Miracle-dz/UniFAR-FTUs huggingface dataset:
REPRODUCTIVE SUCCESS OF FOREST-DEPENDENT SONGBIRDS NEAR AN AGRICULTURAL CORRIDOR IN SOUTH-CENTRAL INDIANA

Abstract Potential source populations of forest-breeding Neotropical migrant birds may be threatened by anthropogenic changes that increase brood parasitism by Brown-headed Cowbirds (Molothrus ater) and nest predation in heavily forested breeding areas. In south-central Indiana, corridors of agriculture and rural development, ranging from <50 m to several thousand meters in width, penetrate interior portions of the heavily forested landscape. These corridors provide habitat for cowbirds and nest predators. We monitored breeding success of six species of Neotropical migrants and one resident species near an agricultural corridor and in interior forest. We found that nest survival was lower near the agricultural corridor for most of the species in the nestling stage, but no consistent difference in nest survival was detected during the egg stage. Levels of cowbird parasitism were generally elevated near the agricultural corridor. Estimates of the number of fledglings per nesting attempt indicated that seasonal productivity was lower near the agricultural corridor for six of the seven species. Status of populations of birds in south-central Indiana as sources in the Midwest may be compromised by extensive intrusion of agricultural corridors within the contiguous, heavily forested landscape.
Pulmonary embolism in COVID-19 patients: a French multicentre cohort study

Abstract Aims While pulmonary embolism (PE) appears to be a major issue in COVID-19, data remain sparse. We aimed to describe the risk factors and baseline characteristics of patients with PE in a cohort of COVID-19 patients. Methods and results In a retrospective multicentre observational study, we included consecutive patients hospitalized for COVID-19. Patients without computed tomography pulmonary angiography (CTPA)-proven PE diagnosis and those who were directly admitted to an intensive care unit (ICU) were excluded. Among 1240 patients (58.1% men, mean age 64 ± 17 years), 103 (8.3%) patients had PE confirmed by CTPA. The ICU transfer and mechanical ventilation were significantly higher in the PE group (for both P < 0.001). In an univariable analysis, traditional venous thrombo-embolic risk factors were not associated with PE (P > 0.05), while patients under therapeutic dose anticoagulation before hospitalization or prophylactic dose anticoagulation introduced during hospitalization had lower PE occurrence [odds ratio (OR) 0.40, 95% confidence interval (CI) 0.14–0.91, P = 0.04; and OR 0.11, 95% CI 0.06–0.18, P < 0.001, respectively]. In a multivariable analysis, the following variables, also statistically significant in univariable analysis, were associated with PE: male gender (OR 1.03, 95% CI 1.003–1.069, P = 0.04), anticoagulation with a prophylactic dose (OR 0.83, 95% CI 0.79–0.85, P < 0.001) or a therapeutic dose (OR 0.87, 95% CI 0.82–0.92, P < 0.001), C-reactive protein (OR 1.03, 95% CI 1.01–1.04, P = 0.001), and time from symptom onset to hospitalization (OR 1.02, 95% CI 1.006–1.038, P = 0.002). Conclusion PE risk factors in the COVID-19 context do not include traditional thrombo-embolic risk factors but rather independent clinical and biological findings at admission, including a major contribution to inflammation.
Phototaxis and the evolution of isogamy and 'slight anisogamy' in marine green algae : insights from laboratory observations and numerical experiments

The evolution of anisogamy in marine algae was studied through numerical simulations of gamete mating behaviour in three dimensions, using observed traits of marine green algae as input parameters. The importance of phototaxis became apparent from the numerical experiments: all gametes with phototactic systems are favoured over those without, but this advantage is reduced with increasing tank depth or shorter search times. Phototactic gametes were advantaged over non-phototactic gametes if the water was shallower than about 30–40 mm when the time available for gamete encounter was 1000 time steps (5.55 min). If gametes of both sexes are positively phototactic, slightly anisogamous species are at a disadvantage to isogamous species, which invalidates the sperm-limitation theory as a driver for the evolution of slight anisogamy. Conflicting selection forces of search efficiency and zygote fitness may be needed. © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society, 2004, 144, 321–327.
Priming of tomato seedlings with 2-oxoglutarate induces arsenic toxicity alleviatory responses by involving endogenous nitric oxide.

