Miracle-dz/UniFAR-FTUs huggingface dataset:
Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research

The interaction between nutrition and human infectious diseases has always been recognized. With the emergence of molecular tools and post-genomics, high-resolution sequencing technologies, the gut microbiota has been emerging as a key moderator in the complex interplay between nutrients, human body, and infections. Much of the host–microbial and nutrition research is currently based on animals or simplistic in vitro models. Although traditional in vivo and in vitro models have helped to develop mechanistic hypotheses and assess the causality of the host–microbiota interactions, they often fail to faithfully recapitulate the complexity of the human nutrient–microbiome axis in gastrointestinal homeostasis and infections. Over the last decade, remarkable progress in tissue engineering, stem cell biology, microfluidics, sequencing technologies, and computing power has taken place, which has produced a new generation of human-focused, relevant, and predictive tools. These tools, which include patient-derived organoids, organs-on-a-chip, computational analyses, and models, together with multi-omics readouts, represent novel and exciting equipment to advance the research into microbiota, infectious diseases, and nutrition from a human-biology-based perspective. After considering some limitations of the conventional in vivo and in vitro approaches, in this review, we present the main novel available and emerging tools that are suitable for designing human-oriented research.
Ultrasound-Guided Microinvasive Trigger Finger Release Technique Combined With Three Tests to Confirm a Complete Release

Supplemental digital content is available in the text. Objective Trigger finger at the A1 pulley is a common cause of hand pain leading to functional limitations. This study evaluated the outcomes of patients treated with a microinvasive ultrasound-guided trigger finger release technique using an 18 blade and described three tests that confirm a complete release. Design A retrospective chart review and cross-sectional study of 46 cases of A1 pulley trigger finger releases in 28 patients performed at a private, sports medicine clinic using this technique were completed, meeting power criteria. The primary outcome measure was the resolution of mechanical catching/locking; secondary outcome measures were reduction in visual analog scale for pain and improvement of function in the modified Nirschl scale. Results Complete release was achieved in all patients, with no recurrence of catching/locking during the first year (P < 0.0001). Ninety-eight percent of patients had significant pain and functional improvement (P < 0.0001). There were no complications perioperatively and postoperatively. The three confirmatory tests ensured that all cases obtained a successful outcome. Conclusion This technique combined with confirmatory tests resulted in full resolution of the locking for all patients and statistically significant reduction in pain and improvement in function.
Selective estrogen receptor modulators (SERMS): keys to understanding their function

Abstract Selective estrogen receptor modulators (SERMs) are an increasingly important therapeutic modality that are used by clinicians on a daily basis. Unfortunately, clinicians have a limited understanding regarding the underlying mechanism(s) of how SERMs function and their increasingly useful role in the treatment of estrogen-responsive target tissues such as the breast, bone, vagina, uterine endometrium, and brain. This review will provide a basic understanding of our current knowledge of SERM pharmacodynamics and will highlight the clinical applications of Food and Drug Administration–approved SERMs in the treatment of vasomotor symptoms, osteoporosis, genitourinary syndrome of menopause, infertility, and breast cancer and its prevention. SERMs under development and natural phytoestrogens will also be reviewed.
BiRRE: Learning Bidirectional Residual Relation Embeddings for Supervised Hypernymy Detection

The hypernymy detection task has been addressed under various frameworks. Previously, the design of unsupervised hypernymy scores has been extensively studied. In contrast, supervised classifiers, especially distributional models, leverage the global contexts of terms to make predictions, but are more likely to suffer from “lexical memorization”. In this work, we revisit supervised distributional models for hypernymy detection. Rather than taking embeddings of two terms as classification inputs, we introduce a representation learning framework named Bidirectional Residual Relation Embeddings (BiRRE). In this model, a term pair is represented by a BiRRE vector as features for hypernymy classification, which models the possibility of a term being mapped to another in the embedding space by hypernymy relations. A Latent Projection Model with Negative Regularization (LPMNR) is proposed to simulate how hypernyms and hyponyms are generated by neural language models, and to generate BiRRE vectors based on bidirectional residuals of projections. Experiments verify BiRRE outperforms strong baselines over various evaluation frameworks.
Neutrophil Extracellular Traps in Periodontitis

