Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein and Microbial Biomarkers in Sputum Discern Acute and Latent Tuberculosis in Investigation of Pastoral Ethiopian Cohort

Differential diagnosis of tuberculosis (TB) and latent TB infection (LTBI) remains a public health priority in high TB burden countries. Pulmonary TB is diagnosed by sputum smear microscopy, chest X-rays, and PCR tests for distinct Mycobacterium tuberculosis (Mtb) genes. Clinical tests to diagnose LTBI rely on immune cell stimulation in blood plasma with TB-specific antigens followed by measurements of interferon-γ concentrations. The latter is an important cytokine for cellular immune responses against Mtb in infected lung tissues. Sputum smear microscopy and chest X-rays are not sufficiently sensitive while both PCR and interferon-γ release assays are expensive. Alternative biomarkers for the development of diagnostic tests to discern TB disease states are desirable. This study’s objective was to discover sputum diagnostic biomarker candidates from the analysis of samples from 161 human subjects including TB patients, individuals with LTBI, negative community controls (NCC) from the province South Omo, a pastoral region in Ethiopia. We analyzed 16S rRNA gene-based bacterial taxonomies and proteomic profiles. The sputum microbiota did not reveal statistically significant differences in α-diversity comparing the cohorts. The genus Mycobacterium, representing Mtb, was only identified for the TB group which also featured reduced abundance of the genus Rothia in comparison with the LTBI and NCC groups. Rothia is a respiratory tract commensal and may be sensitive to the inflammatory milieu generated by infection with Mtb. Proteomic data supported innate immune responses against the pathogen in subjects with pulmonary TB. Ferritin, an iron storage protein released by damaged host cells, was markedly increased in abundance in TB sputum compared to the LTBI and NCC groups, along with the α-1-acid glycoproteins ORM1 and ORM2. These proteins are acute phase reactants and inhibit excessive neutrophil activation. Proteomic data highlight the effector roles of neutrophils in the anti-Mtb response which was not observed for LTBI cases. Less abundant in the sputum of the LTBI group, compared to the NCC group, were two immunomodulatory proteins, mitochondrial TSPO and the extracellular ribonuclease T2. If validated, these proteins are of interest as new biomarkers for diagnosis of LTBI.
Structure of the Interaction Networks Between Bats (Mammalia: Chiroptera) and Ectoparasite Flies (Diptera: Streblidae, Nycteribiidae) on a Latitudinal Gradient

The study of parasites and their distributions is an important tool to understand the problems related to population dynamics and the evolution of the interactions between parasites and their hosts. Due in part to the unique adaptations of this group, bats are parasitized by many arthropod lineages, and the flies of the Streblidae and Nycteribiidae families are considered the most conspicuous. Network analysis is an approach that has been growing in recent decades and has contributed greatly to the understanding of ecological systems. The objective of this study is to analyze if the structure of the bat-ectoparasitic networks are consistent along a latitudinal gradient on a global scale. We searched the scientific literature for information about the relationship of bats and their ectoparasitic dipterans of Streblidae and Nycteribiidae using the Scopus, Google Scholar and PubMed databases. For each publication, nesting, connectivity, and modularity parameters were calculated for each network of bats and flies. In order to evaluate if the structure of the networks varies along the latitudinal gradient, we constructed generalized linear models. In general, we observed that the ectoparasite-bat interaction networks have a highly modular structure with low nesting and connectivity values, which is a pattern commonly presented by networks of antagonistic interactions. We also observed that the size of the network significantly influenced the nesting, connectivity and modularity, possibly due to the highly specialized nature of the ectoparasite-bat interaction. The latitude was positively correlated to the connectivity, which can be explained by the lower diversity observed in temperate regions.
First Record of the Genus Plecotus from Southeast Asia with Notes on the Taxonomy, Karyology and Echolocation Call of P. homochrous from Vietnam