Metal toxicity to crop plants is a matter of scientific concern. Therefore, in recent years efforts are being made to minimize metal toxicity in crop plants. Out of various strategies, priming of seedlings with certain chemicals like donors of signaling molecules, nutrients, metabolites, plant hormones etc. has shown encouraging results. However, mechanisms related with the priming-induced mitigation of metal toxicity are still poorly known. Hence, we have tested the potential of 2-oxoglutarate (2-OG) priming in enhancing the arsenate (AsV ) toxicity tolerance in tomato seedlings along with deciphering the probable role of nitric oxide (NO) in accomplishing this task. Arsenate decreased growth, endogenous NO, nitric oxide synthase-like activity but enhanced the accumulation of As, which collectively led to root cell death. Arsenate toxicity also decreased some photosynthetic characteristics (i.e. Fv /fm, qP, Fv /F0 and Fm /F0 , and total chlorophyll) but enhanced NPQ. However, priming with 2-OG alleviated the toxic effect of AsV on growth, endogenous NO, cell death and photosynthesis. Moreover, arsenate inhibited the activities of enzymes of the nitrogen metabolism (i.e. nitrate reductase, nitrite reductase, glutamine synthetase and glutamine 2-oxoglutarate aminotransferase) but increased the activity of glutamate dehydrogenase and NH4 + content. Superoxide radicals, hydrogen peroxide, lipid peroxidation, protein oxidation and membrane damage increased upon AsV exposure, but the antioxidant enzymes (i.e. superoxide dismutase, catalase and glutathione-S-transferase) showed differential responses. Overall, our results showed that 2-OG is capable of alleviating AsV toxicity in tomato seedlings but the involvement of endogenous NO is probably required. This article is protected by copyright. All rights reserved.
Cannabidiol induces osteoblast differentiation via angiopoietin1 and p38 MAPK

In this study, we report the potential of cannabidiol, one of the major cannabis constituents, for enhancing osteoblastic differentiation in U2OS and MG‐63 cells. Cannabidiol increased the expression of Angiopoietin1 and the enzyme activity of alkaline phosphatase in U2OS and MG‐63. Invasion and migration assay results indicated that the cell mobility was activated by cannabidiol in U2OS and MG‐63. Western blotting analysis showed that the expression of tight junction related proteins such as Claudin1, Claudin4, Occuludin1, and ZO1 was increased by cannabidiol in U2OS and MG‐63. Alizarin Red S staining analysis showed that calcium deposition and mineralization was enhanced by cannabidiol in U2OS and MG‐63. Western blotting analysis indicated that the expression of osteoblast differentiation related proteins such as distal‐less homeobox 5, bone sialoprotein, osteocalcin, type I collagen, Runt‐related transcription factor 2 (RUNX2), osterix (OSX), and alkaline phosphatase was time dependently upregulated by cannabidiol in U2OS and MG‐63. Mechanistically, cannabidiol‐regulated osteoblastic differentiation in U2OS and MG‐63 by strengthen the protein‐protein interaction among RUNX2, OSX, or the phosphorylated p38 mitogen‐activated protein kinase (MAPK). In conclusion, cannabidiol increased Angiopoietin1 expression and p38 MAPK activation for osteoblastic differentiation in U2OS and MG‐63 suggesting that cannabidiol might provide a novel therapeutic option for the bone regeneration.
Intraepithelial tumour infiltrating lymphocytes are associated with absence of tumour budding and immature/myxoid desmoplastic reaction, and with better recurrence‐free survival in stages I–III colorectal cancer

Tumour budding (TB), desmoplastic reaction (DR) and intraepithelial tumour infiltrating lymphocytes (iTILs) are recently recognised prognostic factors in colorectal cancer (CRC). In this study, we evaluated their significance and relationship to each other and their cumulative effect on survival.
Novel and extended HLA class I and II alleles encountered in Kashmiri Brahmin population from North India

