Miracle-dz/UniFAR-FTUs huggingface dataset:
Authors' response

In this intriguing article, Fidder et al report on the long-term follow-up of a cohort of subjects with inflammatory bowel disease (IBD) managed at a tertiary care institution. The authors conclude that IBD patients exposed to infliximab are at no higher risk for mortality or being diagnosed as having malignancy than controls with no prior infliximab exposure. These results would appear to confirm the safety of this drug in the treatment of IBD, as suggested by other studies of IBD cohorts followed over the long-term. However, it appears that this study may contain significant biases which may call these results into question. The issue is that of immortal time bias. In brief, immortal time bias may occur when (1) the criterion for enrolment in the each of the person-time cohorts (in this case infliximab exposure vs non-exposure) does not occur at the same point in time, (2) the occurrence of the outcome in the unexposed group (in this case, death or malignancy) would have prevented future exposure, and (3) the researchers do not account for this ‘immortal person time’ in the enumeration of the total unexposed person-time. In this study, the accrual of person-time for exposed subjects started on the day of the initial infusion of infliximab, which could have occurred anytime from 1994 until 2008. However, person-time was accrued for all unexposed subjects from 1994 onward. However, given our current practice of not administering infliximab to the deceased, one may presume that a subject who received infliximab in 1999 survived at least to that point in time. However, if we accept the counterfactual argument that if that same person instead had died in 1997, he would have been included as an outcome for the exposed group. It does not appear that this ‘immortal person time,’ being the time between 1994 and receipt of the first dose of infliximab, was included in the aggregate person-time for the unexposed cohort. The failure to include this additional person-time would have the effect of decreasing the value of the denominator, thereby overestimating the mortality and malignancy incidence rate in the unexposed cohort. The failure to appropriately account for immortal person time has led to erroneous conclusions being reached in numerous published studies, with treatment effects overestimated by up to 50% over the true value. 4 Assuming for a moment that the dates of the first infliximab infusion were evenly distributed over time for the exposed subjects, 2212 person years of additional person time would need to be added to the 6704 person years reported in the study, resulting in an 33% overestimation of the incidence of adverse outcomes in the control group. Before we can make any conclusions on the long-term safety of infliximab, it would be useful to see a reanalysis of the data, this time with immortal person-time taken into account.
Sexual size dimorphism in relation to female polygamy and protandry in butterflies: a comparative study of Swedish Pieridae and Satyridae

In a number of insects male size has been shown to be positively correlated with mating success. Since variance in male mating success should increase with the degree of female polygamy, sexual selection for large male size may be stronger under polyandry than under monandry. To test this hypothesis we correlated male/female sexual size dimorphism, defined as male/female forewing length, with the degree of female polygamy, assessed by counting the number of spermatophores in wild-caught females. Both sets of data were assessed from 23 species of butterflies, 11 in the Pieridae and 12 in the Satyridae. There was a positive correlation between male/ female sexual size dimorphism and female polygamy in both families. Although size is affected by many factors, we contend that this result is best explained by sperm competition; in butterflies, the mass of the ejaculate delivered by a male is positively correlated with male size, and large ejaculates induce a longer period of female unreceptivity, resulting in sexual selection favouring large male size in species where females mate repeatedly. Although there is an obvious conflict between having a short development time and acquiring large size, the expected negative relationship between sexual size dimorphism and protandry was not statistically significant under direct development in the 8 species tested. This suggests that males under direct development achieve both large size and short development time simultaneously by increasing their growth rate. In diapause generations of 14 species (including overwintering generations of the 8 bivoltine species above) there was, however, such a negative relationship. Since protandry in diapause generations is mainly the result of morphogenesis of the adult during postdiapause pupal development, this is consistent with the tendency for small individuals, males, to require shorter morphogenetic development times than larger individuals, females. We found a weak negative correlation between polyandry and protandry, statistically significant only under diapause development. This suggests that mating with virgin females is more beneficial than mating with non-virgins also under female polygamy, and indicates that selection for early male emergence is only weakly relaxed in species where females mate repeatedly.
A monograph of the freshwater mussels (Mollusca: Pelecypoda) of the Australian region

