Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of three different designed farrowing crates on neonatal piglets crushing: preliminary study

Abstract In swine production, the economic gain in the farrowing room corresponds to the number of weaned piglets/sow per year. Pre-weaning mortality is at least 11–13% of total losses within one herd, considering a previous 7–8% of the stillbirths. Piglet crushing by the sow contributes significantly to the overall piglet mortality. It is caused by multiple factors related to the sow, the piglet and due to modern swine husbandry along the last 50 years. This study aimed to compare three different designs of farrowing crates during the first three days of life in relation to piglet-crushing mortality in intensive herd. One hundred fifty-eight sows with spontaneous deliveries were housed in the following farrowing crates groups: group A (n = 51) farrowing within conventional crates, group B (n = 47) farrowing within the slide cage and group C (n = 60) in the up and down designed, for a total of 2487 live born piglets. In the first three days of life, group C reported the lower crushing mortality rate (0.54%), while groups B and A reported 2.37% and 5.46%, respectively. The comparison between the group C value compared with group A values (p<.001; Chi-square = 36.90) and B (p = .003; Chi-square = 8.81) were statistically significant. In conclusion, the approach to create more space for both mother and litter within an acceptable size of farrowing crates (slide cage and up & down designed) allowed a significant reduction in mortality crushing rate of the piglets during the first three days of life.
Trap-nesting bees and wasps (Hymenoptera, Aculeata) in a Semidecidual Seasonal Forest fragment, southern Brazil

Trap-nesting bee and wasp inventories are common in Brazil but many phytophysiognomies are still poorly studied. The main objective of this study is to survey trap-nesting bees and wasps in a Semidecidual Seasonal Forest fragment. Also, we test the differences on nesting between interior and edge transects. A sum of 1,500 trap nests was made with bamboo cane internodes and two consecutive years were monitored. In the first year 46 nests were occupied by Pachodynerus grandis (19 nests), Pachodynerus guadulpensis (19), Centris analis (two), and Centris tarsata, Megachile fiebrigi, Megachile guaranitica, Megachile susurrans, Trypoxylon sp and Zethus smithii with one nest each. No statistical differences were found between interior and edge transects for richness and occupation rate, but the species composition was different. In the second year 39 nests were occupied by four species, three previously recorded, C. analis (seven nests), P. guadulpensis and P. grandis (six nests each), plus Monobia angulosa with 15 nests. Parasitoids from four families and one cleptoparasite were recorded and the mortality rate was higher in bees than in wasps. These findings reinforce the notion that trap nests assemblages from different studies are not directly comparable for richness and composition.
MHC Genetic Variation Influences both Olfactory Signals and Scent Discrimination in Ring-Tailed Lemurs

Diversity at the Major Histocompatibility Complex (MHC) is critical to health and fitness, such that MHC genotype may predict an individual’s quality or compatibility as a competitor, ally, or mate. Moreover, because MHC products can influence the components of bodily secretions, an individual’s body odor may signal its MHC and influence partner identification or mate choice. To investigate MHC-based signaling and recipient sensitivity, we test for odor-gene covariance and behavioral discrimination of MHC diversity and pairwise dissimilarity, under the good genes and good fit paradigms, in a strepsirrhine primate, the ring-tailed lemur (Lemur catta). First, we coupled genotyping with gas chromatography-mass spectrometry to investigate if diversity of the MHC-DRB gene is signaled by the chemical diversity of lemur genital scent gland secretions. We also assessed if the chemical similarity between individuals correlated with their MHC similarity. Next, we assessed if lemurs discriminated this chemically encoded, genetic information in opposite-sex conspecifics. We found that both sexes signaled overall MHC diversity and pairwise MHC similarity via genital secretions, but in a sex- and season-dependent manner. Additionally, both sexes discriminated absolute and relative MHC-DRB diversity in the genital odors of opposite-sex conspecifics, supporting previous findings that lemur genital odors function as advertisement of genetic quality. In this species, genital odors provide honest information about an individual’s absolute and relative MHC quality. Complementing evidence in humans and Old World monkeys, our results suggest that reliance on scent signals to communicate MHC quality may be important across the primate lineage.
WOOD SCREW WITHDRAWAL RESISTANCE OF SOME IMPORTANT TREE SPECIES GROWING IN EASTERN BLACKSEA REGION

