Miracle-dz/UniFAR-FTUs huggingface dataset:
A review of the energy and protein nutrition of dairy cows through their dry period and its impact on early lactation performance

This review considers the current literature on the energy and protein nutrition of dry cows and its subsequent impact on early lactation performance. Energy intake close to calving appears to be critical to events that occur post-partum, such that a key objective of dry cow feeding should be to maximise or maintain feed intake immediately prior to calving, or at least to minimise the decline in intake. Although a decline in dry matter intake seems to be a normal adaptive event in peri-parturient ruminants, it is the magnitude and duration of the decline that are of concern. Most research has been undertaken using total mixed rations or conserved forage and concentrates, where a wide range of quantities and types of feeds have been used. However, no clear conclusions can be drawn regarding optimum levels of feeding, types of forage, or proportions of concentrates that should be fed to cows in the late dry period to minimise the intake decline. The importance of maintaining energy intake is associated with the reduction of the incidence and severity of metabolic diseases post-partum, by reducing triglyceride mobilisation from adipose tissue, and preventing excessive depletion of hepatic glycogen levels.
Submerged batch culture of the psychrophile Monographella nivalis in a defined medium; growth, carbohydrate utilization and responses to temperature.

An asporogenous strain of the pink snow mould fungus, Monographella nivalis (Schaffnit) E. Müller, anamorph Gerlachia nivalis (Ces. ex Sac.) W. Gams & E. Müller (Syn. Fusarium nivale Ces. ex Sacc.), grew at 5 °C on a denned salts medium plus vitamins and utilized a variety of simple and polymeric carbohydrates as the sole carbon and energy source. Mycelium was grown at temperatures between 3 and 15 °C in aerated submerged fermentation culture in chemically defined medium plus sucrose. Optimum growth rates of 0·035-0·033 h-1 occurred between 9 and 12 °C. Growth in a simple medium showed that all biochemical and physiological processes necessary for growth were functional at 3 °C. The growth performance of the organism at low temperatures was no better than would be expected from extrapolation of mesophilic growth responses to temperature. The optimum growth temperature of 9-12°C showed that some biochemical or physiological process was impaired above 12 °C. Uptake and incorporation of 35 S-methionine by mycelium at different temperatures showed that general protein synthesis increased up to 25 °C, and hence was not responsible per se for the sensitivity to temperatures above 12 °C. Heat shock proteins were synthesized at the relatively low temperature of 25 °C, consistent with the low temperature optimum for growth. When grown with sucrose as the sole carbon source, the mycelium catalyzed the extracellular hydrolysis of sucrose, releasing glucose and fructose together with a small amount of fructan trisaccharides and a trace of tetra- and penta-saccharides. Fructan accumulation was transient, corresponding with maximal rates of sucrose hydrolysis. Most biomass formation occurred in the absence of fructan in the culture, hence fructan was not necessary for growth at low temperature and did not appear to function as a cryoprotectant. Invertase activity was mostly (60-70%) bound to mycelium; the remainder was free in the culture supernatant. The regulation of invertase expression appeared to be by sucrose-induction, rather than by end-product repression. Rates of sucrose hydrolysis in culture were temperature-sensitive and were markedly depressed above 12 °C, indicating inhibition of invertase formation.
Interactive effects of salinity on oxygen consumption, ammonium excretion, osmoregulation and Na+/K+-ATPase expression in the bullseye puffer (Sphoeroides annulatus, Jenyns 1842)

A physiological study was performed to explore the effects in Sphoeroides annulatus (Jenyns 1842) juveniles of exposure to different salinities 10, 17, 23, 29, 35 and 41‰ on oxygen consumption rate (OCR), ammonium excretion rate (AER), the oxygen-nitrogen atomic ratio (O:N), osmoregulation and Na+/K+-ATPase expression. The OCR values ranged from 27.9 to 30.9 mg O2 h−1 kg−1, displaying a Type 1 response pattern Kinne (1977). AER ranged from 0.60 to 0.69 mg h−1 kg−1, and O:N values were from 53.12 to 59.26, indicating that the puffers use proteins and lipids as an energy-substrate. Osmoregulation in S. annulatus was hyposmotic in salinities of 23, 29, 35 and 41‰ and hyperosmotic in a salinity of 10‰. The isosmotic point of the bullseye puffer was 356 mmol kg−1 (10.5‰). The enzyme expression analysis indicates that the fish acclimated to 41‰ had the highest Na+/K+-ATPase expression level, whereas, the lowest expression level was found close to the isosmotic point. Na+/K+-ATPase expression in the gills was found to have a U-shaped relationship with environmental salinity. We conclude that the bullseye puffer is strongly euryhaline and can be cultivated in a wide range of environments that has important economic implications.
Changes in osmolites contents, lipid peroxidation and photosynthetic pigment of Aeluropus lagopoides under potassium deficiency and salinity