This monograph incorporates a systematic revision of the freshwater mussels of the Australian Region (Australia, New Zealand, New Guinea and the Solomon Islands). Previous systematic works are revised and discussed. Details of the taxonomic procedures used in the present work are presented. One aberrant New Guinea genus, Haasodonta, with two species is referred provisionally to the family Unionidae Fleming, subfamily Rectidentinae Modell. The remainder of the Australasian species are assigned to the family Mutelidae Gray. Four subfamilies, Velesunioninae Iredale, Lortiellinae Iredale, Hyridellinae Iredale, and Cucumerunioninae Iredale, are recognized. These include eight genera, Velesunio Iredale, Alathyria Iredale, Weatralunio Iredale, Microdontia Tapparone Canefri, Lortiella Iredale, Hyridella Swainson, Cucumerunio Iredale, and Virgus Simpson. The genus Hyridella includes four subgenera, Hyridella s.s. , Protohyridella Cotton & Gabriel, Nesonaia Haas, and a new subgenus for H. menziesi Gray. These eight genera include 27 species, three of which are polytypic. Three additional species are considered of doubtful validity and two nominal species are listed as nomina dubia. Each taxon is redescribed and all available data of shell morphology, soft anatomy, larval stages, distribution, and type material are presented. The distribution of the Australian and New Guinea species in relation to the fluvifaunal provinces of Iredale and Whitley is considered and a new name is proposed for the fluvifaunula of southern New Guinea. The evolutionary relationships of the Australasian freshwater mussels are discussed and it is suggested that, with one exception, they arose from a single ancestral stock and have subsequently differentiated into four subfamilies within this region. This view is supported by the close anatomical similarity between them.
EXPERIMENTS ON THE SURVIVING MAMMALIAN INTESTINE

Segments of the small intestine have been kept exsected at different temperatures to determine for how long a period the pendulum movements can be revived when the intestine is subsequently put into oxygenated Locke's solution at 37° C. ; also to determine what modifications the pendulum movements undergo when revived under these conditions, and what alterations occur in the effects produced on them by certain drugs. As far as has been found, the maximum time of survival is as follows: 5 days when the isolated intestine is kept at 3° to 7° C. ; over 24 hours when kept at about 15° C. ; at least 8½ hours when kept at 37° C. (without oxygen). The movements of the revived intestine show a gradual diminution of amplitude, but no conspicuous alteration of rate. The reaction of the revived intestine to adrenine and to barium continues unchanged at those temperatures so long as the intestine retains any power of rhythmic movement. Pilocarpine and atropine produce their normal action on the pendulum movements when the intestine is kept for 5 days at 3° to 7° C. ; but lose their effect when it is kept for 3½ hours at 37° C. The results give an indication of the longevity of the receptive substances for those drugs when the intestine is kept at different temperatures, and lead to the conclusion that the receptive substances connected with the sympathetic nerve terminals have a greater vitality than those connected with the parasympathetic nerve terminals. The isolated circular muscle of the cat's small intestine possesses the power of executing rhythmic movements, resembling the pendulum movements, when it is completely separated from the longitudinal muscle on the one side and from the submucosa and mucous membrane on the other. This power is retained even when the outer layers of the circular muscle have also been removed; the inner layers, remote from Auerbach's plexus, still retain the property of spontaneous rhythmicity. Subject to a revision of the accepted conceptions of the localised nature of Auerbach's plexus, the conclusion is drawn that the spontaneous rhythmicity of these movements is an inherent property of the muscle itself. This conclusion is supported by the fact that, when the intestine is kept at different temperatures, the power of executing rhythmic movements and the power of reacting to barium disappear at the same time. The movements of the isolated muscularis mucosae of the cat's small intestine have been recorded and found to consist of regular slow rhythmic contractions, occurring at the rate of one in 27 to 60 seconds. Those movements bear a general resemblance to the rhythmic contractions of the spleen, and probably have a similar function of accelerating the local circulation. Adrenine has a motor effect on the rhythmic contractions of the muscularis mucosae, as on those of the spleen. The benefit of adrenine as a styptic in gastric ulcer may be due partly to its arresting capillary haemorrhage by contracting the muscularis mucosae.
Exploring Hypotheses about the Loss of the Rattle in Rattlesnakes: How Arboreal Is the Isla Santa Catalina Rattleless Rattlesnake, Crotalus catalinensis?

