Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome Differences Suggest Novel Mechanisms for Intrauterine Growth Restriction Mediated Dysfunction in Small Intestine of Neonatal Piglets

Impaired intestinal function is frequently detected in newborns with intrauterine growth restriction (IUGR), whereas the mechanism between transcriptome profiles and small intestinal dysfunction is still unclear. Therefore, this study was conducted by using IUGR neonatal piglets to uncover the mechanism underlying intestinal dysfunction. Neonatal piglets with IUGR and normal birth weight (NBW) were sacrificed at birth. Transcriptomic sequencing was performed on jejunum samples and generated 18,997 and 17,531 genes in NBW and IUGR groups, respectively. A total of 10 differentially expressed genes (DEGs) were identified; of note, only seven were mapped to the genome reference database, with two up-regulated (HSF4 and NR1H4; heat shock transcription factor 4 and nuclear receptor subfamily 1 group H member 4, respectively) and five down-regulated (SLC35C1, BTNL3, BPI, NLRP6, and SLC5A8; Solute carrier family 35 member C1, butyrophilin like 3, bactericidal permeability increasing protein, NLR family pyrin domain containing 6, and solute carrier family 5 member 8, respectively). Combining an enrichment analysis and reverse transcriptase–quantitative polymerase chain reaction validation of DEGs, our results proved the lipid metabolism disorder, intestinal dysfunction, and inflammatory response in IUGR piglets. Here, IUGR piglets presented lower concentration of glucose and triglyceride and higher concentration of total cholesterol and low-density lipoprotein cholesterol in plasma, compared with NBW piglets. Histological analysis revealed decreased mucins and increased apoptosis in both jejunum and ileum for IUGR piglets. Collectively, we found that IUGR induced intestinal dysfunction by altering lipid metabolism, intestinal barrier, and inflammatory response in neonatal piglets at birth, which provides new insights into the prevention and treatment of IUGR that protects against metabolic disorders and inflammatory-related diseases.
Physical and Functional Interactions of Human DNA Polymerase η with PCNA

ABSTRACT Human DNA polymerase η (hPolη) functions in the error-free replication of UV-damaged DNA, and mutations in hPolη cause cancer-prone syndrome, the variant form of xeroderma pigmentosum. However, in spite of its key role in promoting replication through a variety of distorting DNA lesions, the manner by which hPolη is targeted to the replication machinery stalled at a lesion site remains unknown. Here, we provide evidence for the physical interaction of hPolη with proliferating cell nuclear antigen (PCNA) and show that mutations in the PCNA binding motif of hPolη inactivate this interaction. PCNA, together with replication factor C and replication protein A, stimulates the DNA synthetic activity of hPolη, and steady-state kinetic studies indicate that this stimulation accrues from an increase in the efficiency of nucleotide insertion resulting from a reduction in the apparentK m for the incoming nucleotide.
A Human Capital Index for the Italian Provinces

Good health conditions and high quality education are crucial for children development and for their future contribution to the society. Human capital has been recognized as one of the crucial engines of economic growth. Nonetheless, it is often hard to establish a metric that allows to monitor its evolution and contribute to assess the effects of policies. In Italy, the use of such an index at national level may not be enough to have a clear picture of the human capital conditions. Socio-economic characteristics and public services are highly heterogeneous across the Country. There is, therefore, good ground to believe that also the human capital presents substantial differences across the Italian Provinces. To take such a high heterogeneity into consideration, we develop a Human Capital Index for Italy disaggregated at provincial level. The results show very large differences across Italian Provinces in terms of human capital, mostly driven by the variation in the quality of educational. Strikingly, the differences among Italian Provinces span a range that goes from best performers among high income countries to middle and low income countries. Finally, we classify the Italian Provinces in three main clusters according to their HCI and show how the clusters differ in terms of several socio-economic characteristics.
Changes in loblolly pine root growth potential from September to April