Long-eared bats of the genus Plecotus are known to occur predominantly in the Palaearctic Region, and at the margins of the Afrotropical and Indomalayan regions. In 2014, four specimens of the genus Plecotus were collected in a high altitude montane temperate forest in the Hoang Lien National Park, northern Vietnam, representing the first record of Plecotus from the Indochinese subregion, and considerably extending the southern border of the genus' distribution range. Detailed morphological comparisons and phylogenetic reconstructions based on the mitochondrial control region suggest that these specimens can be assigned to P. homochrous, a mountain-dwelling bat from the Himalayas. Moreover, for the first time, we provide information on the species' echolocation call and karyological characteristics. Our results also indicate that the taxonomic status of some Plecotus species recognized by previous studies is doubtful and must be revised. Although rarely encountered, Plecotus is likely to be widely distributed at the higher elevations of the Himalayan chain in southern China and the adjoining northern areas of Vietnam, Laos, and Myanmar. Our findings strongly support the importance of the mountainous areas within the Indo-Burma biodiversity hotspot.
Temporal and Spatial Changes in Myotis lucifugus Acoustic Activity Before and After White-Nose Syndrome on Fort Drum Army Installation, New York, USA

Changes to bat distribution and habitat associations at the local to sub-landscape scale in the post white-nose syndrome (WNS) environment have received little attention to date despite being critical information for managers. To better understand the spatial nature of bat population declines, we modelled both activity patterns and occupancy from acoustic surveys for the Myotis lucifugus (little brown bat) on Fort Drum Military Installation in New York, USA over 15 summers (2003–2017) that span the pre-WNS, WNS-advent (2008) and post-WNS periods, using a set of generalized linear mixed models and geospatial analysis. Our best supported model indicated significant differences between years with significant declines in activity post-WNS. M. lucifugus activity was most closely associated with woody wetland habitats over the study period, however, the spatial patterns of high activity areas were variable over years, with the areal extent of these high activity areas decreasing post-WNS. Our best supported occupancy model varied by year. However, the null occupancy model [Ψ(.)] was either competing (within 2 ΔAIC units) or was the best supported model. Meaning that none of our environmental variables seemed to impact occupancy, and when they did, these differences were not significant. There was high disagreement between our relative activity models and predictions compared to our occupancy models, suggesting that geographic spatial scale and the resolution of the data impacts model outcome. Our results indicate that continued acoustic monitoring of bat species in the Northeast to assess ongoing temporal and spatial changes in habitat associations and to provide direction for future mist-netting studies should rely more on relative activity as the metric of choice rather than site occupancy.
Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements

Microbiology Resource Announcements (MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need for extensive revisions. ABSTRACT Microbiology Resource Announcements (MRA) provides peer-reviewed announcements of scientific resources for the microbial research community. We describe the best practices for writing an announcement that ensures that these publications are truly useful resources. Adhering to these best practices can lead to successful publication without the need for extensive revisions.
Principles of Collaborative Education Research With Stakeholders: Toward Requirements for a New Research and Development Infrastructure

A group of collaborative approaches to education research sits uneasily within the existing infrastructure for research and development in the United States. The researchers in this group hold themselves to account to ways of working with schools, families, and communities that are different from the ways envisioned by models for education research promoted in U.S. policies and endorsed by U.S. federal agencies. Those models, widely supported by funders, privilege the research priorities of individual investigators and regularly yield products and findings with little relevance to educational practice. In this article, we review four collaborative approaches: Community-based Design Research, Design-based Implementation Research, Improvement Science in Networked Improvement Communities, and the Strategic Education Research Partnership. Through a participatory process involving developers and advocates for these approaches, we identified a set of interconnected principles related to collaboration, problem solving, and research. Further, we reviewed evidence of these principles in projects belonging to these four approaches. We contend it is worth attempting to understand, build upon, and support enactments of these principles in research proposals and projects, because there is evidence these approaches can promote agency and equity in education. To do so would require the field to develop criteria for judging quality, which peers can use to evaluate individual studies or sets of research; new outcomes by which to measure progress; new venues for developing and giving accounts of research; and an appreciation for the value of developing and cultivating relationships with educators, families, and communities as an integral part of research.
Diurnal Flying Activity of a Neotropical Bat (Saccopteryx leptura): Effect of Light Intensity, Temperature, and Canopy Cover

