Miracle-dz/UniFAR-FTUs huggingface dataset:
SYSTEMATICS OF BATS OF THE GENUS GLOSSOPHAGA (CHIROPTERA: PHYLLOSTOMIDAE) AND PHYLOGEOGRAPHY IN G. SORICINA BASED ON THE CYTOCHROME-b GENE

Abstract Systematic relationships within the 5 recognized species of Glossophaga were assessed using the complete cytochrome-b gene (1,140 base pairs). Our samples from 4 species, G. commissarisi, G. leachi, G. longirostris, and G. morenoi, show little intraspecific geographic subdivision. Alternatively, G. soricina has a major mtDNA subdivision that may reflect 2 biological species. Our data suggest that G. soricina is the sister taxon to the remainder of the genus, G. leachi and G. longirostris are sister taxa, and the position of G. morenoi is unresolved, placed either with the G. leachi–G. longirostris clade or with the G. commissarisi clade. Distance values among G. morenoi, G. commissarisi, G. longirostris, and G. leachi were similar, suggesting a similar time of speciation for these 4 species.
Rast: Resource-Aware Session Types with Arithmetic Refinements (System Description)

Traditional session types prescribe bidirectional communication protocols for concurrent computations, where well-typed programs are guaranteed to adhere to the protocols. Recent work has extended session types with refinements from linear arithmetic, capturing intrinsic properties of processes and data. These refinements then play a central role in describing sequential and parallel complexity bounds on session-typed programs. The Rast language and system provide an open-source implementation of session-typed concurrent programs extended with arithmetic refinements as well as ergometric and temporal types to capture work and span of program execution. Type checking relies on Cooper’s algorithm for quantifier elimination in Presburger arithmetic with a few significant optimizations, and a heuristic extension to nonlinear constraints. Rast furthermore includes a reconstruction engine so that most program constructs pertaining the layers of refinements and resources are inserted automatically. We provide a variety of examples to demonstrate the expressivity of the language.
Effect of intermediate host size (Cerastoderma edule) on infectivity of cercariae of Himasthla quissetensis (Echinostomatidae: Trematoda)

The edible cockle (Cerastoderma edule), a common marine bivalve in semi-sheltered sandflats, is a natural host for many parasite species of the genus Himasthla (Echinostomatidae: Trematoda). In a previous paper, Wegeberg et al. (1999) showed segregation of cockle infection by three Himasthla species (H. interrupta, H. continua, H. elongata) in relation to host tissue (foot, mantle, siphon) and host size (1·5 to 14 mm shell length). Following the same experimental procedure, a fourth species, H. quissetensis, an introduced dominant parasite of cockles in Arcachon Bay (south-west France) was investigated. The infection pattern was very similar to the patterns shown by H. elongata and H. continua. Cercariae (the free-living stage shed from prosobranch snails and encysting as metacercariae in bivalves) were most successful in the shell-length range of 6–14 mm, where 74% of the added cercariae were recovered as metacercariae. The comparison with the other Himasthla species supports the previous conclusion that the efficiency of cercariae to infect cockles depends on host size.
Aboveground Vegetation, Seed Bank and Soil Analysis of a 31-year-old Forest Restoration on Coal Mine Spoil in Southeastern Ohio

Abstract A 31-y-old forest restoration on coal mine spoil was studied to assess soil chemical composition, percent change in tree density and percent similarity of the seed bank and ground-story vegetation. Seed bank and soil chemistry results were compared to an adjacent unvegetated spoil bank. Of fifteen tree species planted on a barren, coal, spoil bank in 1966, four increased in density (indicating recruitment since 1966), seven decreased in density to 50% and four decreased in density >50% after 31 y. Nine volunteer tree species were recorded on the reforested site since the plantings in 1966. March and July soil collections in 1997 contained seeds of 18 species each, 13 in both collections. Most of the species found in the seed bank were shade-intolerant. No significant difference was found for total seed density between the March (4257 ± 490 seeds/m2) and July (3589 ± 365 seeds/m2) seed banks. Percent similarity between the seed bank and ground-story vegetation from the March and July seed collections was 9.8% and 8.2%, respectively. No seeds were found in soil collections from the adjacent unvegetated spoil bank. Soil pH and ionic content between the reforested study area and the unvegetated spoil bank differed significantly. We believe that the 1966 plantings have provided a habitat for other species to establish by reducing erosion and improving edaphic conditions.
Twins are not alone: a recircumscription of Linnaea (Caprifoliaceae)