Loblolly pine (Pinustaeda L.) 1 + 0 seedlings were periodically hand lifted from a Virginia nursery to determine how root growth potential (RGP) varied between September and April. Several seedling characteristics, RGP, and shoot phenology were recorded for each lift date in 1983–1984 and 1984–1985. An attempt was made to relate RGP variation to changes in the nursery environment and to shoot phenology. Root growth potential variation was consistent between years and was more closely related to shoot phenological changes than to short-term environmental changes. During the development of dormancy, RGP was low, RGP increased when shoot activity resumed during the RGP tests (late winter, early spring), and declined as active shoot elongation began in the nursery. When RGP was low, elongation of existing lateral roots primarily contributed to the new root systems, but as seedling metabolism increased in the late winter, new root initiation also contributed to new root systems. Absolute differences in RGP bet.
Nitrogen use efficiency inwheat in bread wheat (T. aestivum L.) : breeding & gene discovery

In a context of fertiliser reduction, breeding for enhanced nitrogen use efficiency in bread wheat is necessary. This PhD thesis resulting from private-public collaboration between the French National Institute for Agricultural Research and Biogemma aimed providing necessary tools. Analyses were conducted using a dataset of 225 commercial varieties genotyped with 24K SNP and tested in eight combinations of year, location, and nitrogen regimes. We showed that even if past selection increased nitrogen use efficiency at high and moderate nitrogen regimes, genetic progresses need to be accelerated and better balanced between traits. This could be achieved by mixing phenotypic and marker assisted selections. In this sense, we developed a method to define quantitative trait locus from genome-wide association study: 333 chromosomal regions involved in 28 NUE-related traits have been identified. The NAM-A1 gene was located in one of these regions and its natural variants were characterized. We also showed that genomic selection could be improved by pre-selecting SNP based on their significance in a multi-environmental genome-wide association study. Networks of epistasis interactions were also studied and an interesting sub-network was identified. Results and methods are discussed regarding breeding and gene discovery strategy. Further investigations and improvements are suggested.
Robust Reinforcement Learning using Least Squares Policy Iteration with Provable Performance Guarantees

This paper addresses the problem of model-free reinforcement learning for Robust Markov Decision Process (RMDP) with large state spaces. The goal of the RMDPs framework is to find a policy that is robust against the parameter uncertainties due to the mismatch between the simulator model and real-world settings. We first propose Robust Least Squares Policy Evaluation algorithm, which is a multi-step online model-free learning algorithm for policy evaluation. We prove the convergence of this algorithm using stochastic approximation techniques. We then propose Robust Least Squares Policy Iteration (RLSPI) algorithm for learning the optimal robust policy. We also give a general weighted Euclidean norm bound on the error (closeness to optimality) of the resulting policy. Finally, we demonstrate the performance of our RLSPI algorithm on some benchmark problems from OpenAI Gym.
Field trials of baits to control populations of Glossina morsitans morsitans Westwood and G. pallidipes Austen (Diptera: Glossinidae)

An island of 4·5 km 2 in Lake Kariba, Zimbabwe, was stocked with cattle and infested with Glossina morsitans morsitans Westwood and G. pallidipes Austen in 1979. From February 1980 to April 1981, the tsetse populations, estimated by mark, release and recapture, increased about ten times, to contain about 3000 males of G. m. morsitans and 2000 males of G. pallidipes . From May 1981 to May 1983, six traps, with carbon dioxide and acetone as odour attractants, were used to capture 0·1–0·3% per day of the G. m. morsitans population and 1–4% per day of the G. pallidipes population. Captured flies were retained and killed, or were automatically sterilized with metepa and released. In May 1983, when the populations of G. m. morsitans and G. pallidipes had declined by about 90 and 99%, respectively, the traps were replaced by 20 targets with acetone and 1-octen-3-ol as attractants. The targets were coated with dieldrin or, later, deltamethrin and killed about 2% per day of G. m. morsitans and 5% per day of G. pallidipes . Both populations then declined rapidly, G. pallidipes disappearing in 11 weeks and G. m. morsitans in nine months. Targets offer a cheap, simple and effective means of eliminating isolated populations of tsetse.
Conservative and opportunistic settlement strategies in Arctic-breeding shorebirds