Bu calismada; Dogu Karadeniz Bolgesinden (Gumushane, Trabzon, Artvin) elde edilen Dogu Kayini (Fagus orientalis Lipsky.), Sakalli Kizilagac (Alnus glitunosa subsp. barbata (C.A.Mey) Yalt. ), Anadolu Kestanesi (Castenea sativa Mill.), Dogu Ladini (Picea orientalis (L.) Link) ve Saricam (Pinus sylvestris L.) odunlarinin vida tutma direncleri belirlenmistir. Denemeler TS 6094, ASTM-D 143 ve ASTM-D 1761 standartlarina uygun olarak 60’ar ornek uzerinde gerceklestirilmistir. Orneklerin yarisinda rutubet miktarlari % 12, diger yarisinda ise % 30 olarak secilmistir. Orneklerin boyutlari; 50*50*150 mm olarak alinmistir. 4.5 mm capinda ve 40 mm boyunda agac vidalar kullanilmistir. Orneklerin teget kesitinde acilan klavuz deliklerine, iki adet vida 26 mm derinlige kadar vidalanmistir. Sonuc olarak; agac turlerine gore en yuksek vida tutma direnci Dogu Kayininda elde edilmis, onu sirasiyla Sakalli Kizilagac, Anadolu Kestanesi ve Saricam izlemis, en dusuk vida tutma direnci ise Dogu Ladini odunlarinda elde edilmistir. Rutubetin etkisine gore ise; % 12 rutubet miktarindaki orneklerin vida tutma direnc degerleri yuksek cikmistir.
Die afrikanischen Arten der Gattungsgruppe 'Amytta' Karsch (Saltatoria: Tettigoniidae, Meconeminae).

Auf Grund eines sehr umfangreichen, aus 251 Exemplaren bestehenden Materiales aus zwolf Museen und Instituten sowie der Nachuntersuchung samtlicher Typen, von denen sich mehrere als Synonyme erwiesen, werden in der Gattungsgruppe „Amytta" Karsch nunmehr 34 afrikanische Arten und zwei Subspezies unterschieden, von denen 25 Arten und zwei Unterarten als neu beschrieben werden. Diese Arten verteilen sich auf neun Genera, von denen sieben neu errichtet werden. Das Schwergewicht der Gruppe scheint im tropischen West- und Zentralafrika, also in den mehr oder weniger bewaldeten Gebieten zu liegen. Die durchweg relativ kleinen Formen sind von groser habitueller Gleichformigkeit, unterscheiden sich jedoch in beiden Geschlechtern vor allem durch die Gestaltung der Endsegmente und ihrer Anhange, insbesondere der mannlichen Cerci. Der Arbeit ist ein Bestimmungsschlussel zu samtlichen Gattungen, Arten und Unterarten beigegeben.Nomenklatorische Handlungenangulata Chopard, 1945 (Amytta), syn. n. of Amyttosa mutillata (Karsch, 1890)occidentalis Karsch, 1890 (Amytta), syn. n. of Amyttosa mutillata (Karsch, 1890), male, nec femaleukamica Beier, 1965 (Amytta), spec. n.angolensis Beier, 1965 (Amyttacta), spec. n.rhodesica Beier, 1965 (Amyttacta), spec. n.manuata Beier, 1965 (Amyttella), spec. n.pusillula Beier, 1965 (Amyttella), spec. n.congica Beier, 1965 (Amyttina), spec. n.dispersa Beier, 1965 (Amyttina), spec. n.exorbitans Beier, 1965 (Amyttina), spec. n.kivuensis Beier, 1965 (Amyttina), spec. n.rhodei Beier, 1965 (Amyttina), spec. n.schoutedeni Beier, 1965 (Amyttina aliquantula), sspec. n.forcipata Beier, 1965 (Amyttopsis), spec. n.podicaelata Beier, 1965 (Amyttopsis), spec. n.vinculata Beier, 1965 (Amyttopsis), spec. n.bicaudata Beier, 1965 (Anepitacta), spec. n.guineensis Beier, 1965 (Anepitacta), spec. n.nigerica Beier, 1965 (Anepitacta), spec. n.scrofina Beier, 1965 (Anepitacta), spec. n.katangica Beier, 1965 (Anepitacta nigerica), sspec. n.eburnea Beier, 1965 (Proamytta), spec. n.kamerunensis Beier, 1965 (Proamytta), spec. n.reducta Beier, 1965 (Proamytta), spec. n.simillima Beier, 1965 (Proamytta), spec. n.simplicoides Beier, 1965 (Proamytta), spec. n.sincera Beier, 1965 (Proamytta), spec. n.Amyttacta Beier, 1965 (Tettigoniidae), gen. n.Amyttella Beier, 1965 (Tettigoniidae), gen.n. Amyttina Beier, 1965 (Tettigoniidae), gen. n.Amyttopsis Beier, 1965 (Tettigoniidae), gen. n.Amyttosa Beier, 1965 (Tettigoniidae), gen. n.Gonamytta Beier, 1965 (Tettigoniidae), gen. n.Proamytta Beier, 1965 (Tettigoniidae), gen. n.bubianus I. Bolivar, 1906 (Xyphidiopsis), syn. n. of Amyttosa mutillata (Karsch, 1890)mitratus (female) I. Bolivar, 1906 (Xyphidiopsis), syn. n. of Amyttosa mutillata (Karsch, 1890)mitratus (male) I. Bolivar, 1906 (Xyphidiopsis), syn. n. of Gonamytta occidentalis (Karsch, 1889), female
Environmental drivers and phylogenetic constraints of growth phenologies across a large set of herbaceous species

