Miracle-dz/UniFAR-FTUs huggingface dataset:
The dynamics of heterotrophic nanoflagellates and bacterioplankton in a large ultra-oligotrophic Antarctic lake

The abundance of both heterotrophic nanoflagellates (HNAN) and bacterioplankton in a large (9km2) ultraoligotrophic Antarctic lake (Crooked Lake) were investigated from December 1992 until November 1993. HNAN abundance peaked in spring, summer and autumn, falling to lowest numbers during the winter. Numbers ranged between 0 and 50.9×104 l−1. Bacterioplankton abundance was highest during the late summer and then fell progressively towards winter and autumn (range 1.19–4.46×106 l−1) In contrast to numbers, mean cell volumes (MCV) of the bacteria reached their highest in spring, and consequently highest bacterial biomass occurred at this time. MCV ranged between 0.052 and 0. 224μm3. Bacterial production measurements following the incorporation of [3H] thymidine into DNA and [14C] leucine into protein using a doubling-labelling procedure were undertaken in January, June, August, October and November. Rates varied between 2.8 and 52 ng C l1 h1. On occasions, a significant difference in production rates based on the uptake of leucine and thymidine was observed, suggesting unbalanced growth. Highest rates of production coincided with times of high dissolved organic carbon levels in the water column and lowest production with low levels of DOC. HNAN grazing rates were measured by following the uptake of fluorescently labelled bacteria and averaged 4.8 bacterial cells individual1 day1 at 2 and 4°C. Specific growth rates (h1) ranged around 0.00070–0.00077 in both the field and laboratory, giving doubling times of 37.3 and 41.0 days, respectively. These low rates of grazing and growth indicate that there is no adaptation to low temperatures in these freshwater protists. Based on these data, the gross production efficiency is 24%. HNAN removed between 0.1 and 9.7% of bacterial production per day.
Group Choice as a Function of Group Size Differences and Assessment Time in Fish: The Influence of Species Vulnerability to Predation

The shoal-choice behaviour of two species of fish that differ in their vulnerability to predation was compared. Individuals of threespine stickleback, Gasterosteus aculatus, and creek chub, Semotilus astromaculatus, were presented with a simultaneous choice of two equidistant stimulus shoals of conspecifics that differed in membership size (5 vs. 6 fish, 5 vs. 7, 5 vs. 8, 5 vs. 9 and 5 vs. 10). Test fish were allowed to view the stimulus shoals from a standard distance for either 10-20 or 120-150 s before being frightened with a stimulus from an overhead light and released to join either shoal. We observed which shoal (the smaller or the larger one) the test fish approached. Preference for the larger stimulus shoal generally increased with increasing shoal size difference and with the duration of the assessment period, and was more pronounced in chub (the more vulnerable of the two species). For the short assessment period, chub showed a significantly stronger preference for the larger stimulus shoal than sticklebacks, whereas there was no significant difference between species for the long assessment period. Furthermore, chub responded more readily to small differences in shoal size (of 1-3 fish) than sticklebacks, for both short and long assessment periods. The above results are consistent with the hypothesis that chub, as the more vulnerable of the two species (in terms of predation), should be able to identify the larger of two shoals more quickly and should be more sensitive to small differences in shoal size than sticklebacks.
Adaptations in pectoralis muscle, heart mass, and energy metabolism during premigratory fattening in semipalmated sandpipers (Calidris pusilla)

In late summer, semipalmated sandpipers (Calidris pusilla) migrate nonstop from eastern Canada to wintering sites on the northwest coast of South America. Before their transoceanic flight, the birds feed intensively for about 15 days during which time lipids are stored. The fat-free dry mass of the pectoralis muscle increases during the fattening period, probably increasing the maximal power output of the muscle. Plasma free fatty acids and triglycerides, pectoralis muscle lipid content, and the activity of carnitine oleoyl coenzyme A transferase are higher in heavy (fat) than in light (lean) birds. These alterations imply an enhanced capacity to utilize fatty acids as a metabolic fuel during migration. Total pectoralis muscle glycogen levels and the activity of pyruvate kinase increase, suggesting a higher capacity for glycogenolysis, which may be important during intense levels of energy demand. Heart size and protein content per gram of tissue increase in association with an increase in body mass. Howe.
Development and Prospective Validation of a Transparent Deep Learning Algorithm for Predicting Need for Mechanical Ventilation