Abstract Rattle loss in the Isla Santa Catalina (Baja California Sur, México) rattlesnake, Crotalus catalinensis, was hypothesized to be a stealth adaptation for hunting for birds within the vegetation. Recently, however, it was shown that birds are rarely captured by C. catalinensis, while a semi-arboreal mouse is very important in its diet. It was thus suggested that the loss of the rattle could be a stealth adaptation for hunting for mice within the vegetation. But both these hypotheses imply a high degree of arboreality in C. catalinensis, and there is no detailed study on microhabitat use in this species. Here we use field data recently obtained (2005 to 2008) to test the hypothesis of a high degree of arboreality in C. catalinensis. During nine visits to Isla Santa Catalina we searched for snakes in suitable habitats. Of 92 observations in which the snakes were exposed, in seven occasions (7.6%) they were on the vegetation. There was no difference between sexes or between young and adult snakes in the frequency of use of vegetation. Thus, C. catalinensis is a primarily terrestrial rattlesnake which uses the vegetation only occasionally, similar to its sister species Crotalus ruber. Results of a previous phase of our studies at Isla Santa Catalina are similar to those presented herein. These results make the hypothesis of the loss of the rattle as a stealth adaptation for hunting on the vegetation very unlikely, since such a low frequency of use of vegetation may not function as a selective agent that could lead to an adaptive loss of the rattle.
Seasonal dynamics and life histories of pelagic cladocerans (Crustacea; Cladocera) in an acid boreal lake

In the surveyed anthropogenic acidified Lake Gjerstadvann with pH ≈ 5.2 situated in southern Norway, spatial and temporal distribution of three characteristic planktonic cladocerans inhabiting acidified boreal biotopes, Bosmina longispina, Holopedium gibberum, and Diaphanosoma brachyurum, were studied over a period of one year. The major pelagic predator was Eurasian perch, Perca fluviatilis. The local perch probably balanced the cladoceran community and facilitated co-existence of all three species of cladocerans by removing significant portions of B. longispina, which could also be the case in similar types of boreal lakes. Invertebrate predators such as the dipteran larvae Chaoborus flavicans and carnivorous copepods did not seem to influence the cladoceran community. B. longispina was perennial, whereas both H. gibberum and D. brachyurum were recorded only during the ice-free period. The life cycle of these free-living pelagic species ranged from 2-3 in D. brachyurum, 3 in H. gibberum to approximately 6 annual generations in B. longispina. Wintering took place as resting eggs in D. brachyurum and H. gibberum, while B. longispina produced resting eggs in addition to an active planktonic stay. The warm water tolerant D. brachyurum was mainly distributed above the thermocline, whereas H. gibberum also inhabited deeper strata, and B. longispina most vertical strata of the lake. Maximum seasonal clutch volume of B. longispina coincided in time with peak in food abundance and may be a useful parameter to identify planktonic food availability in such lakes. Knowledge of the autecology and life history of species is fundamental for understanding ecosystem stress, such as anthropogenic acidification and recovery through liming or by natural causes. Seasonal depth isoplots combined with life history studies of commonly co-occurring cladoceran species from natural acid and anthropogenic acidified lakes on the Northern Hemisphere seem to be uncommon, and similar type of data is needed to fully understand the processes of acidification and recovery.
The effect of housing conditions on Biceps femoris muscle fibre properties, fatty acid composition, performance and carcass traits of slow-growing rabbits