disorder in the its functions. In the present research, changes of four biochemical parameters (proline, glycinebetaine, photosynthetic pigments and malondialdehyde) have been investigated in Aeluropus lagopoides seedling under salinity and potassium deficiency. Sterile seeds had been cultured on modified Murashige-Skoog containing 0, 1.75 or 100 mM potassium, with or without 600 mM NaCl for 30 days. The results showed that maximum proline content was observed in root and shoot by 600 mM NaCl + 1.75 mM K + treatment. Also in this treatment, amount of carotenoids and chlorophyll a was more decreased. Potassium deficiency caused to reduced MDA and chlorophyll b content. The highest amount of glycinebetaine was measured in the presence of 600 mM NaCl in the company of 100 mM K + . It can conclude that chlorophyll oxidation was occurred in K + deficiency because of increasing lipid peroxidation and disruption of protein-pigment complexes. The accumulation rates of two osmolite in different organ was shown that in A. lagopoides proline and glycinebetaine play more important role in osmotic adjustment of the shoot and root, respectively.
Description of the Nest and Egg of an Atlantic Forest Endemic, the Black-headed Berryeater, Carpornis melanocephala (Cotingidae)

Abstract We describe the nest and egg of the Black-headed Berryeater (Carpornis melanocephala), an Atlantic Forest endemic considered vulnerable to extinction. The nest was in a montane evergreen primary forest area in a tree fork 4.2 m above the ground. It was cup shaped and constructed mainly of leaves and stems, resembling a pile of aerial leaf litter. It held just one egg that was incubated solely by the female. The male was near the nest, and inspected it once while being observed.
Observations préliminaires de la variabilité entre quelques morphotypes de voandzou (Vigna subterranea L. Verdc., Fabaceae) de Côte d’Ivoire

Le voandzou (Vigna subterranea L. Verdc.) est une legumineuse alimentaire cultivee principalement par les femmes pour lesquelles il assure une source de revenus pour le menage. En Cote d’Ivoire, la culture du voandzou est localisee a l’ouest et dans la partie nord du pays. Ces zones sont caracterisees par des conditions agroecologiques contrastees incluant la foret tropicale humide et la savane plus seche. Dans ces zones, le voandzou joue un role important dans l’alimentation et la culture des populations. Quatre morphotypes de Cote d’Ivoire (ICU, BPR, RBU, NFU) ont ete utilises dans un essai preliminaire pour evaluer la variabilite phenotypique entre morphotypes. Pour chaque morphotype, 100 individus ont ete utilises pour analyser 26 caracteres agromorphologiques selectionnes parmi la liste des descripteurs du voandzou. Les resultats de l’analyse statistique ont montre une importante variabilite entre les morphotypes, suggerant ainsi que 22 des caracteres peuvent servir valablement a distinguer la variabilite entre les morphotypes de voandzou de Cote d’Ivoire. Trois morphotypes (ICU, BPR et RBU) ont une phase reproductive plus courte que l’autre (NFU). Les morphotypes a phase reproductive courte ont donne un pourcentage plus eleve de gousses matures (87 a 95 %), par comparaison avec le morphotype NFU (69 %) dans nos conditions d’experimentation. Le morphotype ICU est particulierement precoce, atteignant la maturite 90 jours apres semis (JAS), tandis que le morphotype a phase reproductive longue (NFU) necessite 137 jours. A partir des caracteres agronomiques analyses, les possibilites d’amelioration du rendement du voandzou et la vulgarisation de sa culture en Cote d’Ivoire sont discutees.
Molecular identity, morphology and taxonomy of the Rhynchospio glutaea complex with a key to Rhynchospio species (Annelida, Spionidae)

