , Lian xueqi , lu shuangshuang , huang lei , wang zhimin 
Published: June 2024

Abstract

Esophageal squamous cell carcinoma (ESCC), a primary form of esophageal cancer, is characterized by poor outcomes and limited treatment options. Targeting EGFR with chimeric antigen receptor-modified T cells (EGFR CAR-T) has emerged as a promising therapeutic approach for ESCC. Utilizing nanobodies enhances the specificity of antigen recognition and has become a popular method in CAR-T cell therapy. In this study, we introduced an EGFR-specific nanobody, EGFR-VHH-7D12, into the receptor binding domain of EGFR CAR-T cells and incorporated human interleukin 21 (hIL-21) to boost the efficacy of these cells. Our findings show that EGFR-VHH-7D12-equipped CAR-T cells can accurately target and eliminate EGFR-positive esophageal cancer cells both in vitro and in animal models. The addition of hIL-21 not only increased the proliferation of CAR-T cells but also led to a higher formation of memory T cell subsets in vitro. Furthermore, the presence of hIL-21 in these CAR-T cells resulted in increased expression of IFN-gamma when cultured with various human esophageal cancer cell lines (KYSE-30, KYSE-150, and KYSE-510) in vitro. Notably, CAR-T cells expressing both EGFR-VHH-7D12 and hIL-21 showed superior anti-tumor activity in a KYSE-150 xenograft mouse model. Our results indicate that the combined expression of hIL-21 in 7D12-CAR-T cells significantly enhances their anti-tumor capabilities, making them a highly promising option for ESCC treatment.
Effect of stabilizers on the detection of swine influenza A virus (swIAV) in spiked oral fluids over time
Authors: Grau K. , Lillie-Jaschniski K. , Graaf-Rau A. , Harder T. , Eddicks M. , Zöls S. , Zablotski Y. , Ritzmann M. , Stadler J. 
Published: June 2024

Abstract

Background
Aggregated samples such as oral fluids (OFs) display an animal friendly and time and cost-efficient sample type for swine Influenza A virus (swIAV) monitoring. However, further molecular and biological characterization of swIAV is of particular significance. The reportedly inferior suitability of aggregated samples for subtyping of swIAV presents a major drawback compared to nasal swabs, still considered the most appropriate sample type for this purpose (1). In addition, the viral load in the original sample, storage conditions and characteristics of different swIAV strains might further compromise the eligibility of aggregated samples for molecular detection and subtyping.
Therefore, the present study aimed to evaluate the suitability of stabilizing media to minimize the degradation of viral RNA and thus increase the detection and subtyping rate of swIAV by RT-qPCR in spiked OFs under different conditions (virus strain, storage temperature and viral load in the original sample) over a time span of 14 days.
Results
The use of stabilizing media in spiked OFs resulted in a significant higher probability to detect swIAV RNA compared to OFs without stabilizers (OR = 46.1, p < 0.001). In addition, the probability of swIAV degradation over time was significantly reduced in samples suspended with stabilizer (OR = 5.80, p < 0.001), in samples stored at 4°C (OR = 2.53, p < 0.001) and in samples spiked with the avian derived H1N1 subtype (OR = 2.26, p < 0.01). No significant differences in swIAV RNA detection and degradation of swIAV RNA in spiked OFs over time were observed between the three different stabilizing media.
Conclusion
Addition of stabilizers and storage of samples at cooled conditions highly significantly improved detection and subtyping of swIAV in spiked OFs.
Association between humoral serological markers levels and risk of SARS-CoV-2 infection after the primary COVID-19 vaccine course among ANRS0001S COV- POPART cohort participants
Authors: Chalouni Mathieu , Loubet Paul , Lhomme Edouard , Ninove Laetitia , Barrou Benoit , Blay Jean-Yves , Hourmant Maryvonne , Seze Jérome , Laville Martine , Laviolle Bruno , Lelièvre Jean-Daniel , Morel Jacques , Quoc Stéphanie Nguyen , Spano Jean-Philippe , Terrier Benjamin , Thiebaut Anne , Viallard Jean-Francois , Vrtovsnik François , Circosta Sophie , Barquin Aude , Gharib Mariam , Tartour Eric , Parfait Béatrice , Thiébaut Rodolphe , Meyer Laurence , Lamballerie Xavier , Launay Odile , Wittkop Linda 
Published: June 2024