IMPORTANCE: Objective and early identification of hospitalized patients, and particularly those with novel coronavirus disease 2019 (COVID-19), who may require mechanical ventilation is of great importance and may aid in delivering timely treatment. OBJECTIVE: To develop, externally validate and prospectively test a transparent deep learning algorithm for predicting 24 hours in advance the need for mechanical ventilation in hospitalized patients and those with COVID-19. DESIGN: Observational cohort study SETTING: Two academic medical centers from January 01, 2016 to December 31, 2019 (Retrospective cohorts) and February 10, 2020 to May 4, 2020 (Prospective cohorts). PARTICIPANTS: Over 31,000 admissions to the intensive care units (ICUs) at two hospitals. Additionally, 777 patients with COVID-19 patients were used for prospective validation. Patients who were placed on mechanical ventilation within four hours of their admission were excluded. MAIN OUTCOME(S) and MEASURE(S): Electronic health record (EHR) data were extracted on an hourly basis, and a set of 40 features were calculated and passed to an interpretable deep-learning algorithm to predict the future need for mechanical ventilation 24 hours in advance. Additionally, commonly used clinical criteria (based on heart rate, oxygen saturation, respiratory rate, FiO2 and pH) was used to assess future need for mechanical ventilation. Performance of the algorithms were evaluated using the area under receiver-operating characteristic curve (AUC), sensitivity, specificity and positive predictive value. RESULTS: After applying exclusion criteria, the external validation cohort included 3,888 general ICU and 402 COVID-19 patients. The performance of the model (AUC) with a 24-hour prediction horizon at the validation site was 0.882 for the general ICU population and 0.918 for patients with COVID-19. In comparison, commonly used clinical criteria and the ROX score achieved AUCs in the range of 0.773 - 0.782 and 0.768 - 0.810 for the general ICU population and patients with COVID-19, respectively. CONCLUSIONS and RELEVANCE: A generalizable and transparent deep-learning algorithm improves on traditional clinical criteria to predict the need for mechanical ventilation in hospitalized patients, including those with COVID-19. Such an algorithm may help clinicians with optimizing timing of tracheal intubation, better allocation of mechanical ventilation resources and staff, and improve patient care.
COVID-19 trend in Bangladesh: deviation from epidemiological model and critical analysis of the possible factors

Background: Since its first report on March 08, COVID-19 positive cases and number of deaths are increasing in Bangladesh. In the first month of COVID-19 infection, incidence of daily positive cases did follow the susceptible, infected and recovered (SIR) based predictions we reported in April, but started to deviate in the following month. COVID-19 transmission and disease progression depends on multifaceted determinants e.g. viral genetics, host immunity, social distancing, co-morbidity, socio-demographic and environmental parameters. Therefore deviation in confirmed cases from predicted model may appear and warrant thorough investigation. In this short report, we tried to demonstrate and analyze the possible factors associated with the deviation which included preventive intervention strategies, socioeconomic capabilities, climatic and meteorological indexes, acquired immunity of Bangladeshi population, demographic characteristics, health indicators and food habits. Findings: The key factor responsible for the deviation was found to be the number of tests performed. Having population with low median age, young age groups are being mostly infected. Low prevalence of non-communicable diseases among them and strong immunity compared to the elderly might have kept most of them asymptomatic with silent recovery. Warm temperature, humidity and UV index of Bangladesh during this summer period might have contributed to the slow progression of infection. Longer daylight mediated immunity, fresh air circulations and ventilation, less density in rural areas and certain food habits perhaps helped the large number of populations to restrict the infection. Conclusion: Despite all these helpful determinants in Bangladesh, person to person contact is still the leading risk factor for COVID-19 transmission. Infection may increase rapidly if safe distance and preventive measures are not strictly followed while resuming the normal social and work life. A global second wave may hit in many countries in autumn and as well as in Bangladesh in mid-October when winter starts to approach. Strong collaborative action plans, strategies and implementation are needed immediately to prevent catastrophe.
A novel pair of universal primers for the detection of potyviruses.