Three novel HLA‐A*02:06:01:04, ‐DRB1*12:02:01:02, ‐DQB1*03:01:01:07 and five extended HLA‐B*51:01:05, ‐DRB1*12:02:01:01, ‐DRB1*14:01:01, ‐DRB1*14:04:01:01, ‐DRB1*15:04 alleles.
Prevalence and characteristics of self-reported kratom use in a representative US general population sample

Abstract Background Reports of kratom (Mitragyna speciosa) use, a medicinal plant widely found in Southeast Asia, are on the rise in the US. However, the prevalence and characteristics of individuals who use kratom in the US is unknown. Objective To estimate lifetime prevalence of, and descriptive characteristics associated with, kratom use in a sample of the US general population. Methods A cross-sectional survey was administered online by Qualtrics® research panel aggregator. Utilizing quota-based sampling, data was collected from a US sample aged 18–59 years, representative to age, geographic region, ethnicity, income, and education level. Data was collected regarding respondent demographic/clinical characteristics, as well as frequency/patterns of kratom and other drug use. Results Among 1,842 respondents, 112 (6.1%) reported use of kratom within their lifetime. Respondents who used kratom were largely between 25–44 years old, male, employed, and at higher educational levels. A total of 24.1% to 47.3% of respondents indicated self-reported diagnoses for addiction, and 42.9% reported having previously received treatment for addiction. A total of 71.4% to 92% of respondents who used kratom also reported use of other drugs, including nicotine, cannabis, cocaine, ecstasy, methamphetamine, and heroin. Conclusions To our knowledge, this analysis provides the first estimate of kratom use in the general US population, providing insight on demographic/clinical characteristics of individuals reporting use.
IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

Abstract Motivation The human body hosts more microbial organisms than human cells. Analysis of this microbial diversity provides key insight into the role played by these microorganisms on human health. Metagenomics is the collective DNA sequencing of coexisting microbial organisms in an environmental sample or a host. This has several applications in precision medicine, agriculture, environmental science and forensics. State-of-the-art predictive models for phenotype predictions from metagenomic data rely on alignments, assembly, extensive pruning, taxonomic profiling and reference sequence databases. These processes are time consuming and they do not consider novel microbial sequences when aligned with the reference genome, limiting the potential of whole metagenomics. We formulate the problem of predicting human disease from whole-metagenomic data using Multiple Instance Learning (MIL), a popular supervised learning paradigm. Our proposed alignment-free approach provides higher accuracy in prediction by harnessing the capability of deep convolutional neural network (CNN) within a MIL framework and provides interpretability via neural attention mechanism. Results The MIL formulation combined with the hierarchical feature extraction capability of deep-CNN provides significantly better predictive performance compared to popular existing approaches. The attention mechanism allows for the identification of groups of sequences that are likely to be correlated to diseases providing the much-needed interpretation. Our proposed approach does not rely on alignment, assembly and reference sequence databases; making it fast and scalable for large-scale metagenomic data. We evaluate our method on well-known large-scale metagenomic studies and show that our proposed approach outperforms comparative state-of-the-art methods for disease prediction. Availability and implementation https://github.com/mrahma23/IDMIL.
Visual outcomes of combined cataract and minimally invasive glaucoma surgery.

Minimally invasive glaucoma surgery (MIGS) has become a reliable standard of care for the treatment of glaucoma when combined with cataract surgery. This review describes the MIGS procedures currently combined with and without cataract surgery with a focus on visual outcomes based on the literature and the experience of the ASCRS Glaucoma Clinical Committee.
Diffusion tensor imaging reveals changes in non‐fat infiltrated muscles in late onset Pompe disease