Rhynchospio glutaea (Ehlers, 1897), Rhynchospio arenincola Hartman, 1936 and Rhynchospio arenincola asiatica Chlebovitsch, 1959, originally described from Strait of Magellan, California, and South Kurile Islands respectively, appear similar to each other in adult morphology. These species and subspecies have been considered by some authors as subjective synonyms and are here referred to as members of the R. glutaea complex. Sequence data of four gene fragments (2465 bp in total) of the mitochondrial 16S rDNA, nuclear 18S and 28S rDNA, and Histone 3 have shown that R. glutaea complex individuals from the South West Atlantic (Argentina), North East Pacific (British Columbia and Oregon) and North West Pacific (South Korea) were genetically distant and not conspecific. These data also indicate that R. arenincola from North America and R. aff. asiatica from South Korea are more closely related to each other, and both are closer to R. glutaea from South America than to R. nhatrangi from Vietnam: nhatrangi (glutaea (arenincola-aff. asiatica)). Adults of the R. glutaea complex are hermaphrodites and the arrangement of gametes is suggested to be a crucial reproductive character for distinguishing these species. Based on this character, two species of the complex are apparent in the North West Pacific: R. asiatica Chlebovitsch, 1959 stat. nov. from the Kurile Islands (not analysed here) and an unnamed species from the mainland coast of Asia (here referred to as R. aff. asiatica). Adult morphology of R. asiatica stat. nov. is briefly described and illustrated. The lectotype and the type locality of the species on Iturup Is. are established for the first time. An identification key is provided to the 10 currently recognized Rhynchospio species.
Capture–recapture models with heterogeneity to study survival senescence in the wild

Detecting senescence in wild populations and estimating its strength raise three challenges. First, in the presence of individual heterogeneity in survival probability, the proportion of high-survival individuals increases with age. This increase can mask a senescence-related decrease in survival probability when the probability is estimated at the population level. To accommodate individual heterogeneity we use a mixture model structure (discrete classes of individuals). Second, the study individuals can elude the observers in the field, and their detection rate can be heterogeneous. To account for detectability issues we use capture-mark-recapture (CMR) methodology, mixture models and data that provide information on indi-viduals' detectability. Last, emigration to non-monitored sites can bias survival estimates, because it can occur at the end of the individuals' histories and mimic earlier death. To model emigration we use Markovian transitions to and from an unobservable state. These different model structures are merged together using hidden Markov chain CMR models, or multievent models. Simulation studies illustrate that reliable evidence for survival senescence can be obtained using highly heterogeneous data from non site-faithful individuals. We then design a tailored application for a dataset from a colony of black-headed gull Chroicocephalus ridibundus. Survival probabilities do not appear individually variable, but evidence for survival senescence becomes significant only when accounting for other sources of heterogeneity. This result suggests that not accounting for heterogeneity leads to flawed inference and/or that emigration heterogeneity mimics survival heteroge-neity and biases senescence estimates.
PHYLOGENETIC RELATIONSHIPS IN BEARDED MANAKINS (PIPRIDAE: MANACUS) INDICATE THAT MALE PLUMAGE COLOR IS A MISLEADING TAXONOMIC MARKER

Abstract The piprid genus Manacus is composed of four allospecies that are readily distinguishable by differences in male plumage color. Electrophoretic data for two populations of each of the four forms plus seven outgroup piprid taxa were collected from 32 isozyme loci and used to infer phylogenetic relationships. Each Manacus form was monophyletic, with the exception of M. manacus, in which the trans-Andean (west of the Andes) population was sister to M. vitellinus, rather than to its conspecific cis-Andean (east of the Andes) population. This controversial relationship, supported by the synapomorphic allele PGM-2b as well as allele frequencies at ADA, GOT-1 and LGG, is consistent with general biogeographic patterns in the region, but indicates that male plumage color is an unreliable taxonomic marker. Reconstruction of male plumage color on the tree confirms that gold plumage is a derived state in M. vitellinus, a finding consistent with the possibility that gold plumage is an evolutionary novelty in vitellinus which has spread recently under positive selection. Among piprids, there was strong support for a group composed of Antilophia, Chiroxiphia, and Corapipo, and for a group composed of Pipra mentalis, P. fasciicauda, and Dixiphia pipra. Manacus is more closely related to the P. mentalis + P. fasciicauda + D. pipra group. The isozymes supported Lepidothrix as the basal taxon of those examined.
Progress on novel immunomodulatory agents for HIV-1 infection and other infectious diseases