A novel pair of universal primers was developed to detect potyvirus species after conserved sites were identified using all full-length potyvirus sequences available by 2005. The breadth of specificity of the new primers, NIb2F and NIb3R, was investigated and compared with the specificity of two routinely used primer pairs in plant virus diagnostic laboratories. RNA from 40 potyvirus isolates representing 23 recognized and three possible new species was tested. Reactions with NIb2F and NIb3R produced amplicons of 350 bp from all 40 virus isolates tested. Reactions with the previously published WCIEN and Potyvirid primers amplified cDNA from 32 and 21 isolates, representing possibly 21 and 15 species, respectively. The identity of 12 unknown potyvirus isolates was confirmed by sequencing and three were found to be potentially distinct potyvirus species. Gel banding patterns from reactions with NIb2F and NIb3R were simpler to interpret than those from reactions with the other two primer sets; fewer products were visible and the cDNA fragments were less variable in size. RT-PCR with the novel primers is predicted to be able to detect virus isolates from all major groups within the genus Potyvirus and its reliability makes it well suited for use as a routine diagnostic assay.
Psychological consequences of the Flint Water Crisis: A systematic review.

Given the COVID-19 outbreak, these unprecedented times pose many urgent dilemmas about how to support the mental health of communities. The goal of this research is to summarize existing literature on the mental health impact of the recent Flint Water Crisis. In March 2020, we searched five databases for literature exploring the psychological consequences of the crisis. Main findings were extracted. 132 citations were screened and eleven included in the review. Results suggest a negative psychological effect caused by the water crisis, including anxiety and health worries, exacerbated by lowered trust in public health officials, uncertainty about the long-term impacts of the crisis, financial hardships, stigma, and difficulties seeking help. There was evidence that concerns about tap water continued even after the state of emergency was lifted. With a possible compounded effect to residents of Flint with the recent COVID-19 pandemic, the results highlight the need for more resources for psychological health interventions in Flint as well as a need for local governments and health authorities to regain the trust of those affected by the Flint Water Crisis.
Some aspects of the absorption of picloram by gorse (Ulex europaeus L.)

Summary: Plants of Ulex europaeus were grown from cuttings and studies made of the absorption of 14C-picloram applied with unlabelled 2,4,5-T. In vivo experiments in a growth chamber showed that absorption ceased after 10 h, but was resumed on wetting. In in vitro experiments the Q10 and the activation energy for uptake decreased with increasing temperature. Absorption was increased by addition of non-ionic surfactants, by lowering the pH and by removal of cuticular wax. Gorse shoots were shown to have a high wax content but scanning electron microscopy revealed no obvious wax structures and the contact angle of spray droplets was less than 900, indicating that the surfaces were not difficult to wet. Resume: Quelques aspects de l'absorption du piclorame par le genet (Ulex europaeus L.) Des plantes d'Ulex europaeus ont ete cultivees a partir de boutures et des etudes ont ete faites sur l'absorption du piclorame marque au 14C, applique avec du 2,4,5-T non marque. Des experiences in vivo en chambre climatisee montrerent que l'absorption cessait apres 10 heures mais reprenait avec l'arrosage. Dans ces experiences in vitro, le Q10 et l'energie d'activation pour l'absorption diminuerent avec l'augmentation de la temperature. L'absorption fut accrue par l'addition d'agents de surface non ioniques, par l'abaissement du pH et par l'enlevement de la cire cuticulaire. Les pousses de genet montrerent une teneur elevee en cire mais l'examen au microscope electronique ne revela pas de structures cireuses evidentes et l'angle de contact des gouttelettes de pulverisation fut inferleur a 90°, ce qui indique que les surfaces n'etaient pas difficiles a mouiller. Zusammenfassung Einige Aspckte der Absorption von Picloram durck Stechginster (Ulex europaeus L.) Pflanzen von Ulex europaeus wurden aus Stecklingen gezogen und die Absorption von 14C-Picloram untersucht, das zusammen mit 2,4,5-T appliziert wurde. In vivo versuche in der Klimakammer zeigten, dass die Absorption nach 10 Stunden aufhorte, aber durch Befeuchtung wieder anfing. Bei in vitro versuchen nahm der Q10-Wert und die Aktivierungsenergie fur die Aufnahme mit steigender Temperatur ab. Durch Zusatz von nichtionischen Netzmitteln, durch Erniedrigen des pH und durch Entfernung des kutikularen Wachses wurde die Absorption erhoht. Es wurde gezeigt, dass die Stechginsterslengel einen hohen Wachsgehalt haben. Raster-Elektronenmikroskopie zeigte jedoch keine deutlichen Wachsstrukturen und der Kontaktwinkel der Spritztropfchen war kleiner als 90°, was darauf hinweist, dass die Oberflachen nicht schwer bcnetzbar sind.
Habitat specificity, restricted range and metapopulation persistence of the slender scotch burnet moth Zygaena loti in western Scotland