MRI is a helpful tool for monitoring disease progression in late‐onset Pompe disease (LOPD). Our study aimed to evaluate if muscle diffusion tensor imaging (mDTI) shows alterations in muscles of LOPD patients with <10% fat‐fraction. We evaluated 6 thigh and 7 calf muscles (both legs) of 18 LOPD and 29 healthy controls (HC) with muscle diffusion tensor imaging (mDTI), T1w, and mDixonquant sequences in a 3T MRI scanner. The quantitative mDTI‐values axial diffusivity (λ1), mean diffusivity (MD), radial diffusivity (RD), and fractional anisotropy (FA) as well as fat‐fraction were analyzed. 6‐Minute Walk Test (6‐MWT) data were correlated to diffusion metrics. We found that mDTI showed significant differences between LOPD and HC in diffusion parameters (P < .05). Thigh muscles with <10% fat‐fraction showed significant differences in MD, RD, and λ1‐3. MD positively correlated with 6‐MWT (P = .06). To conclude, mDTI reveals diffusion restrictions in muscles of LOPD with and without fat‐infiltration and reflects structural changes prior to fatty degeneration.
Interactions of dietary polyphenols with epithelial lipids: advances from membrane and cell models in the study of polyphenol absorption, transport and delivery to the epithelium

Abstract Currently, diet-related diseases such as diabetes, obesity, hypertension, and cardiovascular diseases account for 70% of all global deaths. To counteract the rising prevalence of non-communicable diseases governments are investing in persuasive educational campaigns toward the ingestion of fresh fruits and vegetables. The intake of dietary polyphenols abundant in Mediterranean and Nordic-type diets holds great potential as nutritional strategies in the management of diet-related diseases. However, the successful implementation of healthy nutritional strategies relies on a pleasant sensory perception in the mouth able to persuade consumers to adopt polyphenol-rich diets and on a deeper understanding on the chemical modifications, that affect not only their chemical properties but also their physical interaction with epithelial lipids and in turn their permeability, location within the lipid bilayer, toxicity and biological activity, and fate during absorption at the gastro-intestinal epithelium, transport in circulation and delivery to the endothelium. In this paper, we review the current knowledge on the interactions between polyphenols and their metabolites with membrane lipids in artificial membranes and epithelial cell models (oral, stomach, gut and endothelium) and the findings from polyphenol-lipid interactions to physiological processes such as oral taste perception, gastrointestinal absorption and endothelial health. Finally, we discuss the limitations and challenges associated with the current experimental approaches in membrane and cell model studies and the potential of polyphenol-rich diets in the quest for personalized nutritional strategies (“personalized nutrition”) to assist in the prevention, treatment, and management of non-communicable diseases in an increasingly aged population.
A Pooled Analysis to Compare the Clinical Characteristics of Human Papillomavirus–positive and -Negative Cervical Precancers

Given that high-risk human papillomavirus (HPV) is the necessary cause of virtually all cervical cancer, the clinical meaning of HPV-negative cervical precancer is unknown. We, therefore, conducted a literature search in Ovid MEDLINE, PubMed Central, and Google Scholar to identify English-language studies in which (i) HPV-negative and -positive, histologically confirmed cervical intraepithelial neoplasia grade 2 or more severe diagnoses (CIN2+) were detected and (ii) summarized statistics or deidentified individual data were available to summarize proportions of biomarkers indicating risk of cancer. Nineteen studies including 3,089 (91.0%) HPV-positive and 307 (9.0%) HPV-negative CIN2+ were analyzed. HPV-positive CIN2+ (vs. HPV-negative CIN2+) was more likely to test positive for biomarkers linked to cancer risk: a study diagnosis of CIN3+ (vs. CIN2; 18 studies; 0.56 vs. 0.24; P < 0.001) preceding high-grade squamous intraepithelial lesion cytology (15 studies; 0.54 vs. 0.10; P < 0.001); and high-grade colposcopic impression (13 studies; 0.30 vs. 0.18; P = 0.03). HPV-negative CIN2+ was more likely to test positive for low-risk HPV genotypes than HPV-positive CIN2+ (P < 0.001). HPV-negative CIN2+ appears to have lower cancer risk than HPV-positive CIN2+. Clinical studies of human high-risk HPV testing for screening to prevent cervical cancer may refer samples of HPV test–negative women for disease ascertainment to correct verification bias in the estimates of clinical performance. However, verification bias adjustment of the clinical performance of HPV testing may overcorrect/underestimate its clinical performance to detect truly precancerous abnormalities.
AdipoGauge software for analysis of biological microscopic images