Neutrophils are key cells of the immune system and have a decisive role in fighting foreign pathogens in infectious diseases. Neutrophil extracellular traps (NETs) consist of a mesh of DNA enclosing antimicrobial peptides and histones that are released into extracellular space following neutrophil response to a wide range of stimuli, such as pathogens, host-derived mediators and drugs. Neutrophils can remain functional after NET formation and are important for periodontal homeostasis. Periodontitis is an inflammatory multifactorial disease caused by a dysbiosis state between the gingival microbiome and the immune response of the host. The pathogenesis of periodontitis includes an immune-inflammatory component in which impaired NET formation and/or elimination can be involved, contributing to an exacerbated inflammatory reaction and to the destruction of gingival tissue. In this review, we summarize the current knowledge about the role of NETs in the pathogenesis of periodontitis.
Variability in reactions of Pacific harbor seals, Phoca vitulina richardsi, to disturbance

In many locations, disturbance is an important factor affecting the haulout patterns of harbor seals, Phoca vitulina. Disturbance is defined as any activity that alters normal behavior. In the United States, disturbance of marine mammals by humans is regulated by the Marine Mammal Protection Act of 1972. In contrast to pelagic marine mammals, changes in the behavior of pinnipeds on haul-out sites related to disturbance is relatively simple to measure. Long-term effects of disturbance, however, are often difficult to assess. The effects of disturbance may be quite mild or may cause displacement and even mortality. Bighorn sheep (Ovis canadensis) and whitetailed deer exposed to snowmobile traffic have shown increased heart rate but no visible change in behavior (MacArthur et al., 1982; Moen et al., 1982). Humpback whale (Megaptera novaeangliae) femalecalf pairs in Hawaii have avoided nearshore areas of intense human recreational activities (Salden, 1988; Glockner-Ferrari and Ferrari 1 ). Disturbance-related mortality in harbor seals can result from stampeding and pup abandonment (Johnson 2 ). Disturbance from low-flying aircraft may have caused mortality of more than 200 (10%) harbor seal pups on Tugidak Island, Alaska, in
Spatiotemporal evolution of case fatality rates of COVID-19 in Brazil, 2020

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome (SARS) coronavirus 2, was initially identified in the city of Wuhan, capital of the Hubei province of China, in December of 2019. (1) On March 11, 2020, the World Health Organization characterized the disease as a pandemic. (2) As of April 26, there were approximately 3 million confirmed cases of COVID-19 and 206,000 deaths attributed to the disease worldwide. The highest numbers of confirmed cases were in the United States (n = 963,379) and Spain (n = 226,629), whereas the highest numbers of deaths were in Italy (n = 26,644) and France (n = 23,190). (3)
Graphene Nanoplatelets for the Development of Reinforced PLA–PCL Electrospun Fibers as the Next-Generation of Biomedical Mats

Electrospun scaffolds made of nano- and micro-fibrous non-woven mats from biodegradable polymers have been intensely investigated in recent years. In this field, polymer-based materials are broadly used for biomedical applications since they can be managed in high scale, easily shaped, and chemically changed to tailor their specific biologic properties. Nonetheless polymeric materials can be reinforced with inorganic materials to produce a next-generation composite with improved properties. Herein, the role of graphene nanoplatelets (GNPs) on electrospun poly-l-lactide-co-poly-ε-caprolactone (PLA–PCL, 70:30 molar ratio) fibers was investigated. Microfibers of neat PLA–PCL and with different amounts of GNPs were produced by electrospinning and they were characterized for their physicochemical and biologic properties. Results showed that GNPs concentration notably affected the fibers morphology and diameters distribution, influenced PLA–PCL chain mobility in the crystallization process and tuned the mechanical and thermal properties of the electrospun matrices. GNPs were also liable of slowing down copolymer degradation rate in simulated physiological environment. However, no toxic impurities and degradation products were pointed out up to 60 d incubation. Furthermore, preliminary biologic tests proved the ability of the matrices to enhance fibroblast cells attachment and proliferation probably due to their unique 3D-interconnected structure.
Transmission modes affect the population structure of potato virus Y in potato