ABSTRACT Shorebirds seem to have evolved a number of strategies for adapting to and exploiting the unpredictable and inhospitable Arctic environment. Two such strategies put forth by Holmes and Pitelka suggest that species either conservatively or opportunistically select breeding locations based on local environmental conditions. “Conservative” species were characterized by strong site fidelity and territoriality, consistent population densities, relatively even spacing of individuals, and monogamous mating systems, while “opportunistic” species exhibited opposite traits and were polygamous. Here, we assessed whether 10 shorebird species consistently exhibited these settlement strategies over a 10-year period (2003–2012) near Barrow, Alaska, by comparing annual estimates of site fidelity, territoriality, and population density. Additionally, we determined the relative importance of past and current environmental and social conditions in predicting annual breeding densities of these same species. Data from 1,413 captured adults and 1,946 shorebird nests indicated that most species conformed to 1 of the 2 settlement strategies, while others exhibited traits of both strategies, and a few had settlement patterns inconsistent with that predicted for their mating system. We suggest that deviations from these strategies may occur depending on a species' location within its breeding range. For some species, however, described settlement patterns may be too simplistic. Species with the same settlement strategy seem to respond similarly to environmental cues but differently than species with the alternative strategy. However, we were unable to determine a common environmental cue for species with the same settlement strategy, although lemming abundance, overall nest survival rate, and presence of conspecifics or heterospecifics did seem to influence settlement decisions in some species. Results from this study indicate that understanding how species settle may have important consequences for implementing monitoring or conservation actions.
Testing for Expected Return and Market Price of Risk in Chinese A-B Share Market: A Geometric Brownian Motion and Multivariate GARCH Model Approach

There exist dual-listed stocks which are issued by the same company in some stock markets. Although these stocks bare the same firm-specific risk and enjoy identical dividends and voting policies, they are priced differently. Some previous studies show this seeming deviation from the law of one price can be solved due to different expected return and market price of risk for investors holding heterogeneous beliefs. This paper provides empirical evidence for that argument by testing the expected return and market price of risk between Chinese A and B shares listed in Shanghai and Shenzhen stock markets. Models with dynamic of Geometric Brownian Motion are adopted, multivariate GARCH models are also introduced to capture the feature of time-varying volatility in stock returns. The results suggest that the different pricing can be explained by the difference in expected returns between A and B shares in Chinese stock markets. However, the difference between market prices of risk is insignificant for both markets if GARCH models are adopted.
Analysis of total flavonoids and phenolics in different fractions of bark and needle extracts of Pinus roxburghii and Pinus wallichiana

Total flavonoid and phenolic content was estimated quantitatively by using colorimetric method in various fractions of bark and needle extracts of Pinus roxburghii and Pinus wallichiana . Flavonoids may exist as free aglycone, but usually they are bound to sugar as glycosides and any one aglycone may occur in single plant in several combinations. For the measurement of total flavonoid content, original plant extract was hydrolysed and aglycone was measured before and after hydrolysis to calculate the presence of free aglycone content. Flavonoid contents (aglycone) of the extracts, in terms of quercetin equivalent (the standard curve equation: y = 0.0877× -0.0595, r 2 = 0.9981), were in the range of 60.1 ± 4.5 to 484 ± 2.5 before and after hydrolysis. As such, the values fell in the range of 76.9 ± 3.2 to 943 ± 2.6. The total phenol varied from 394 + 0.03 to 1331 + 0.24 measured in terms of gallic acid equivalent (with standard equation: y = 0.0197 × -0.0076, r 2 = 0.9997).
Intercontinental and intracontinental biogeography—patterns and methods

Intercontinental and intracontinental biogeography— patterns and methods 1Jun WEN∗ 2Qiu-Yun (Jenny) XIANG 3Hong QIAN 4Jianhua LI 5Xiao-Quan WANG 6Stefanie M. ICKERT-BOND 1(Department of Botany, MRC-166, Smithsonian Institution, PO Box 37012, Washington DC 20013-7012, USA) 2(Department of Plant Biology, North Carolina State University, Raleigh, NC 27695-7612, USA) 3(Research and Collections Center, Illinois State Museum, Springfield, IL 62703, USA) 4(Biology Department, Hope College, Holland, MI 49423, USA) 5(State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) 6(UA Museum of the North Herbarium and Department of Biology and Wildlife, University of Alaska Fairbanks, Fairbanks, AK 99775-6960, USA)
Phylogeny and historical biogeography of the cynipoid wasp family Ibaliidae (Hymenoptera)