ABSTRACT Obesity is a complex disease of global epidemic proportions. Adipose tissue expansion and chronic low-grade inflammation, locally and systemically, are hallmark features of obesity. Obesity is associated with several other chronic diseases, which are also characterized by inflammation. Determination of adipocyte size and macrophage content in adipose tissue is a critical step in assessing changes in this tissue with obesity. Here, we introduce a complete standalone software package, AdipoGauge, to analyse microscopic images derived from haematoxylin and eosin (H&E)-stained and immunofluorescently stained histology sections of adipose tissue. The software package is a user-friendly application that does not require a vast knowledge of computer science or costly commercial tools. AdipoGauge includes analysing tools that are capable of cell counting and colour separation. Furthermore, it can quantify the cell data in images both with and without clear boundaries around the cells. It can also remove objects from the image that are not intended for analysis, such as blood vessels or partial cells at edges of slide sections. The simple and state-of-the-art graphical user interface requires minimal time and learning.
Use of tocilizumab in kidney transplant recipients with COVID-19

Acute respiratory distress syndrome associated with coronavirus infection is related to a cytokine storm with large interleukin‐6 (IL‐6) release. The IL‐6‐receptor blocker tocilizumab may control the aberrant host immune response in patients with coronavirus disease 2019 (COVID‐19) . In this pandemic, kidney transplant (KT) recipients are a high‐risk population for severe infection and showed poor outcomes. We present a multicenter cohort study of 80 KT patients with severe COVID‐19 treated with tocilizumab during hospital admission. High mortality rate was identified (32.5%), related with older age (hazard ratio [HR] 3.12 for those older than 60 years, P = .039). IL‐6 and other inflammatory markers, including lactic acid dehydrogenase, ferritin, and D‐dimer increased early after tocilizumab administration and their values were higher in nonsurvivors. Instead, C‐reactive protein (CRP) levels decreased after tocilizumab, and this decrease positively correlated with survival (mean 12.3 mg/L in survivors vs. 33 mg/L in nonsurvivors). Each mg/L of CRP soon after tocilizumab increased the risk of death by 1% (HR 1.01 [confidence interval 1.004‐1.024], P = .003). Although patients who died presented with worse respiratory situation at admission, this was not significantly different at tocilizumab administration and did not have an impact on outcome in the multivariate analysis. Tocilizumab may be effective in controlling cytokine storm in COVID‐19 but randomized trials are needed.
The effects of magnetic water on milk and blood components of lactating Saanen goats

Change in milk and blood components of lactating Saanen goats when consuming magnetic water were studied. Twelve goats in a completely randomized design with 3 treatments including 1. ) Control, 2. ) Consuming conditioned water with 1200 Gauss permanent magnet and 3. ) Consuming conditioned water with 3600 Gauss permanent magnet, were used. Results indicated that conditioning of the water did not affect blood metabolites (glucose and urea), blood ions (Na, K, Mg and P) and milk composition (fat, protein, lactose, solid not fat and total solid) significantly. Key words: Saanen goats, magnetic water, blood metabolites, blood ions, milk composition.
Ultra-high field 7 T imaging in multiple sclerosis.

PURPOSE OF REVIEW Ultra-high field 7 T MRI has multiple applications for the in vivo characterization of the heterogeneous aspects underlying multiple sclerosis including the identification of cortical lesions, characterization of the different types of white matter plaques, evaluation of structures difficult to assess with conventional MRI (thalamus, cerebellum, spinal cord, meninges). RECENT FINDINGS The sensitivity of cortical lesion detection at 7 T is twice than at lower field MRI, especially for subpial lesions, the most common cortical lesion type in multiple sclerosis. Cortical lesion load accrual is independent of that in the white matter and predicts disability progression.Seven Tesla MRI provides details on tissue microstructure that can be used to improve white matter lesion characterization. These include the presence of a central vein, whose identification can be used to improve multiple sclerosis diagnosis, or the appearance of an iron-rich paramagnetic rim on susceptibility-weighted images, which corresponds to iron-rich microglia at the periphery of slow expanding lesions. Improvements in cerebellar and spinal cord tissue delineation and lesion characterization have also been demonstrated. SUMMARY Imaging at 7 T allows assessing more comprehensively the complementary pathophysiological aspects of multiple sclerosis, opening up novel perspectives for clinical and therapeutics evaluation.