Availability of a vast array of recombinant and synthetic immunomodulators represents a significant milestone toward the development of effective therapies for infectious diseases. This is attested by the licensing of several recombinant human cytokines, including colony-stimulating factors, interleukins, interferons and erythropoietin, for clinical use in patients. The identification of the essential role of coreceptors for the entry of HIV into the host cell focused attention on chemokines as important targets for pharmacological intervention. This generated an intense search for molecules possessing therapeutic potential as inhibitors of chemokine receptors and several new compounds have been advocated. Diverse combinations with interferons and other cytokines for the treatment of various viral infections, including hepatitis B and C, have been proposed. Considerable advances have been made on compounds exhibiting cytokine inhibitory properties useful for new treatments of infectious and inflammatory diseases. Many of the major developments and current trends in the area of cytokine biology and therapy are highlighted in this review. Novel strategies based on the engineering of cytokines and inhibitors are poised to revolutionise therapeutic options in the coming decades.
CLEARCUT STAND SIZE AND SCRUB-SUCCESSIONAL BIRD ASSEMBLAGES

Abstract We investigated the effects of clearcut stand size on species richness, reproductive effort, and relative abundance of scrub-successional birds and the entire bird assemblage at the Savannah River Site in South Carolina. We used standardized mist-net grids to mark and recapture birds in clearcuts replanted with longleaf pine (Pinus palustris) in stands of 2 to 57 ha that were two to six years old. Species richness for the entire bird assemblage was not explained by stand size (P = 0.67), stand age (P = 0.95), or the interaction of these two variables (P = 0.90). Similarly, species richness of scrub-successional birds was not explained by stand size (P = 0.63), stand age (P = 0.55), or the interaction of stand size and stand age (P = 0.35). Regressing species richness on clearcut stand size, we found a significant negative relationship between these variables for the entire bird assemblage (P = 0.01) and for scrub-successional birds (P = 0.02). The ratio of juveniles to adults in mist-net samples varied by year (P = 0.04), but neither clearcut size (P = 0.23) nor the interaction of clearcut size and year (P = 0.25) was related to the ratio of juveniles to adults in the sample. We found no relationship between the frequency of capture of any category of birds and stand size (scrub-successional, P = 0.52; woodland, P = 0.77; combined sample, P = 0.55). Neither bird-species richness, reproductive effort, nor relative abundance differed across clearcut stand sizes. Clearcut stand size does not appear to be an important management variable if variation in species richness, reproductive effort, or relative abundance are objectives. We suggest that even-aged forestry is a useful tool for managing birds in the southeastern United States.
Genetic Diversity Among Popular Historical Southern U.S. Soybean Cultivars Using AFLP Markers

ABSTRACT Modern soybean [Glycine max (L.) Merr. ] breeding extensively uses as crossing parents superior cultivars and breeding lines with locally adapted desirable traits, which may lead to declined genetic diversity and increased frequency of fixed common alleles. The main objective of this research was to evaluate, via amplified fragment length polymorphism (AFLP) markers, the genetic diversity and the genetic relationships among the 38 most popular cultivars and lines in the southern United States. Genetic analysis using AFLP markers with 16 primer combinations revealed an average genetic distance of 0.124 among the 38 genotypes examined. Genetic diversity declined among cultivars released during the 1950s and 1960s compared to those released before the 1950s, but increased in the 1970s and peaked in the 1980s, followed by a decline again in the 1990s and 2000s. While 34 unique bands were identified, allelic frequency analysis revealed 50.8% of the 754 loci examined to be fixed in all 38 genotypes. Future parent selection for crossing should consider using genotypes of greater genetic distance and avoid using lines with common genetic background.
Identification of Parentage of Japanese Pear 'Housui'