Nocturnal behavior is a critical life-history trait associated with the evolutionary success of bats. Avian predation, competition with birds, and hyperthermia may explain the origin of this behavior, but it is difficult to assess the validity of these hypotheses due to the rarity of diurnal activity in bats. In Gorgona National Natural Park, Colombia, the population of the lesser sac-winged bat (Emballonuridae: Saccopteryx leptura) has an unusual daylight flight activity, which provides an opportunity to learn about the origin of nocturnality in bats. We described the daylight activity of S. leptura in Gorgona Island and explored the influence of environmental factors at different spatiotemporal scales, potentially involved in this particular behavior. We registered the variation of light intensity and temperature across days, months, and different vegetation canopy covers and assessed their effects on the number of daylight flights. We found that the daytime activity of this insular population increases with vegetation cover, decreases with light intensity and temperature, and varies seasonally. These responses of flying activity to environmental temperature and light intensity seem to be related to avoiding the risk of overheating. Furthermore, bats were also active at night, and daytime flights included echolocation and feeding, which suggest that daytime activity complements but does not replace night-time activity. Consequently, our results provide empirical support for the notion that the nocturnality in bats can reflect the actions of avoiding overheating during the day.
Gap junctions: historical discoveries and new findings in the Caenorhabditis elegans nervous system

ABSTRACT Gap junctions are evolutionarily conserved structures at close membrane contacts between two cells. In the nervous system, they mediate rapid, often bi-directional, transmission of signals through channels called innexins in invertebrates and connexins in vertebrates. Connectomic studies from Caenorhabditis elegans have uncovered a vast number of gap junctions present in the nervous system and non-neuronal tissues. The genome also has 25 innexin genes that are expressed in spatial and temporal dynamic pattern. Recent findings have begun to reveal novel roles of innexins in the regulation of multiple processes during formation and function of neural circuits both in normal conditions and under stress. Here, we highlight the diverse roles of gap junctions and innexins in the C. elegans nervous system. These findings contribute to fundamental understanding of gap junctions in all animals. Summary: Studies from C. elegans have illustrated many roles of gap junctions in neural connectivity and circuit regulation, during normal conditions and under stress.
Technical Perspective

From a historical perspective, relational database management systems (RDBMSs) have integrated many specialized systems and data models back into the RDBMS over time. New workloads motivated specialized systems for performance, but over time, general-purpose RDBMSs absorbed this functionality to avoid boundary crossing. We already witnessed this process for object-relational functionality, XML and JSON data types, OLAP/HTAP systems, and RDF/graph processing, while for natural language processing (NLP), time series, and machine learning (ML), the outcomes remain unclear. Interestingly, graph processing, NLP, and time series are largely ML workloads too. For this reason, integrating data management and ML is of high practical relevance and has been addressed by (1) integrating ML into RDBMSs, and (2) specialized ML systems. The paper "Declarative Recursive Computation on an RDBMS" [3] by Jankov et al. makes a very valuable contribution by reconciling these two areas and showing the potential of recursive computations on an RDBMS, as the backend-not necessarily frontend-for large-scale machine learning.
Reproductive Isolation and Morphological Discrimination of Myotis myotis Macrocephalicus and M. Blythii s.l. (Chiroptera: Vespertilionidae) in Turkey