Because perennial herbs of temperate climates develop their above‐ground parts every year anew, their success critically depends on the timing and speed of this growth (growth phenology). These parameters can play a role in species coexistence and may differ along environmental gradients. Still, we know little about them, as most phenological data come from observations of flowering and to a lesser degree leafing onset. We collected data on growth phenology of about 400 perennial herbs in a botanical garden to make the results independent of local differences in climatic drivers as much as possible. Using these data, we determined species‐specific parameters of Day of peak growth, Day of maturity and two types of growth rates associated with the change in plant size. Environmental conditions in which these species occur in the field were assessed using Ellenberg indicator values, which express species’ optima along gradients of moisture, nutrients and temperature. Both timing and speed of growth estimated in the common garden were affected by light and moisture conditions of the habitats where the species typically occur. All parameters showed phylogenetic conservatism. We identified two relationships among these parameters of growth phenology: (1) species with early peak growth had high relative growth rates in contrast to late species; (2) tall species showed later peak growth than short species. The first relationship is associated with survival under forest canopy, where species are selected to grow early and fast before trees leaf out, which restricts their size. The latter is associated with (asymmetric) competition for light in open habitats, where the main selection factor is for tall stature, which cannot be attained early in the season. Synthesis. We show that large differences in size growth dynamics among herbaceous species are constrained by a few key trade‐offs involving height at maturity, rate of growth and time when maximum height is attained. These trade‐offs correspond to major selective forces acting on herbaceous plants in temperate climates.
Repurposing of archived CO1 sequence data reveals unusually high genetic structure between North American and European zebra mussels (Dreissena polymorpha)

Abstract The invasion of the zebra mussel, Dreissena polymorpha in the Great Lakes of North America is regarded as one of the most catastrophic ecological events in recent history. Previous studies showed a close kinship between European zebra mussels and their invasive cohorts in the Great Lakes. In this study, we repurposed and reanalyzed archived CO1 sequence data from Lake Superior and multiple sites in Europe that were collected between 1991 and 2011 to illustrate an interesting pattern of genetic isolation that was overlooked in previous studies. The results showed extreme genetic isolation of Lake Superior zebra mussels as evident by high ϕST values and strong geographic patterning of Lake Superior haplotypes.
Relationship between incidence of Leucinodes orbonalis (Guenee) and Chlorophyll content in leaves of Brinjal (Solanum melongena L.)

The present study on biochemical basis of resistance against Leucinodes orbonalis infestation was conducted during the year 2011-2012. The results revealed that highest chlorophyll-â€˜aâ€™- content of 0.497 mg/gfw was recorded in the susceptible genotype SHB-1.The lowest amount of 0.319 and 0.381 mg/gfw was observed in the resistant genotypes Brinjal-85 and Local long respectively, which were significantly different from other evaluated genotypes. The chlorophyll â€˜aâ€™content was positively correlated with the brinjal shoot and fruit borer infestation. Thehighest chlorophyll -â€˜bâ€™- content of 0.442 mg/gfw was recorded at 70 DAT (days after transplanting). The amount of chlorophyll -â€˜bâ€™- varied significantly among the genotypes at different ages and decreased with the age of crop. The average highest amount of chlorophyll -â€˜bâ€™- was estimated in the genotype SBH-1 which was significantly at par with hybrid SBH-2. The lowest chlorophyll -â€˜bâ€™- content was recorded at 40 DAT in the genotype Brinjal-85 followed by Local Long. The lowest amount of total chlorophyll was estimated in the resistant variety as compared to susceptible therefore exhibiting lowest level of infestation.
Shell decomposition rates in relation to shell size and habitat conditions in contrasting types of Central European forests