Transmission is a crucial part of a viral life cycle and transmission mode can have an important impact on virus biology. It was demonstrated that transmission mode can influence the virulence and evolution of a virus; however, few empirical data are available to describe the direct underlying changes in virus population structure dynamics within the host. Potato virus Y (PVY) is an RNA virus and one of the most damaging pathogens of potato. It comprises several genetically variable strains that are transmitted between plants via different transmission modes. To investigate how transmission modes affect the within-plant viral population structure, we have used a deep sequencing approach to examine the changes in the genetic structure of populations (in leaves and tubers) of three PVY strains after successive passages by horizontal (aphid and mechanical) and vertical (via tubers) transmission modes. Nucleotide diversities of viral populations were significantly influenced by transmission modes; lineages transmitted by aphids were the least diverse, whereas lineages transmitted by tubers were the most diverse. Differences in nucleotide diversities of viral populations between leaves and tubers were transmission mode-dependent, with higher diversities in tubers than in leaves for aphid and mechanically transmitted lineages. Furthermore, aphid and tuber transmissions were shown to impose stronger genetic bottlenecks than mechanical transmission. To better understand the structure of virus populations within the host, transmission mode, movement of the virus within the host, and the number of replication cycles after transmission event need to be considered. Collectively, our results suggest a significant impact of virus transmission modes on the within-plant diversity of virus populations and provide quantitative fundamental data for understanding how transmission can shape virus diversity in the natural ecosystems, where different transmission modes are expected to affect virus population structure and consequently its evolution.
Parasitic infestation of Synodontis batensoda (Rüppell, 1832, Siluriformes, Mockokidae) at Rivers Niger-Benue Confluence, Nigeria

The Mockokid, upside down catfish, Synodontis batensoda caught with various fishing gears were studied for parasites for a period of 12 months (March 2007 to February 2008) in Rivers Niger and Benue at the Confluence. Out of 84 fish specimens examined, 61 (72.6%) fish hosts were infected, while 23 (27.4%) were uninfected. The total parasites recovered were 1196, comprising one protozoan ciliate (Trichodinids), two Digeneans ( Allocreadim ghanensis and Metacercariae of Pygidiopsis genata ), four Cestodes ( Monobothrioides woodlandi, Bothriocephalus acheilognathii, Proteocephalus largoploglotis and Caryophyleus sp.), six Nematodes ( Procamallanus laevionchus, Rhabdochona congolensis, Spinitectus guntheri, Oxyuris equi, Contracaecum microcephalum, Strongylides sp and larval Nematodes) and the Acanthocephalans ( Acanthocephalus sp., Neoechinorhynchus prolixum and Acanthella sp. - the immature stages). Acanthocephalans had the highest prevalence among the parasites recovered. All parasites were recovered from the intestines except the Trichodinids which were recovered from the gills and skin of fish hosts. The relationship of host weight and parasite infection showed infection was highly significant (p 0.01) difference between the male and female fish hosts, both being equally infected. Multiple infections were recorded in several fish hosts, an indication of the rich parasitic fauna of the localities. This study provides an overview of parasites of S. batensoda in Rivers Niger and Benue at the Confluence. Keywords : Parasites, protozoan, helminths, nematodes, cestodes, acanthocephalans, Synodontis batensoda , Rivers Niger-Benue Confluence, Nigeria African Journal of Biotechnology Vol. 12(20), pp. 3029-3039
Immunoadsorption for Treatment of Patients with Suspected Alzheimer Dementia and Agonistic Autoantibodies against Alpha1a-Adrenoceptor—Rationale and Design of the IMAD Pilot Study