The Ibaliidae are a small family of cynipoid wasps, the members of which parasitize woodboring siricid larvae in hardwoods and conifers. The 19 currently recognized extant species occur mainly in the Northern Hemisphere. No fossils are known despite the presumed old age of the family. We present a cladistic analysis of ibaliid relationships at the species‐level, mainly based on external skeletal characters of adults. The results indicate that the three genera (Eileenella, Heteribalia, Ibalia) and two subgenera of Ibalia (Ibalias. str. and Tremibalia) recognized in the current classification are monophyletic. Three different categories of characters were compared for their phylogenetic usefulness. Homoplasy was found to be lowest for main structures, higher for sculptural characters, and still higher for colour differences. The historical biogeography of the family was reconstructed using dispersal–vicariance analysis in combination with palaeogeographical data. The results suggest that the family primarily diversified within the eastern Palaearctic–northern Oriental region. The nominate subgenus of Ibalia dispersed early to the western Nearctic, where it radiated; two species later spread throughout the Holarctic. The other subgenus of Ibalia shows an early eastern Palaearctic–eastern Nearctic disjunction which presumably dates back to the Eocene–Oligocene transition.
A DOUBLE-OBSERVER APPROACH FOR ESTIMATING DETECTION PROBABILITY AND ABUNDANCE FROM POINT COUNTS

Abstract Although point counts are frequently used in ornithological studies, basic assumptions about detection probabilities often are untested. We apply a double-observer approach developed to estimate detection probabilities for aerial surveys (Cook and Jacobson 1979) to avian point counts. At each point count, a designated “primary” observer indicates to another (“secondary”) observer all birds detected. The secondary observer records all detections of the primary observer as well as any birds not detected by the primary observer. Observers alternate primary and secondary roles during the course of the survey. The approach permits estimation of observer-specific detection probabilities and bird abundance. We developed a set of models that incorporate different assumptions about sources of variation (e.g. observer, bird species) in detection probability. Seventeen field trials were conducted, and models were fit to the resulting data using program SURVIV. Single-observer point counts generally miss varying proportions of the birds actually present, and observer and bird species were found to be relevant sources of variation in detection probabilities. Overall detection probabilities (probability of being detected by at least one of the two observers) estimated using the double-observer approach were very high (>0.95), yielding precise estimates of avian abundance. We consider problems with the approach and recommend possible solutions, including restriction of the approach to fixed-radius counts to reduce the effect of variation in the effective radius of detection among various observers and to provide a basis for using spatial sampling to estimate bird abundance on large areas of interest. We believe that most questions meriting the effort required to carry out point counts also merit serious attempts to estimate detection probabilities associated with the counts. The double-observer approach is a method that can be used for this purpose.
The melatonin receptor antagonist luzindole induces the activation of cellular stress responses and decreases viability of rat pancreatic stellate cells

In this study, we have examined the effects of luzindole, a melatonin receptor‐antagonist, on cultured pancreatic stellate cells. Intracellular free‐Ca2+ concentration, production of reactive oxygen species (ROS), activation of mitogen‐activated protein kinases (MAPK), endoplasmic reticulum stress and cell viability were analyzed. Stimulation of cells with the luzindole (1, 5, 10 and 50 μm) evoked a slow and progressive increase in intracellular free Ca2+ ([Ca2+]i) towards a plateau. The effect of the compound on Ca2+ mobilization depended on the concentration used. Incubation of cells with the sarcoendoplasmic reticulum Ca2+‐ATPase inhibitor thapsigargin (1 μm), in the absence of Ca2+ in the extracellular medium, induced a transient increase in [Ca2+]i. In the presence of thapsigargin, the addition of luzindole to the cells failed to induce further mobilization of Ca2+. Luzindole induced a concentration‐dependent increase in ROS generation, both in the cytosol and in the mitochondria. This effect was smaller in the absence of extracellular Ca2+. In the presence of luzindole the phosphorylation of p44/42 and p38 MAPKs was increased, whereas no changes in the phosphorylation of JNK could be noted. Moreover, the detection of the endoplasmic reticulum stress‐sensor BiP was increased in the presence of luzindole. Finally, viability was decreased in cells treated with luzindole. Because cellular membrane receptors for melatonin have not been detected in pancreatic stellate cells, we conclude that luzindole could exert direct effects that are not mediated through its action on melatonin membrane receptors.
Long-term changes in performance and meat quality of Danish Landrace pigs: a study on a current compared with an unimproved genotype