1. Many species have highly localized distributions in the British Isles and have persisted for considerable periods of time in isolation from their main ranges on the European continent. Many of these have survived in warm man-made refugia in southern England. 2. The slender scotch burnet moth Z. loti is one of many insects that are confined in the British Isles to small areas of western Scotland. Its ecology was studied to identify its conservation requirements and factors explaining its persistence and restricted distribution. 3. Most populations were small and the majority occurred in herb-rich grassland on vegetated talus slopes below south-facing Tertiary basalt cliffs. Mobility was limited, but nevertheless the colonies form a metapopulation. Female oviposition and larval behaviour were concentrated around patches of bare soil and small foodplants, amongst short, dark vegetation suggesting that a specialized microclimate is important. The requirements of Z. loti are similar to butterflies at the north-west limits of their European ranges in southern England. 4. The vegetation of the thin soils was early successional and exhibited signs of frequent disturbance. Soils were more developed, and densities of moths were lower, on colonies that were more heavily vegetated. Suitable areas are created by rockfalls or slope slippage and maintained by small-scale disturbance or by grazing. The thin soils and high grazing levels suggest that vegetation colonization is slow, so although site occupancy is limited ultimately by vegetation succession, suitable conditions may persist for long periods if local disturbance continues. 5. Colonies have persisted in isolation for so long and on such small sites because of the low turnover of sites caused by slow succession, the instability of the basalt slopes and regular grazing. A recent reduction in grazing pressure has led to a contraction in the range of the species to the most unstable sites. 6. The enhanced microclimate associated with habitat aspect, local shelter and short vegetation, as well as soils influenced by basalt, help explain the restriction of Z. loti and related species to this part of the western seaboard of Scotland. But the unusually oceanic climate of this region probably explains the presence of these and many other species that are separated from their main ranges elsewhere in Britain and Europe.
Evolution and the Diversity of Life: Selected Essays

General Introduction I. EVOLUTION Introduction: Darwin Vindicated Basic Concepts of Evolutionary Biology The Evolution of Living Systems Typological versus Population Thinking Accident or Design: The Paradox of Evolution Selection and Directional Evolution Population Size and Evolutionary Parameters From Molecules to Organic Diversity Sexual Selection and Natural Selection The Emergence of Evolutionary Novelties II. SPECIATION Introduction Darwin and Isolation Darwin, Wallace, and the Origin of Isolating Mechanisms Karl Jordan on Speciation Sympatric Speciation Bird Speciation in the Tropics Change of Environment and Speciation Geographical Character Gradients and Climatic Adaptation III. HISTORY OF BIOLOGY Introduction Lamarck Revisited Agassiz, Darwin, and Evolution The Nature of the Darwinian Revolution Karl Jordan on the Theory of Systematics and Evolution Where Are We? The Recent Historiography of Genetics IV. PHILOSOPHY OF BIOLOGY Introduction Cause and Effect in Biology Explanatory Models in Biology Theory Formation in Developmental Biology Teleological and Teleonomic: A New Analysis V. THEORY OF SYSTEMATICS Introduction The Challenge of Diversity The Role of Systematics in Biology Theory of Biological Classification Cladistic Analysis or Cladistic Classification VI. THE SPECIES Introduction Toward a Modern Species Definition Karl Jordan and the Biological Species Concept Species Concepts and Definitions Sibling or Cryptic Species among Animals The Biological Meaning of species VII. MAN Introduction Taxonomic Categories in Fossil Hominids VIII. BIOGEOGRAPHY Introduction What Is a Fauna? History of the North American Bird Fauna Inferences Concerning the Tertiary North American Bird Faunas The Origin and History of the Polynesian Bird Fauna Land Bridges and Dispersal Facilities Wallace's Line in the Light of Recent Zoogeographic Studies Fragments of a Papuan Ornithogeography The Ornithogeography of the Hawaiian Islands The Nature of Colonization of Birds IX. BEHAVIOR Introduction Behavior and Systematics Behavior Programs and Evolutionary Strategies INDEX
Amylase activities in insect (Aelia and Eurygaster) damaged wheat