In order to facilitate taxonomic identification and assess reproductive isolation between Myotis myotis macrocephalicus and M. blythii s.l. , at the interface between the Balkan Peninsula and Middle East, we analyzed microsatellite markers and a fragment of the mitochondrial hyper-variable control region. We also examined two external morphological traits of the sampled bats, length of upper tooth row (CM3) and forearm (FA) length, to assess the reliability of distinguishing them morphologically. Myotis blythii s.l. had higher allelic and haplotype richness than M. m. macrocephalicus, supporting the hypothesis that the former was present in Asia Minor before the arrival of M. myotis from Europe. The microsatellite markers analyses suggested that all sampled individuals were ‘pure’ forms of either species. Both species, however, shared a few mitochondrial haplotypes, which seem to document past introgression events rather than the recurrent interbreeding. Length of CM3 and FA increased with longitude in both species. A binary logistic regression model, using CM3 measurements and longitude of the sampling locality, correctly assigned 98% of genetically identified individuals. The sex-specific binary regression models, based on FA measurements and longitude were correct for 96% females and 98% males.
The Limpopo River Exerts a Powerful but Spatially Limited Effect on Bat Communities in a Semi-Arid Region of South Africa

Although the Limpopo River is not perennial in its upper stretches in South Africa, the presence of a narrow riparian forest zone is expected to enhance bat diversity by promoting a wider range of foraging types, but the scale at which this effect may operate is not known. A recent, fine-scale model of bat diversity in Africa suggested that rivers may enhance species richness of bats, but that strong gradients in richness would occur next to rivers especially in savanna areas. We tested this idea by conducting acoustic surveys with bat detectors around six water bodies at distances from 0–12 km from the Limpopo River in two adjacent protected areas, the Mapungubwe National Park and the Venetia Limpopo Nature Reserve. We used a paired design, with each water body having detectors placed at and just away (500–750 m) from it. We found enhanced species richness, diversity and activity at MNP sites closer to the Limpopo (0–5 km) compared with VNR sites located 9–12 km from the Limpopo. Moreover, at VNR but not MNP, the bat community was dominated (32% of calls) by an arid-adapted generalist species, the Cape serotine (Neoromica capensis). Consistent with the proximity of structurally complex riparian vegetation, slow flying, clutter-feeding horseshoe bats (Rhinolophus spp.) were relatively more abundant (12% of calls) at MNP compared with VNR (0.7% of calls). This effect was highly accentuated when correcting for detectability of different species to bat detectors. Proximity to small, natural and artificial water bodies significantly enhanced both species richness and activity, but this effect was much more pronounced at sites > 5 km from the Limpopo compared with sites < 2 km from the Limpopo. We conclude that while major rivers with riparian zones can exert a significant impact on species richness, diversity, activity and community structure of insectivorous bats, this effect may only extend a few kilometres from the river. Protection of riparian zones along rivers in savannas is therefore critical to conserving intact and diverse bat communities.
Plants sustain the terrestrial silicon cycle during ecosystem retrogression

Terrestrial biogeochemistry of silicon Silicon is an important element in plant tissues and contributes to structural defenses against herbivores and other stresses. However, the terrestrial biogeochemical cycling of silicon is poorly understood, particularly the relative importance of geochemical and biological mechanisms in its regulation. de Tombeur et al. studied this question in 2-million-year chronosequences of soil and vegetation in Western Australia. Sites became progressively more weathered and infertile as they aged, indicating that the silicon cycle shifts from geochemical to biological control as the ecosystem develops (see the Perspective by Carey). They found that foliar silicon concentrations increase continuously during ecosystem development, even though rock-derived silicon is depleted in the older soils. By contrast, other major rock-derived nutrients showed decreasing concentrations in plants. Hence, biological silicon cycling allows plants to maintain concentrations even under conditions of extreme soil infertility. Science, this issue p. 1245; see also p. 1161 Plants retain and accumulate silicon when soil reserves are depleted, thereby sustaining silicon cycling. The biogeochemical silicon cycle influences global primary productivity and carbon cycling, yet changes in silicon sources and cycling during long-term development of terrestrial ecosystems remain poorly understood. Here, we show that terrestrial silicon cycling shifts from pedological to biological control during long-term ecosystem development along 2-million-year soil chronosequences in Western Australia. Silicon availability is determined by pedogenic silicon in young soils and recycling of plant-derived silicon in old soils as pedogenic pools become depleted. Unlike concentrations of major nutrients, which decline markedly in strongly weathered soils, foliar silicon concentrations increase continuously as soils age. Our findings show that the retention of silicon by plants during ecosystem retrogression sustains its terrestrial cycling, suggesting important plant benefits associated with this element in nutrient-poor environments.
Genome Sequences of Four Potentially Therapeutic Bacteriophages Infecting Shiga Toxin-Producing Escherichia coli