Abstract

Background We assessed the prognostic value of serological humoral markers measured one month after the last dose of the primary COVID-19 vaccine course for predicting the risk of severe acute respiratory syndrome coronavirus 2 SARS-CoV-2 infection over the following six months in specific populations.Methods ANRS0001SCOV-POPART (NCT04824651) is a French nationwide multicenter prospective observational cohort study assessing the immune response to Covid-19 vaccines routinely administered to 11 subgroups of patients with chronic disease and a control group. Participants from the ANRS0001S COV-POPART were included if they received at least two doses of Covid-19 vaccine for the primary vaccine course, had measurements of anti-Spike, anti-receptor binding domain (RBD) IgG-specific or neutralizing antibodies one month after the end of the primary vaccine course, without being infected by SARS-CoV-2 before the measurement. SARS-CoV-2 infections defined by a positive PCR/antigenic test or seroconversion to detectable anti nucleocapsid antibodies were evaluated until the first COVID-19 booster injection. Cox proportional hazards models taking into account interval-censored data were implemented to estimate the association between each antibody level and the risk of SARS-CoV-2 infection. Predictive performances were evaluated by the area under the receiving operating characteristic curve (AUROC).Results 2,570 adults with a chronic disease and 1,123 without a condition of interest were included. The cumulative probabilities of SARS-CoV-2 infections at five months were 6.0% 95% confidence interval: [5.0; 7.9] and 10.1% [8.3; 11.9], respectively. Higher levels of anti-Spike IgG antibody were associated with a lower risk of SARS-CoV-2 infections in participants without a condition of interest, but not in the specific populations. Among the specific populations, AUROC were 74.5%, 74.9%, and 72.4% for anti-Spike IgG, anti-RBD IgG, and neutralizing antibodies, respectively. AUROC were superior in participants without a condition of interest, 82.0%, 81.2%, and 81.4% for anti-Spike IgG, anti-RBD IgG, and neutralizing antibodies, respectively.Conclusions Vaccine-induced antibody response after the primary course of Covid-19 infection only moderately discriminated between participants developing a SARS-CoV-2 infection during the Omicron wave.
Outcome after nintedanib therapy for fibrosing interstitial lung disease in patients without dyspnea
Authors: Okamoto Masaki , Yanagihara Toyoshi , Fujimoto Kiminori , Chikasue Tomonori , Tabata Kazuhiro , Zaizen Yoshiaki , Tominaga Masaki , Sumi Akiko , Nishii Yuuya , Matsuo Norikazu , Nouno Takashi , Kawaguchi Atsuhi , Hoshino Tomoaki 
Published: June 2024

Abstract

The effectiveness and tolerability of antifibrotic drugs for asymptomatic patients with fibrosing interstitial lung disease (FILD) are unknown. We compared outcomes after starting nintedanib between 17 patients without dyspnea and 56 with dyspnea, adjusting for confounding factors associated with prognosis of FILD. At baseline, there were no significant differences in the incidence of > 4% decrease (69% vs. 89%, P = 0.11) or decrease to < 90% (25% vs. 54%, P = 0.051) in SpO2 in 6-minute walk test. The incidence of annual progression [defined as > 10% decrease in forced vital capacity (FVC) or 15% decrease in diffusing capacity of lungs for carbon monoxide (DLCO), developing acute exacerbation, or FILD-related death] was significantly lower in non-dyspnea than dyspnea group (18% vs. 52%, adjusted P = 0.044). The relative change in DLCO was significantly slower in non-dyspnea group (adjusted P = 0.044), but FVC was not (adjusted P = 0.079). Overall survival defined by FILD-related death was longer in non-dyspnea group (adjusted P = 0.010). The discontinuation rate and therapeutic period of nintedanib were not significantly different between the two groups. Asymptomatic patients with FILD can have severe exercise-induced hypoxia and better outcome after nintedanib therapy compared with symptomatic patients. Antifibrotic drug therapy should not be avoided solely based on absence of symptoms.
A Comparative assessment of ant species richness under different shade coverages in the Coffee agroecosystem
Authors: Venugopal Remya , Swaran P R 
Published: June 2024