The genus Linnaea is reviewed and expanded to include the genera Abelia (excluding section Zabelia ), Diabelia , Dipelta , Kolkwitzia and Vesalea , making it monophyletic and comprising 16 species. The history of the generic name is discussed. An updated description for the genus Linnaea is provided and new combinations or names for all taxa are provided in Linnaea .
Guidance and Patient Instructions for Proning and Repositioning of Awake, Nonintubated COVID‐19 Patients

Prior studies on proning awake, non-intubated patients with hypoxemic acute respiratory failure, as well as evolving study of similar COVID-19 patients, coupled with experience and dramatic anecdotal evidence from the COVID-19 pandemic, suggest the importance of proning all such patients with COVID-19 to improve oxygenation and reduce respiratory effort. Literature and experience from healthcare teams in the midst of the pandemic suggest that any COVID-19 patients with respiratory compromise severe enough to warrant admission should be considered for proning. We additionally suggest these patients should be considered for proning as well as ongoing patient re-positioning (e.g. right lateral decubitus, seated, and left lateral decubitus positions). Figure 1 represents the proning and positioning instructions developed at New York City Health + Hospitals/Elmhurst, a large, inner-city, tertiary public hospital in the epicenter of the COVID-19 pandemic in New York City, and later adapted and utilized at facilities across the United States.
Spectral Analysis in Ecology

Ecologists, like other biologists, are involved with the study of living systems, and they, again like other biologists, are handicapped in their work by the inadequacy of the conceptual framework to which they must relate their quantitative results, and within which they must generate new and testable hypotheses. One way in which the weakness of this structure manifests itself is in the lack of a theoretical approach consistently applicable to a wide variety of living systems, and able to lead to powerful predictions of high generality. Various such approaches have been tried and found wanting; for example, the most recent candidate, the systems analysis method, requires colossal labor· and expense to produce a solution that is self­ consistent for a particular data set, but for which is guaranteed neither the unique­ ness in the original data set nor the self-consistency in any other data set that may be drawn from the same system ensemble, regardless of the boundary conditions. In other words, both the predictive power and the generality of this inelegant approach are very low. A new foundation for a theoretical biology has been proposed based on nonlinear statistical mechanics (49). This method, which is neither strictly holism nor wholly reductionism, is emerging from attempts to find a general mathematical approach that would account for living as well as nonliving phenomena. It identifies as the most important characteristic of complex systems the property' that the differential equations describing the functional relationships between the system components be of the nonlinear kind. A crucial characteristic of nonlinear systems is their disposition toward periodic behavior, even for non periodic boundary conditions. Therefore, they tend to a periodic (cyclic) organization in time, in space, or in both. According to this view, the biosystem is seen as an ensemble of nonlinear oscillators, coupled together in various functional configurations at each hierarchic level of system description. The
DISTURBANCES IN HAEMATOLOGY, FLUID VOLUME DISTRIBUTION AND CIRCULATORY FUNCTION ASSOCIATED WITH LOW ENVIRONMENTAL pH IN THE RAINBOW TROUT, SALMO GAIRDNERI

Exposure of adult rainbow trout to low pH (4.0–4.5) for 3 days resulted in progressive increases in heart rate, mean arterial blood pressure and haematocrit. The haematocrit increase resulted from erythrocyte swelling, a reduction in plasma volume and a mobilization of erythrocytes from the spleen. Erythrocyte swelling probably resulted from plasma acidosis and a reduction in plasma ions (McDonald & Wood, 1981). There was an associated redistribution of body water from extracellular to intracellular compartments, but maintenance of total body water content. Erythrocyte mobilization was reflected in an increase in reticulocyte and erythrocyte counts, and a depletion of splenic blood reserves. Haemoconcentration caused large increases in blood viscosity, which contributed to the rise in blood pressure. Pharmacological analysis revealed an adrenergic component to the cardiovascular disturbance. These events are thought to play a key role in the toxic syndrome.
Comparative analyses of the genetic diversity among bread wheat genotypes based on RAPD and SSR markers