Empty mollusc shells provide evidence of the species’ presence over various temporal and spatial scales. However, the persistence of the shell can differ depending on the levels of soil pH and soil humidity. Although this is generally known, there are virtually no experimental data on shell decomposition rate and its relation to shell size and site conditions. Here we study disappearance and degradation rates of shells of nine common species covering the variation in shell size and ecological requirements of temperate European land snails. These shells were exposed to decomposition during a 3-year field experiment in six forest types, representing a gradient of soil pH and humidity. Rates of disappearance and (in larger species) of degradation were estimated by removing the exposed shells and measuring their condition after 6, 12, 24 and 36 months. The disappearance rate was modelled by generalized linear models in relation to species and forest type. The data showed an increase in shell disappearance rate from dry alkaline through to wet acidic forests, but the effect of species size outweighed that of habitat. While shells of large species only started to disappear after 3 years in wet acidic sites, most shells of small species had already disappeared by that time. In contrast, in dry habitats the loss of small shells only started after 3 years. The results clearly support the benefits of using empty shells in mollusc research, especially less damaged shells, which represent the individuals that were alive less than 2 years ago, regardless of shell size and habitat type. However, the marked differences in decomposition rate related to shell size and habitat also highlight the need to take these into account if a studied parameter is confounded with variation in shell size and/or site alkalinity or humidity.
In vitro digestion of caprine whey proteins by human gastrointestinal juices : Effect of whey hydrolysates and peptides on in vitro cell responses

The aim of this study was to characterise the individual human gastric and duodenal juices to be used in in vitro model digestion and to examine the storage stability of the enzymes. Gastroduodenal juices were aspirated, and individual variations in enzymatic activities as well as total volumes, pH, bile acids, protein and bilirubin concentrations were recorded. Individual pepsin activity in the gastric juice varied by a factor of 10, while individual total proteolytic activity in the duodenal juice varied by a factor of 5. The duodenal amylase activity varied from 0 to 52.6 U/ml, and the bile acid concentration varied from 0.9 to 4.5 mM. Pooled gastric and duodenal juices from 18 volunteers were characterised according to pepsin activity (26.7 U/ml), total proteolytic activity (14.8 U/ml), lipase activity (951.0 U/ml), amylase activity (26.8 U/ml) and bile acids (4.5 mM). Stability of the main enzymes in two frozen batches of either gastric or duodenal juice was studied for 6 months. Pepsin activity decreased rapidly and adjusting the pH of gastric juice to 4 did not protect the pepsin from degradation. Lipase activity remained stable for 4 months, however decreased rapidly thereafter even after the addition of protease inhibitors. Glycerol only marginally stabilised the survival of the enzymatic activities. These results of compositional variations in the individual gastrointestinal juices and the effect of storage conditions on enzyme activities are useful for the design of in vitro models enabling human digestive juices to simulate physiological digestion.
The complete mitochondrial genome of Dabry’s sturgeon (Acipenser dabryanus)

Abstract The complete mitochondrial genome of Dabry’s sturgeon (Acipenser dabryanus) was first determined in this study. The mitochondrial DNA is circular molecule (16,437 bp in length) with a typical vertebrate mitochondrial gene arrangement, including 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 non-coding control region (D-loop). All genes were encoded on the heavy strain except for ND6 and eight tRNA genes. The overall base composition of the heavy strain was A (30.2%), T (23.7%), C (29.7%), G (16.4%), and with an AT bias of 53.9%. Phylogenetic analysis based on the mitochondrial genomes of 10 related species using MEGA 5.1 indicated that A. dabryanus and A. sinensis are the most closely related species.
Functional analysis of a Midgut Proteolytic Gene in Tsetse Fly (Glossina pallidipes) by RNA Interference