The 84 cross combinations used in the Japanese pear breeding program in 1953-1955 were investigated to identify the parents of 'Housui' (syn. 'Hosui'). Twenty-one putative parent cultivars were investigated for their S genotypes and skin types. The S genotypes of 75 out of 84 cross combinations could not have sired 'Housui' (S3S5) because neither putative parent has an S3 nor S5 allele. Skin types of all cultivars used for 9 cross combinations selected from S genotype analysis were russet types. For this reason, 9 cross combinations are possible sources for the putative parents of 'Housui'. These 9 cross combinations were investigated by utilizing 10 SSR markers developed from Japanese and European pears. The SSR analysis indicated that only two parental crosses, 'Kousui' (syn. 'Kosui') × '1-33' and '1-33' × 'Kousui' were possible; the other 7 parentages had discrepancies at the 2-6 loci. The two assumed parents of 'Housui', 'Kousui' and 'I-33' were investigated by using 51 more SSR markers. A total of 61 SSR marker analyses confirmed the parent-offspring relationships because 'Housui' inherited SSR alleles from 'Kousui' and '1-33' without any discrepancy. Chloroplast DNA (trnL-F region) was investigated to determine whether 'Kousui' or '1-33' was the female parent. The nucleotide sequence at the trnL-F region of 'Housui' was exactly the same as that of 'Kousui', but was different from that of '1-33'. Therefore, we conclude that 'Kousui' is the female parent of 'Housui' and '1-33' is the male parent.
Pharmacokinetics and pharmacodynamics of acetylcholinesterase inhibition: Can acetylcholine levels in the brain be improved in alzheimer's disease?

Up to 20% or more of individuals who will be 80 years of age will develop senile dementia of the Alzheimer type (SDAT). In SDAT patients cholinergic neurons in the basal forebrain undergo profound damage, which is reflected in decreased acetylcholine synthesis, choline acetyltransferase activity, acetylcholinesterase activity, and choline uptake in cortical terminals. Physostigmine has been widely used to increase brain acetylcholine concentration by inhibiting acetylcholinesterase. The pharmacokinetics of physostigmine and its effects on acetylcholine concentration are not well studied. Our studies of physostigmine pharmacokinetics in dogs, rats, and humans suggest that a “slow‐release formulation” may be necessary to achieve increases in acetylcholine concentrations that will have therapeutic effects in SDAT. To investigate one potential “slow release formulation” of physostigmine we have studied direct injection into the lateral ventricles of the brain.
Retrieval of the ground surface reflectance along coast zone and island with MODIS image

A new method based on lookup tables (LUTs) for retrieval of the ground surface reflectance along coastal zones and islands with MODIS (Moderate-resolution imaging spectroradiometer) image was descibed.Through simulation of the AHMAD radiative transfer model, we can retrieve the aerosol optical character with water pixels of MODIS image. Postulating the background is cloudless and the atmosphere on the water is the same as that on the island, we can use the 6S radiative transfer model to compute the LUT about the ground surface reflectance, then use the interpolate method to get the reflectance of the ground surface along coastal zones and islands through the reflectance of the land pixels of MODIS image, the geometric condition and the aerosol optical thickness. The LUT method is applied to determine the ground surface reflectance in Xiamen’s zone from the MODIS image. At last, the results were analyzed and its expectation errors were reported.
Using geographic profiling to locate elusive nocturnal animals: a case study with spectral tarsiers

We thank Operation Wallacea for supporting S.C. F. in thisproject and for providing logistical support for the fieldwork,and Aidan Kelsey for invaluable assistance in the field. Wethank the Indonesian Institute of Sciences (LIPI) andKementerian Riset dan Teknologi Republik Indonesia(RISTEK) for providing permission to undertake the work(RISTEK permit no. 211/SIP/FRP/SM/VI/2013, and BalaiKonservasi Sumber Daya Alam (BKSDA) for theirassistance.
Methylation and intratumoural heterogeneity of 14-3-3 σ in oral cancer

14-3-3 sigma has been a major G2/M checkpoint control gene and has demonstrated that its inactivation in various cancers occurs mostly by epigenetic hypermethylation, not by genetic change. This study investigated the methylation status and expression of the 14-3-3 sigma gene in 46 oral squamous cell carcinomas by methylation-specific polymerase chain reaction, reverse transcriptase-polymerase chain reaction, Western blotting and immunohistochemistry. Exons of the p53 gene were examined for mutations by sequencing analysis and CyclinD1 by immunohistochemistry. Methylation of the 14-3-3 sigma gene was detected in 13% (6/46) of the oral tumours, but not in corresponding adjacent non-malignant and normal gingival tissues. Intratumoural heterogeneity was found in the tumour tissues including three 14-3-3 sigma-methylated samples. Methylation of 14-3-3 sigma was detected in 3 SCC with p53 mutations and 3 with wild-type p53. Our major findings are: (a) methylation of 14-3-3 gene promoter is a rare event in oral cancer; (b) it is not always associated with 14-3-3 protein levels and there is no clear relationship between its methylation and p53 mutation; (c) loss of 14-3-3 sigma expression is associated with reduced CyclinD1 gene expression.