Abstract

Ants play key role in environment management due to their abundance, Diversity and functional importance. The present study examined the ant species diversity and relative abundance in coffee agro-ecosystem of Wayanad region of the Western Ghats (110.27’00”&110.58’52” and the East Longitude 750.47’50”&760.27’35”) under different intensity of canopies. Ants were recorded from August 2022 to September 2023 from all three sampling locations belonging to six coffee plantations ie; Site 1-Highly Shaded (HSC), Site 2-Moderately Shaded (MSC) and Site 3 -open (OC) coffee plantation. Ants were sampled by using pitfall traps, honey baits, litter sifting, soil core extraction, and transect sampling methods. During the study period, a total of 5311 individual ants were collected representing 51 species in 26 genera, and six subfamilies. The distribution of ants in different subfamily showed a dominance of Formicinae with seventeen morpho-species (32%) followed by Myrmicinae (28%). Shannon-Weiner (H1) diversity index value of site 1 has 3.435 while site 2 has an H1 value of 3.477and site 3 has 3.197. Site 2 has a slightly higher H1 value than site 1 owing to its high species richness of 48 ant species and site 3 has lowest H1 value with 38 ant species. Site 3 has higher Simpson’s (D) diversity index value than site 2 and site 1. High species dominance in habitat would automatically mean that there would be low evenness.
Research on the correlation between rash and complement C3, C4 levels and the occurrence and development of lupus nephritis
Authors: luo fei , Chen Yongkang , Xie Jingzhi , Zeng Yanzhen , Wei Jingwen , Liu Runzhi , Yin Hanqiu , Yin Songlou , Duan Lili , Zhou Dongmei 
Published: June 2024

Abstract

Objective
We here investigate the relationship between the appearance of skin rash, complement, and the risk of systemic lupus erythematosus and lupus nephritis.
Methods
All data were collected from 71 patients with SLE (without LN) and 200 patients with LN treated at our hospital from August 2018 to August 2023. The latter group was further categorized into a high eGFR group (eGFR ≥ 60 ml/min; 100 cases) and a low eGFR group (eGFR < 60 ml/min; 100 cases). Basic clinical characteristics such as gender, age, fever, joint pain, rash, hair loss, along with laboratory indicators including cystatin C, complement C3, complement C4, and anti-dsDNA titers were gathered. The differences in clinical characteristics and hematological indicators between the SLE group and the LN group, as well as between the high eGFR group and the low eGFR group patients, were compared. Binary logistic regression analysis was employed to identify independent risk factors for the progression from SLE to LN and independent risk factors for the deterioration of renal function in LN. Correlation studies were conducted to elucidate the relationship between independent factors and the disease. The predictive value of risk was assessed using ROC curves.
Results
Compared to the SLE group, the absence of skin rash and low complement C3 levels were significantly associated with the occurrence of LN. Multifactor analysis revealed that both skin rash (OR: 0.231, P < 0.001) and complement C3 (OR: 0.080, P < 0.001) were influencing factors for the development of lupus nephritis, while SLEDAI scores consistently showed no statistical significance. The combination of no skin rash and low complement C3 levels had an area under the curve (AUC) of 0.708 in relation to LN, with a diagnostic sensitivity of 0.83 and specificity of 0.70, demonstrating good predictive efficacy. In the progression of LN, the absence of skin rash and low levels of complement C3 and C4 were significant in differential and correlation analyses; however, in multifactor analysis, low levels of complement C3 and C4 showed no statistical significance with p-value > 0.05. SLEDAI scores remained statistically insignificant, possibly due to treatment-induced differences.
Conclusion
The absence of skin rash and low levels of complement C3 are risk factors for the occurrence of LN, and their combined predictive diagnostic value is higher. Disease activity may not necessarily be the sole factor for further deterioration of kidney function.
Correlations between lichen planus and autoimmune diseases: A mendelian randomization study
Authors: Long Xuan , Zhang Guiying , Wang Qiaolin , Liao Jieyue , Zhou Wenyu 
Published: June 2024