Trypanosomiasis a devastating disease for human and animals in sub-Saharan Africa is transmitted via a tsetse fly (Genus: Glossina) bite. In absence of vaccine, effective and affordable drugs, the disease control relies heavily on vector control strategies because trypanosomes require an obligatory passage through the vector. Understanding the factors involved in tsetse-trypanosome interactions such as the midgut proteolytic genes that are known to be potential barriers to the initial trypanosome establishment stands to enhance vector control. However, very few in vivo studies have been undertaken to analyze such genes. The study describes functional analysis of a midgut Glossina proteolytic gene (GPL) by RNA interference to establish its influence on tsetse fly feeding success and survival. The coding region of the gene was amplified by RT-PCR and sequenced. The gene classified as a serine protease belonging to the trypsin family, with> 90% identity to the previously reported GPL genes from G. austeni and G. f fuscipes. Sequence prediction showed it has a pi of 4.99, molecular weight of 29.47 KD and a hydrophobic leader peptide (16aa) indicating it is secretory in nature. When compared to other serine protease of Diptera origin, it exhibited close phylogenetic relatedness to those of other haematophagous insects. A reverse genetic approach to study the isolated gene function was limited by the short lived nature of the achieved knockdown as confirmed by semi quantitative RT-PCR. The highest transcript reduction (60%) lasted for two days, feeding success in this group was not significantly impaired (p<0.05) but, it improved with time as the transcripts level recovered. Also, the observed mortality was low and survival of the fly was normal when compared to the uninjected control group. The short lived GPL knockdown suggests it is crucial to tsetse fly physiology and may contribute to bloodmeal digestion. The study results through targeted transcript knockdown together with GPL dual role during trypanosome establishment could provide a foundation for the development of a genetic approach to control trypanosomiasis based on this gene.
Massive Sequencing: A New Tool for the Control of Alcoholic Fermentation in Wine?

In wine industry, there is a prevalent use of starter cultures to promote a controlled and efficient alcoholic fermentation preventing the growth of spoilage microbes. However, current trends in enology aim to combine the guaranteed success of monitored process and the complexity of fermentations either by inoculating autochthonous starters or by performing spontaneously to produce distinctive wines. To understand the complex roles of microorganisms on wine fermentation, we must understand their population dynamics and their relationships with wine quality and metabolome. Current metagenomics techniques based on massive sequencing are gaining relevance to study the diversity and evolution of microbial population on every stage of the wine making process. This new tool and technique increases the throughput and sensitivity to study microbial communities. This review focuses on the current knowledge about wine alcoholic fermentation, the contribution of massive sequencing techniques and the possibility of using this tool for microbial control.
Characteristics, Histories, and Future Succession of Northern Pinus pungens Stands

Abstract Pinus pungens (Table Mountain pine) stands are rare conifer-dominated communities that occur on xeric ridges and upper slopes throughout the central and southern Appalachian Mountains. At the northern end of this range, this uncommon forest community is essentially unstudied. Therefore, in 2006 I initiated a dendroecology study of three Pinus pungens stands growing in Pennsylvania to better understand their current conditions, histories, and likely future succession. These stands contained from four to 14 tree species with Pinus pungens or Quercus montana (chestnut oak) dominating the main canopy. Quercus coccinea (scarlet oak), Acer rubrum (red maple), or Nyssa sylvatica (black gum) were the primary species of the midstory. Kalmia latifolia (mountain laurel) was the principal understory shrub. Two of the communities had Pinus pungens and Quercus montana trees dating back into the mid-1800s and were likely heavily influenced by the charcoal iron industry of that century. Periodic fire was also part of their history. The other Pinus pungens community arose following abandonment of an agricultural field in the 1910s and fire does not seem to have been a factor in its ecological history. Two of the communities appear to be losing their Pinus pungens component as their understories are dominated by hardwood saplings or shrubs and there are no pine seedlings present. Perpetuating these and other Pinus pungens communities in Pennsylvania will require reducing the understory vegetation and creating suitable seed beds for Pinus pungens seedling establishment.
Histone demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction

Nutrient limitation may elicit adaptive epigenetic changes but the nature and mechanisms of the cellular response to specific nutrient deficiencies are incompletely understood. We report that depriving human cells of amino acids (AAs) induces specific loss of H4K20me1 from gene bodies and elevated binding of c-MYC at promoters genome-wide. These effects are most pronounced at ribosomal protein and translation initiation genes, which are upregulated, leading to enhanced protein synthetic capacity. Combination of H4K20 methyltransferase depletion and c-MYC over-expression in rich media is required and sufficient to recapitulate the effects of AA restriction. Our data reveal an unexpected and epigenetically implemented increase in translational capacity when AAs are limiting, likely to safeguard the proteome by making effective use of limited resources. One Sentence Summary: Combination of H4K20me1 demethylation and c-MYC activation enhance translational capacity in response to amino acid restriction.