Two different DNA-based techniques viz, randomly amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to estimate genetic diversity among bread wheat. A total of 188 clear and repeatable bands were amplified from 17 selected RAPD primers, and 101 fragments were detected from 35 SSR primer pairs. The level of polymorphism was 88% with RAPDs compared to 100% with SSRs. Mean genetic similarity was estimated to be 0.88 based on RAPDs and 0.85 using SSRs. The wide range of genetic similarity was obtained by SSR than RAPD, reflecting the hypervariability of SSR markers and their high resolution power. Matrix correlation analyses suggested that a good representation of the relationships among the bread wheat cultivars/lines can be obtained by using RAPDs alone or in combination with SSRs, but SSRs alone cannot be used for this purpose. Both techniques discriminated the genotypes very effectively. On the hand, RAPDs were able to discriminate the cultivars Alvand and Ghods, whereas the cultivars Sardari and Ghods were discriminated only by SSRs. The use of PCRbased assays having advantage of being quick, easy to use and refractory to many environmental influences can complement traditional methods of germplasm characterization.
Soil–atmosphere exchange of CH4, CO, N2O and NOx and the effects of land‐use change in the semiarid Mallee system in Southeastern Australia

The semiarid and arid zones cover a quarter of the global land area and support one‐fifth of the world's human population. A significant fraction of the global soil–atmosphere exchange for climatically active gases occurs in semiarid and arid zones yet little is known about these exchanges. A study was made of the soil–atmosphere exchange of CH4, CO, N2O and NOx in the semiarid Mallee system, in north‐western Victoria, Australia, at two sites: one pristine mallee and the other cleared for approximately 65 years for farming (currently wheat). The mean (± standard error) rates of CH4 exchange were uptakes of −3.0 ± 0.5 ng(C) m−2 s−1 for the Mallee and −6.0 ± 0.3 ng(C) m−2 s−1 for the Wheat. Converting mallee forest to wheat crop increases CH4 uptake significantly. CH4 emissions were observed in the Mallee in summer and were hypothesized to arise from termite activity. We find no evidence that in situ growing wheat plants emit CH4, contrary to a recent report. The average CO emissions of 10.1 ± 1.8 ng(C) m−2 s−1 in the Mallee and 12.6 ± 2.0 ng(C) m−2 s−1 in the Wheat. The average N2O emissions were 0.5 ± 0.1 ng(N) m−2 s−1 from the pristine Mallee and 1.4 ± 0.3 ng(N) m−2 s−1 from the Wheat. The experimental results show that the processes controlling these exchanges are different to those in temperate systems and are poorly understood.
Taxonomy of the Genus Microcyclus Ørskov 1928: Reintroduction and Emendation of the Genus Spirosoma Migula 1894 and Proposal of a New Genus, Flectobacillus

The type strains of the three currently recognized species of the genus Microcyclus Orskov 1928 (M. aquaticus Orskov, strain ATCC 25396; M. major Gromov, strain BKM 859; and M. flavus Raj, strain ATCC 23276), together with strains apparently belonging to each species, were examined to determine their taxonomic relationships. There were many differences between the type strains in their morphological and physiological characteristics as well as in the guanine-plus-cytosine (G+C) contents of their deoxyribonucleic acids (DNAs). Therefore, we propose to split the genus Microcyclus into three genera, each containing a single species. M. aquaticus, the type species of Microcyclus, remains as the only species in the genus. It is characterized by the formation of cellular rings which are produced when the ends of the curved cells overlap. It is nonpigmented and is respiratory in its metabolism; the G+C content of its DNA ranges from 66.3 to 68.4 mol%. M. flavus ATCC 22376 and three similar strains were found to possess characters in agreement with those given in the original description of Spirosoma linguale, and they were placed in that species. The name M. flavus Raj 1970 thus becomes a later subjective synonym of Spirosoma linguale (Eisenberg 1891) Migula 1894. This species is characterized by the formation of wavy and coiled filaments, yellow pigmentation on Microcyclus-Spirosoma (MS) agar, and respiratory metabolism. The G+C content of its DNA ranges from 51.0 to 52.9 mol%. Strain DSM 74 is designated as the neotype strain of S. linguale. M. Major BKM 859 and one similar strain were placed in a new genus, Flectobacillus. F. major (Gromov) comb, nov., the type species, is composed of rods which are straight to curved, the degree of curvature varying among individual cells within a culture. The cells may form long, sinuous filaments and rings. Colonies on MS agar are pale pink to rose-colored. Metabolism is respiratory, and the G+C content of its DNA ranges from 39.5 to 40.3 mol%. The type strain of F. major is strain BKM 859.
Involvement of Tumor Necrosis Factor-α in the Pathogenesis of Autoimmune Orchitis in Rats1