Four phages infecting Shiga toxin-producing Escherichia coli (STEC) strains of different serotypes were isolated from wastewater samples. Their virion DNAs range from 51 to 170 kbp, are circularly permuted or have defined terminal repeats, and can encode 82 to 279 proteins. Despite their high similarity to other phages, only about 30% of their genes have a predicted function. ABSTRACT Four phages infecting Shiga toxin-producing Escherichia coli (STEC) strains of different serotypes were isolated from wastewater samples. Their virion DNAs range from 51 to 170 kbp, are circularly permuted or have defined terminal repeats, and can encode 82 to 279 proteins. Despite their high similarity to other phages, only about 30% of their genes have a predicted function.
The Business Cycle Mechanics of Search and Matching Models

This paper estimates a real business cycle model with unemployment driven by shocks to labor productivity and the job separation rate. We make two contributions. First, we develop a new identification scheme based on the matching elasticity that allows the model to perfectly match a range of labor market moments, including the volatilities of unemployment and vacancies. Second, we use our model to revisit the importance of shocks to the job separation rate and highlight how their correlation with labor productivity affects their transmission mechanism.
Comparison of fractional exhaled nitric oxide, spirometry, and Asthma Control Test, in predicting asthma exacerbations: A prospective cohort study

Context: Fractional exhaled nitric oxide (FeNO) is a noninvasive test for airway inflammation in asthma. The usefulness of FeNO in predicting exacerbations is uncertain. Aims: The study aims to assess and compare the ability of FeNO, spirometry, and asthma control test (ACT) in predicting future exacerbations of asthma and their correlation with each other. Settings and Design: This prospective, cohort study was conducted at the Department of Respiratory Medicine, Kasturba Medical College, Manipal. Materials and Methods: Adult asthma patients of age 18–65 years were included. Patients with a smoking history of >10 pack-years and those in whom spirometry was contraindicated were excluded. Patients who consented underwent FeNO and spirometry. The control of asthma was assessed using the ACT questionnaire. We captured the number of exacerbations in the follow-up period of 4 months. Statistical Analysis Used: Mann–Whitney test was used to compare the utility of FeNO, spirometry, ACT in predicting exacerbations and Spearman's correlation coefficient was used to ascertain the correlation among them. Results: Of 154 study patients, 28% had exacerbations. We found that there was no significant difference in FeNO in patients with and without exacerbations. The median (interquartile range [IQR]) FEV1% in the patients with and without exacerbations were 68 (55–79) and 75 (65–88), respectively (P = 0.013). The median (IQR) ACT score in patients with exacerbations was 12 (10–16) which was significantly lower than in those without exacerbation in whom it was 16 (14–18) (P = 0.003). There was a negative correlation of ACT with FeNO (Correlation coefficient: −0.167, P = 0.038). The median (IQR) FeNO level (ppb) was lower in patients who were on inhaled corticosteroid (ICS) than in the other group values being 22 (14–38) and 30 (17–58), respectively (P = 0.05). Conclusions: In our study, FEV1% and ACT score could predict exacerbations of asthma whereas FeNO could not. FeNO level correlated inversely with ACT score. FeNO level decreased with inhaled corticosteroid usage.