An experiment was conducted in 1995 in order to examine muscle growth, muscle histochemical properties, muscle metabolism and meat quality of two types of Danish Landrace pigs representing the growth potential of years 1976 and 1995, respectively. Danish Landrace pigs representing 1976 (slow-growing, SG) originated from a breeding station where the population was maintained without being selected for production traits such as daily gain, food conversion ratio and meat content. Pigs representing Danish Landrace of 1995 (fast-growing, FG) were bought from certified Danish pig breeders. The pigs were simultaneously tested for performance from 40 to 95 kg live weight. The daily gain, food conversion ratio and meat content of the carcass were improved proportionately by 0·43, 0·24 and 0·03 in FG pigs compared with SG pigs. In m. longissimus dorsi (LD), the cross-sectional area of muscle fibres was smaller in FG pigs compared with SG pigs indicating increased muscle fibre number. Data further suggest increased satellite cell proliferation in muscles of FG pigs. Serum from FG pigs stimulated the proliferation of C2C12 muscle cells to a greater extent than serum from SG pigs, although the serum level of insulin-like growth factor 1 did not differ between pig types. The effect of serum on protein turn-over of C2C12 myotubes did not depend on pig type. The glycogen concentration in the LD did not differ significantly between pig types, while the activity of citrate synthase, 3-OH-acyl-CoA-dehydrogenase, and lactate dehydrogenase were higher in the LD of SG pigs compared with FG pigs. Pork chop colour of FG pigs was proportionately 0·09 lighter (L ⋆ ) and 0·13 less red (a ⋆ ) than pork chops of SG pigs. The total muscle pigment concentration in the LD, m. biceps femoris and m. vastus intermedius was proportionately reduced by 0·17, 0·19 and 0·11, respectively, in FG pigs compared with SG pigs. In the LD, the concentration of myoglobin was proportionately reduced by 0·17 in FG pigs. The chemical composition of the LD differed between pig types such that the water content was higher and protein content lower in LD from FG pigs compared with SG pigs. The pH of the LD measured 45 min and 24 h post mortem, drip loss and thawing loss were similar for both pig types. Meat tenderness of conditioned pork chops of FG pigs was slightly reduced in accordance with a decreased intensity of the 31 kDa peptide band and increased cooking loss. The present study suggests that increased muscle fibre number and rate of muscle DNA deposition (satellite cell proliferation) have contributed to the increased muscle growth as a result of selection for performance in pigs under Danish conditions. However, the increase in growth performance was accompanied by deterioration in muscle colour and slightly reduced tenderness.
GEOGRAPHIC CALL VARIATION AND NOTES ON REPRODUCTION AND ABUNDANCE OF AMEEREGA FLAVOPICTA (ANURA, DENDROBATIDAE)

Ameerega flavopicta (=Epipedobates flavopictus) (Lutz, 1925) is a distinctive dendrobatid species which reproduces in open environments subject to broad variations in humidity and temperature (Costa, Facure & Giaretta, 2006). As presently recognized, this species presents a wide distribution in the Brazilian states of Minas Gerais, Goias, Tocantins, Para, and Maranhao (Haddad & Martins, 1994; Colli, Bastos & Araujo, 2002; Costa, Facure & Giaretta, 2006; Giaretta et al., 008). Inter populational differences have been reported in color pattern (Haddad & Martins, 1994), and in call (Haddad & Martins, 1994; Costa, Facure & Giaretta, 2006). Eterovick et al., 2005) suggested a populational decline of this species at Serra do Cipo (MG).