The aim of the present work was to evaluate the effect of stocking density on the biceps femoris (BF) muscle fibre properties, meat quality, the growth performance and carcass traits of Czech White rabbits. A total of 20 rabbits (40 days old, 10 rabbits per treatment, sex ratio 1/1) were reared in cages at different stocking densities (10 rabbits/m2 or 4 rabbits/m2) for 49 days. Stocking density had no significant effect on the growth performance. There were no significant differences between groups with regard to hot carcass weight (HCW) or dressing-out percentage. The proportions of both perirenal (9.5 vs. 15.9 g/kg HCW; P=0.010) and total dissectible fat (14.9 vs. 25.1 g/kg HCW; P=0.001) were lower in rabbits reared at the lower stocking density. No significant differences in ultimate pH values, meat colour or proximate composition were observed. The hind leg meat of rabbits reared at the lower stocking density contained significantly less lauric (4.6 vs. 6.7 mg/100 g of muscle; P=0.008) and myristic acid (52.2 vs. 64.4 mg/100 g of muscle; P=0.033). Significantly higher percentages of βR fibres (16.3 vs. 6.5 %, P=0.001) and αR fibres (24.5 vs. 14.2 %; P=0.001) and a significantly lower percentage of αW fibres (59.2 vs. 79.3 %; P=0.001) were also observed in these rabbits. The mean cross-sectional area (1882 vs. 2744 μm2; P=0.001) and diameter (47.9 vs. 58.5 μm; P=0.001) of βR fibres were smaller in rabbits reared at the lower stocking density. Thus, the lower stocking density favourably affected the medium-chain fatty acid profile of meat and fibre characteristics of the rabbits' biceps femoris muscle.
Effects of Temperature and Time of Day on the Resting Metabolic Rates of Paedomorphic and Metamorphic Mole Salamanders,Ambystoma talpoideum

Abstract Mole salamanders, Ambystoma talpoideum, are one of several species that exhibit facultative paedomorphosis. Many characteristics of paedomorphs and metamorphs have been compared in an effort to understand the ecological and evolutionary significance of facultative paedomorphosis, but few physiological comparisons have been made. We measured resting metabolic rates (oxygen consumption) of paedomorphic and metamorphic mole salamanders, under aquatic (both morphs) and terrestrial (metamorphs) conditions in an effort to compare maintenance energy expenditures of these phenotypes. There were no statistically significant differences in metabolic rates between morphs during aquatic trials. Under aquatic conditions, size adjusted oxygen consumption rates ranged from a low of 0.085 ml/h to 0.194 ml/h. There was a trend for oxygen consumption to increase with temperature, and at night compared to day, but significant interactions among time of day, temperature, and phenotype revealed complex responses. Most interesting, although metamorphs and paedomorphs had indistinguishable metabolic rates in water, both morphs in water consumed 2–4 times as much oxygen as did metamorphs in air. Our results suggest that metamorphs, while in a terrestrial environment, may expend significantly less energy for maintenance than aquatic paedomorphs.
Dynamics of a Managed Oak Woodland in Northeastern Illinois

Abstract We examined the current composition and structure of a woodland in northeastern Illinois and evaluated the early effect of two prescribed burns. In an effort to increase white oak (Quercus alba L.) regeneration, managers are reintroducing fire into the woodland understory. We assessed canopy species and compared understory vegetation and light, along with soil nutrient characteristics, between a burned and an unburned area. In addition, we monitored transplanted white oak seedlings to better understand their growth and survivorship in the woodland. The canopy was dominated by white oak, but non-oak species, particularly slippery elm (Ulmus rubra Muhl.), ash (Fraxinus spp. L), and black cherry (Prunus serotina Ehrh.), dominated the smaller size classes. There were no differences in woody and herbaceous vegetation, soil, and light characteristics between the burned and unburned area. White oak regeneration was poor which appeared to be due to low understory light levels associated with high density of the shrub prickly ash (Zanthoxylum americanum Mill.) and high numbers of non-oak saplings. Transplanted seedlings also performed poorly, with low survival rates throughout the woodland as a whole. Mammalian herbivory is a likely cause of additional stress to white oak regeneration. Evidence of browsing of transplanted white oak seedlings was apparent throughout the study area. If white oak is to be a component of the future woodland, managers should consider: (1) implementing a more intensive management program aimed at reducing competition from non-oak species and (2) increasing light in the understory.
Diversity in chemical composition and yield of essential oil from two Iranian landraces of sweet basil