Background: agonistic autoantibodies (agAABs) against G protein-coupled receptors (GPCR) have been linked to cardiovascular disease. In dementia patients, GPCR-agAABs against the α1- and ß2-adrenoceptors (α1AR- and ß2AR) were found at a prevalence of 50%. Elimination of agAABs by immunoadsorption (IA) was successfully applied in cardiovascular disease. The IMAD trial (Efficacy of immunoadsorption for treatment of persons with Alzheimer dementia and agonistic autoantibodies against alpha1A-adrenoceptor) investigates whether the removal of α1AR-AABs by a 5-day IA procedure has a positive effect (improvement or non-deterioration) on changes of hemodynamic, cognitive, vascular and metabolic parameters in patients with suspected Alzheimer’s clinical syndrome within a one-year follow-up period. Methods: the IMAD trial is designed as an exploratory monocentric interventional trial corresponding to a proof-of-concept phase-IIa study. If cognition capacity of eligible patients scores 19–26 in the Mini Mental State Examination (MMSE), patients are tested for the presence of agAABs by an enzyme-linked immunosorbent assay (ELISA)-based method, followed by a bioassay-based confirmation test, further screening and treatment with IA and intravenous immunoglobulin G (IgG) replacement. We aim to include 15 patients with IA/IgG and to complete follow-up data from at least 12 patients. The primary outcome parameter of the study is uncorrected mean cerebral perfusion measured in mL/min/100 gr of brain tissue determined by magnetic resonance imaging with arterial spin labeling after 12 months. Conclusion: IMAD is an important pilot study that will analyze whether the removal of α1AR-agAABs by immunoadsorption in α1AR-agAAB-positive patients with suspected Alzheimer’s clinical syndrome may slow the progression of dementia and/or may improve vascular functional parameters.
REVERSAL OF NITROGEN SATURATION AFTER LONG‐TERM DEPOSITION REDUCTION: IMPACT ON SOIL NITROGEN CYCLING

An ongoing roof experiment, where N and acid inputs were reduced to the recommended critical load levels, has been conducted since 1991 in an N-saturated spruce stand in Solling, Germany. Our study was aimed at (1) quantifying the changes in gross rates of microbial N cycling under ambient and reduced N conditions, and (2) relating the soil N dynamics to the changes in N leaching and N status of trees. Two roofs were used, one to achieve “ambient” and the other reduced (“clean rain”) inputs, with a roofless plot as a control for possible roof effects. In 2001, the ambient roof and ambient no-roof plots showed an apparent decrease in gross N mineralization rates and significantly lower microbial NH4+ immobilization rates and turnover rates of NH4+ and microbial N pools. The microbial NO3− immobilization rates and NO3− pool turnover rates were lower than the microbial NH4+ immobilization rates and NH4+ pool turnover rates, showing that less NO3− cycled through microorganisms than NH4+. There was also low abiotic NO3− immobilization. High NO3− input from throughfall and low microbial turnover rates of the NO3− pool, combined with low abiotic NO3− retention, may have contributed to the high NO3− leaching losses in these ambient plots. The clean rain plot showed a slight increase in gross N mineralization rates and significantly higher microbial NH4+ immobilization rates and turnover rates of NH4+ and microbial N pools. Neither nitrification nor soil NO3− was detectable. There was an increase in abiotic NO3− immobilization. Foliar N concentration had decreased but was still adequate. An efficient cycling of NH4+ through microorganisms, combined with the high abiotic NO3− immobilization, indicated efficient mineral N retention in the clean rain plot. These results indicated that long-term reduction of throughfall N and acid inputs had induced high but tightly coupled microbial NH4+ cycling and an increase in abiotic NO3− retention, which contributed to the reversal of N saturation.
Effectively managing angler satisfaction in recreational fisheries requires understanding the fish species and the anglers

Whenever satisfied anglers are an important objective of recreational fisheries management, understanding how trip outcomes influence satisfaction reports is critical. While anglers, generally, prefer high catch rates and large fish, the relative importance of these catch outcomes for catch satisfaction has not been established across species and angler types. We examined relationships between angler specialization, trip outcomes (both catch and non-catch characteristics such as crowding), and catch satisfaction across six freshwater fish species in northern Germany. As expected, catch satisfaction was primarily determined by catch rate and fish size in all fish species; however, the relative importance of these two outcomes varied considerably across species and among angler types that differed by commitment to fishing. We found a diminishing marginal return of satisfaction for increasing catch rate for all but small-bodied cyprinid species, while increasing size of largest retained fish monotonically in.
Effects of insect cadavers infected by Heterorhabditis bacteriophora and Steinernema diaprepesi on Meloidogyne incognita parasitism in pepper and summer squash plants