The extent of modification of wheat amylase activities caused by Aelia and Eurygaster attack on wheat grain was determined in different Spanish cultivars subjected to varying degrees of attack. High variation in diastatic activity and α-amylase and β-amylase activities was found between cultivars, but no relationship could be established between these activities and bug damage within cultivars. Scanning electron micrographs of the cross-section of damaged kemels showed an empty cavity under the bite point. The surrounding cell walls and protein matrix were absent, but the starch granules were intact. Since wheat damaged by Aelia and Eurygaster does not have altered amylase activities, it appears that amylolytic enzymes are not involved in the alteration of bug-damaged wheat. L'etendue des modifications des activites amylasiques du ble causees par l'attaque de Aelia et Eurygaster sur le grain de ble est determinee dans des cultivars espagnols sujets a differents degres d'attaque. De grandes variations dans les activites diastase, α et β amylase sont observees entre les cultivars mais aucune relation ne peut etre etablie avec les dommages causes par les insectes. Les resultats indiquent que les enzymes amylolytiques ne sont pas impliquees dans l'alteration du ble endommage par les insectes.
Growth, Morphology and Microherbivore Faunas of Pelvetia fastigiata (Phaeophyta, Fucaceae) at La Jolla, California, U.S.A.

Age-size relationships of Pelvetia fastigiata on bedrock ridges at La Jolla, California were established by measuring individuals of known ages on four occasions during 1974-1977. Such relationships indicate that P. fastigiata individuals commonly grow 1-2 cm in length, or approximately 10 cm in volume (space occupied) per 30 d. The age-size relationships, however, exhibit high variance because some individuals grow 3-4 cm per 30 d but others, especially larger plants, become smaller between surveys. Specimens of P. fastigiata collected from six different sites demonstrate that thallus lengths are positively related to other size parameters (weights and volumes) but that relationships among such parameters can vary with plant size and distribution. Variations in length/weight relationships and in bushiness suggest that net growth rates are lower for isolated (non-contiguous) than for aggregated P. fastigiata in the same area. Invertebrates that wound P. fastigiata (the amphipod Ampithoe tea and perhaps gastropods and decapods) arid often other microherbivores are relatively abundant on "bushy", isolated P. fastigiata. Therefore, although grazing effects are not known quantitatively, such distributions suggest that microherbivores as well as physical factors may affect the morphology, growth and perhaps reproduction of P. fastigiata at La Jolla.
Interspecific Differences in the Direct and Indirect Effects of Two Neotropical Hylid Tadpoles on Primary Producers and Zooplankton

Herbivores can both consume and facilitate primary producers with important consequences for community structure. How differences in herbivore foraging ecology alter the relative importance of such effects is not well understood, especially in tropical lentic systems. To address this issue, we manipulated the density of two herbivores with different foraging strategies to evaluate their effects on primary producers and other consumers. Specifically, we examined the effects of the tadpoles of two common Neotropical hylid frogs at two densities on conspecific growth, periphyton and phytoplankton, and zooplankton. We found that the tadpoles of the pantless treefrog, Dendropsophus ebraccatus, reduced periphyton and increased phytoplankton abundances, whereas they had no affect on zooplankton. The red‐eyed treefrog, Agalychnis callidryas, also reduced periphyton and increased phytoplankton, but to a greater extent, and they also had strong impacts on zooplankton by altering the composition, size structure, and total abundances of the zooplankton community. Differences between both species' impacts on these food webs were independent of tadpole biomass, as size‐selective filter feeding and nutrient cycling seems to drive the impacts of A. callidryas on phytoplankton and zooplankton, while the role of D. ebraccatus is more limited. Species level differences in the strength and direction of top‐down and bottom‐up effects on food webs suggest that the ecological roles of tadpoles may be diverse and important to aquatic communities.