Abstract We studied the testicular macrophages of rats with experimental autoimmune orchitis (EAO) and analyzed whether the tumor necrosis factor-α (TNFα) is involved in germ cell apoptosis and in Leydig cell steroidogenesis. The EAO was induced in adult male Sprague-Dawley rats by active immunization with testicular homogenate and adjuvants. In the experimental group, a severe orchitis was observed 80 days after the first immunization. ED1- and ED2-positive macrophages were quantified by immunohistochemistry. The TNFα concentration of conditioned media from testicular macrophages (TMCM) was determined by ELISA. The number of apoptotic TNF receptor 1 (TNFR1)-positive germ cells was identified by combining in situ end labeling of apoptotic DNA and immunohistochemical techniques. The effect of TNFα on Leydig cell testosterone production was determined by RIA. In rats with EAO, we observed a significant increase in the number of TNFα-positive testicular macrophages, the TNFα concentration in TMCM, and the number of TNFR1-positive germ cells. Sixty percent of TNFR1-positive germ cells were apoptotic. These results suggest that TNFα could be involved in the pathogenesis of EAO. Acting together with other local factors such as Fas-FasL, TNFα could trigger germ cell apoptosis. We also demonstrated that TNFα inhibited in vitro testosterone production in basal and hCG-stimulated Leydig cells from rats with orchitis.
Salvianic acid A alleviates chronic alcoholic liver disease by inhibiting HMGB1 translocation via down‐regulating BRD4

Alcoholic liver disease (ALD) is the major cause of chronic liver disease and a global health concern. ALD pathogenesis is initiated with liver steatosis, and ALD can progress to steatohepatitis, fibrosis, cirrhosis and even hepatocellular carcinoma. Salvianic acid A (SAA) is a phenolic acid component of Danshen, a Chinese herbal medicine with possible hepatoprotective properties. The purpose of this study was to investigate the effect of SAA on chronic alcoholic liver injury and its molecular mechanism. We found that SAA significantly inhibited alcohol‐induced liver injury and ameliorated ethanol‐induced hepatic inflammation. These protective effects of SAA were likely carried out through its suppression of the BRD4/HMGB1 signalling pathway, because SAA treatment largely diminished alcohol‐induced BRD4 expression and HMGB1 nuclear translocation and release. Importantly, BRD4 knockdown prevented ethanol‐induced HMGB1 release and inflammatory cytokine production in AML‐12 cells. Similarly, alcohol‐induced pro‐inflammatory cytokines were blocked by HMGB1 siRNA. Collectively, our results reveal that activation of the BRD4/HMGB1 pathway is involved in ALD pathogenesis. Therefore, manipulation of the BRD4/HMGB1 pathway through strategies such as SAA treatment holds great therapeutic potential for chronic alcoholic liver disease therapy.
Increasing Fatty Acid Oxidation Prevents High-Fat Diet–Induced Cardiomyopathy Through Regulating Parkin-Mediated Mitophagy