E. E. Del Valle, P. Lax, J. Rondan Duenas, and M. E. Doucet. 2013. Effects of insect cadavers infected by Heterorhabditis bacteriophora and Steinernema diaprepesi on Meloidogyne incognita parasitism in pepper and summer squash plants. Cien. Inv. Agr. 40(1):109-118. The effects of insect cadavers infected with three isolates of Heterorhabditis bacteriophora and one isolate of Steinernema diaprepesi on a population of Meloidogyne incognita in pepper (Capsicum annuum) and summer squash (Cucurbita maxima) were evaluated in greenhouse experiments carried out in Santa Fe (Argentina). Insect cadavers were obtained for the experiments from last instar larvae of Galleria mellonella and Tenebrio molitor that had been infected with entomopathogenic nematodes. Two six-day-old insect cadavers per pot were placed below the soil surface, and the soil was inoculated with 100 second-stage juveniles of M. incognita. Sixty days after inoculation, the following parameters were recorded for each plant: number of leaves; dry weight of aerial parts; numbers of galls, egg masses and eggs; and numbers of galls, egg masses and eggs g -1 of root fresh matter. In pepper, the only variable affected by the infected cadavers with respect to control was the number of eggs in the treatment involving T. molitor cadavers infected with the H. bacteriophora isolate Rama Caida. In summer squash, several treatments using infected cadavers resulted in a decrease in the numbers of galls and egg masses. Only the treatment involving G. mellonella cadavers infected with the H. bacteriophora isolate Rama Caida proved to be efficient in reducing the number of M. incognita eggs. Our results indicated that the application of insect cadavers infected with the entomopathogenic nematodes studied might reduce M. incognita damage in pepper and summer squash plants.
Pyramid: A Layered Model for Nested Named Entity Recognition

This paper presents Pyramid, a novel layered model for Nested Named Entity Recognition (nested NER). In our approach, token or text region embeddings are recursively inputted into L flat NER layers, from bottom to top, stacked in a pyramid shape. Each time an embedding passes through a layer of the pyramid, its length is reduced by one. Its hidden state at layer l represents an l-gram in the input text, which is labeled only if its corresponding text region represents a complete entity mention. We also design an inverse pyramid to allow bidirectional interaction between layers. The proposed method achieves state-of-the-art F1 scores in nested NER on ACE-2004, ACE-2005, GENIA, and NNE, which are 80.27, 79.42, 77.78, and 93.70 with conventional embeddings, and 87.74, 86.34, 79.31, and 94.68 with pre-trained contextualized embeddings. In addition, our model can be used for the more general task of Overlapping Named Entity Recognition. A preliminary experiment confirms the effectiveness of our method in overlapping NER.
Developmental Gene Expression of Nutrient Transporters in the Small Intestine of Chickens from Lines Divergently Selected for High or Low Juvenile Body Weight

Nutrient transporters in the small intestine are responsible for dietary nutrient assimilation and therefore the expression of these transporters can influence the overall nutrient status as well as the growth and development of the animal. This thesis examined correlated responses to selection in the developmental gene expression of the peptide transporter PepT1, the glutamate/aspartate transporter EAAT3, the sodiumdependent glucose transporter SGLT1, and the fructose transporter GLUT5 in the small intestine of chickens from lines divergently selected for high (HH) or low (LL) eightweek body weight and their reciprocal crosses, (HL and LH). Chicks were weighed and killed on embryonic day 20 (E20), day of hatch (DOH with no access to feed), and days 3 (D3), 7(D7), and 14 (D14) post hatch. Duodenum, jejunum, ileum and liver were collected. DNA extracted from liver was used to sex birds by PCR. RNA was extracted from the intestinal segments of four males and four females from each mating combination (MC) and time point except E20 HL males (n = 3) and D7 LL females (n = 2). Expression of nutrient transporters was assayed by real-time PCR using the relative quantification method. In comparing HH and LL males and females there was a line by segment interaction in PepT1 gene expression, with no segment difference in HH and greatest expression in the ileum of the LL (P < 0.05). There was also a MC by age by sex interaction for PepT1 gene expression (P < 0.0001) with peak gene expression occurring on DOH for LL females, on D7 for HH females, on D7 for LL males and D14 for HH