Ocimum basilicum L. belongs to the family Lamiaceae is an herb that is extensively cultivated in some countries. Areal parts, especially leaves of sweet basil are widely used to enhance the flavour of foods such as salads, pasta, tomato products, vegetables, pizza, meat, soups, marine foods, confectioneries and other products. Essential oil yield and chemical components of two Iranian landraces of sweet basil including “Purple” and “Green” grown south-central of Iran (Isfahan province) were investigated. The hydro-distillated oils were analyzed by GC-MS. The oil yields were obtained from the aerial of Purple with 0.56 ml/100 g dry matter and the aerial of Green with 0.48 ml/100 g dry matter. Results indicated significant differences (p < 0.01) among the aerial for the main constituents in the essential oil from two Iranian landraces of sweet basil. The major constituents of the essential oil from the aerial of Purple landrace were methyl chavicol or estragol (63.32%) and linalool (7.96%). The main compositions of the essential oil from the aerial of Green landrace were methyl chavicol (31.82%), geranial (24.60%) and neral (22.65%). Genarlly, a comparison of our results with the previous reports suggests differences in the essential oil compositions and oil yield of the plant material could be attributed to genetic diversity in two Iranian landraces of sweet basil.
Ash yellows : geographic range and association with decline of white ash

Ash yellows was found to occur from Iowa and Missouri eastward to the Ottawa Valley of Canada and the Atlantic Coast in southern New England, as well as in scattered localities outside this range. New distribution areas recorded include Connecticut, Kentucky, Michigan, Missouri, Ohio, Pennsylvania, Utah, and the province of Quebec. In Utah, velvet ash was affected, a new host record. The association of MLOs with decline in white ash was studied on 88 sites in four states and southern Ontario. MLOs were detected by fluorescence microscopy in ash at 35 of 51 sites where severe dieback was common but at only five of 37 sites where dieback was scarce or absent (.)
Evaluation of the biogenic amine content and some chemical and microbiological properties of Urfa and Van herby cheeses.

In this study, the biogenic amine contents and some microbiological and chemical properties of Urfa and Van herby cheeses obtained from local supermarkets in Urfa and Van provinces were investigated. Tryptamine, β-phenylethylamine, putrecine, cadaverine, histamine and tyramine levels were detected in these cheeses. In addition some chemical properties (pH, total solids, fat-in-dry matter and salt-in-dry matter, protein, ripening coefficient, water soluble nitrogen and water activity) and some microbiological properties (total aerobic mesophilic bacteria, lactic acid bacteria and Enterobacteriaceae) were determined. Tyramine, cadaverine, histamine and putrecine were predominant biogenic amines in Urfa and Van herby cheese, respectively. β-phenylethylamine and tryptamine in Urfa cheese, were predominant in Van herby cheeses. The amounts of tyramine in Urfa and Van herby cheeses were found to be the highest with an average of 1.80 mg 100 g-1, 0.56 mg 100 g-1, respectively. None of the detected biogenic amines was higher than the toxic limit.
Effect of mine spoil on native soil of Lower Gondwana coal fields: Raniganj coal mines areas, India

Mine spoil characteristics of the dump area and the native soil are analyzed critically to evaluate any deterioration in soil properties. The required level of soil nutrient of mine spoil is less than that of the native soil. Available nutrients (N, P, K), exchangeable cation (Ca, Mg, Na, K) of the native soil suggest that open cast mining changes the soil quality. Other physical properties of the mine spoil such as bulk density, water holding capacity, moisture content are lower than those of native soil. Mining method alters the soil texture from siltyloam to sandy soil, but old mine spoil at Belbad has regenerated from sandy to silty-loam type. There have been no such significant differences in trace metal content in mine spoil and native soil.