Supplemental Digital Content is available in the text. Background: Increased fatty acid oxidation (FAO) has long been considered a culprit in the development of obesity/diabetes mellitus–induced cardiomyopathy. However, enhancing cardiac FAO by removing the inhibitory mechanism of long-chain fatty acid transport into mitochondria via deletion of acetyl coenzyme A carboxylase 2 (ACC2) does not cause cardiomyopathy in nonobese mice, suggesting that high FAO is distinct from cardiac lipotoxicity. We hypothesize that cardiac pathology–associated obesity is attributable to the imbalance of fatty acid supply and oxidation. Thus, we here seek to determine whether further increasing FAO by inducing ACC2 deletion prevents obesity-induced cardiomyopathy, and if so, to elucidate the underlying mechanisms. Methods: We induced high FAO in adult mouse hearts by cardiac-specific deletion of ACC2 using a tamoxifen-inducible model (ACC2 iKO). Control and ACC2 iKO mice were subjected to high-fat diet (HFD) feeding for 24 weeks to induce obesity. Cardiac function, mitochondria function, and mitophagy activity were examined. Results: Despite both control and ACC2 iKO mice exhibiting a similar obese phenotype, increasing FAO oxidation by deletion of ACC2 prevented HFD-induced cardiac dysfunction, pathological remodeling, and mitochondria dysfunction, as well. Similarly, increasing FAO by knockdown of ACC2 prevented palmitate-induced mitochondria dysfunction and cardiomyocyte death in vitro. Furthermore, HFD suppressed mitophagy activity and caused damaged mitochondria to accumulate in the heart, which was attenuated, in part, in the ACC2 iKO heart. Mechanistically, ACC2 iKO prevented HFD-induced downregulation of parkin. During stimulation for mitophagy, mitochondria-localized parkin was severely reduced in control HFD-fed mouse heart, which was restored, in part, in ACC2 iKO HFD-fed mice. Conclusions: These data show that increasing cardiac FAO alone does not cause cardiac dysfunction, but protects against cardiomyopathy in chronically obese mice. The beneficial effect of enhancing cardiac FAO in HFD-induced obesity is mediated, in part, by the maintenance of mitochondria function through regulating parkin-mediated mitophagy. Our findings also suggest that targeting the parkin-dependent mitophagy pathway could be an effective strategy against the development of obesity-induced cardiomyopathy.
Involvement of sphaeractinomyxon in the life cycle of mugiliform-infecting Myxobolus (Cnidaria, Myxosporea) reveals high functionality of actinospore morphotype in promoting transmission

Abstract Four new actinospore types belonging to the sphaeractinomyxon collective group (Cnidaria, Myxosporea) are described from the coelomic cavity of a marine Baltidrilus sp. (Oligochaeta, Naididae) inhabiting a northern Portuguese estuary. Host identification supports the usage of marine oligochaetes, namely of the family Naididae Ehrenberg, 1828, as definitive hosts for myxosporeans inhabiting estuarine/marine environments. The absence of mixed infections in the host specimens analysed is suggested to reflect the influence of host-, parasite- and environmental-related factors regulating myxosporean–annelid interactions. Molecular analyses matched the SSU rDNA sequences of three of the four new types with those of mugiliform-infecting Myxobolus spp. , namely Myxobolus mugiliensis and a Myxobolus sp. from flathead grey mullet Mugil cephalus, and Myxobolus labrosus from thicklip grey mullet Chelon labrosus. These results directly link, for the first time, the sphaeractinomyxon collective group to a myxospore counterpart, further confirming their previously hypothesized specific involvement in the life cycle of myxobolids that infect mullets. Acknowledging this life cycle relationship, the functionality of the sphaeractinomyxon morphotype is suggested to have been decisive for the evolutionary hyperdiversification of the genus Myxobolus in mullets. Unlike other actinospore morphotypes, sphaeractinomyxon lack valvular processes, which implies a limited capability for buoyancy. Considering the benthic-feeding nature of mullets, this feature is most likely crucial in promoting successful transmission to the vertebrate host.
Differentiating Groups of Abies Species With a Simple Molecular Marker

Abstract The unambiguous identification of closely related species is useful for many practical purposes in forest tree species. For example, international laws require timber identification and the control of the origin of forest reproductive material. In this paper, we present a mitochondrial DNA marker which can be used to differentiate among groups of fir species (Abies spp.). Eight Mediterranean and one North American fir species (used as reference) were analysed at the fourth intron of the NAD subunit 5 gene. A total of six different haplotypes was identified, one in the American Abies concolor, the other five in Mediterranean species. Two different haplotypes were found each in the widespread A. alba and in A. cephalonica, one haplotype being shared among the two species. A single species specific haplotype was found in the near-eastern A. cilicica. The two southwestern species A. pinsapo and A. numidica shared one haplotype. The fifth haplotype was shared by all remaining eastern Mediterranean firs, A. cephalonica, A. bornmuelleriana, A. equi-troiani, and A. nordmanniana. Differences in haplotype sequences were mainly due to large insertions/deletions. Agarose gel electrophoresis thus provides a fast, cheap and reliable diagnosis method for species or species group identification.