Abstract

Background
Previous observational studies have found that lichen planus (LP) is associated with autoimmune diseases. To determine the association between LP and 15 autoimmune diseases, we applied the Mendelian randomization (MR) approach, which uses genetic variants as a tool to improve causal inference.
Methods
We performed a two-sample MR with the genetic instruments identified for 15 autoimmune diseases. Genome-wide association study (GWAS) data for LP was sourced from the FinnGen (1,865 cases and 212,242 non-cases). The instrumental variables (IVs) for LP were genetic variations highly associated (P < 5 × 10− 6) with LP in the European population. UK Biobank, FinnGen data and IEU Open GWAS database were utilized for autoimmune diseases GWAS data. To calculate causal effects, odds ratios (ORs) with 95% confidence intervals (CIs) are employed.
Results
We found genetic liability to LP was associated with a decreased risk of atopic dermatitis and ankylosing spondylitis, OR [95%CI] = 0.96[0.94, 0.99], PIVW = 0.013 and OR [95%CI] = 0.88[0.77, 0.99], PIVW = 0.047, respectively. Furthermore, it presents increased risk of higher odds ratios in: Type 1 diabetes (OR [95%CI] = 1.07[1.01, 1.14], PIVW = 0.027).
Conclusion
The MR study suggests that there may not be a significant association for LP contributing to the development of vitiligo, thyroid disease, SLE and Sjogren’s syndrome. On the contrast, we found that patients with LP are at decreased risk of AD and ankylosing spondylitis. no strong causal evidence of LP on the risk of vitiligo, thyroid disease, SLE and Sjogren’s syndrome.
Early administration of anamorelin improves cancer cachexia in patients with gastrointestinal cancer: An observational study
Authors: Matsumoto Toshihiko , Cho Sien , Nakasya Akio , Nagai Hiroki , Satake Hironaga , Yasui Hisateru 
Published: June 2024

Abstract

Purpose
To report the efficacy of anamorelin in patients with colorectal and gastric cancer with cachexia and in those receiving systemic chemotherapy.
Methods
We retrospectively collected real-world data from patients diagnosed with colorectal and gastric cancers experiencing cachexia who were treated with anamorelin. We evaluated the efficacy of treatment by measuring the improvements in appetite and body weight (BW) gain.
Results
Between June 2021 and October 2022, 43 cancer patients with cachexia—23 with gastric cancer and 20 with colorectal cancer—were treated with anamorelin. Median observation period was 7.3 months. The participants were 25 males with median age of 71 years and median BMI of 19.7. The ECOG PS distribution was 4, 33, 6 for grades 0, 1, and 2, respectively. Seven patients received supportive care only, while 36 received anamorelin with chemotherapy. Thirty-four had received chemotherapy previously (≤ 2 regimens) and nine had received ≥ 3 regimens. Median anamorelin treatment duration was 2.8 months; overall survival was 7.3 months. After 3 weeks, 24 experienced appetite improvement and 21 gained weight; after 12 weeks, 20 experienced appetite improvement and 15 gained weight. Multivariate analysis showed that anamorelin treatment before second-line chemotherapy and colorectal cancer correlated with appetite improvement and weight gain at 3 weeks. In the univariate analysis, anamorelin treatment before second-line chemotherapy correlated with weight gain at 12 weeks and with improved overall survival in patients with weight gain at 12 weeks.
Conclusion
Early anamorelin treatment contributes to appetite improvement and BW gain in colorectal and gastric cancers with cachexia.