Miracle-dz/UniFAR-FTUs huggingface dataset:
Models for Predicting Specific Gravity and Ring Width for Loblolly Pine from Intensively Managed Plantations, and Implications for Wood Utilization

Loblolly pine (Pinus taeda L.) is increasingly grown on intensively managed plantations that yield high growth rates. Wood properties, including specific gravity (SG), change with cambial age, and thus intensively managed trees contain a high proportion of low density corewood when harvested because of reduced rotation lengths. This study was undertaken to develop models of ring-level properties (SG and width) in intensively managed loblolly pine plantations. Ninety-three trees from five stands aged from 24 to 33 years were harvested, and 490 disks were obtained from in between the 5.2-m logs that were cut, and at the merchantable top. The disks were cut into pith-to-bark radial strips that were scanned on an X-ray densitometer, and the resultant data analyzed using non-linear mixed-effects models. The fixed effects of the models, which included cambial age and for some models disk height and ring width, were able to explain 56, 46, 54, 16, and 46 percent of the within-tree variation for ring SG, ring width, latewood SG, earlywood SG, and latewood percent, respectively. To assess implications for wood utilization, a modeled tree was built by using height, diameter, and taper equations and these models were linked with the developed ring SG model to produce a tree properties map. The linked information was also used to generate tree and log SG and proportion of corewood values for different rotation ages. The results from this study are a step towards integrating wood quality models into growth-and-yield modeling systems that are important for loblolly pine plantation management.
Spotting the path that leads nowhere: Modulation of human theta and alpha oscillations induced by trajectory changes during navigation

The capacity to take efficient detours and exploit novel shortcuts during navigation is thought to be supported by a cognitive map of the environment. Despite advances in understanding the neural basis of the cognitive map, little is known about the neural dynamics associated with detours and shortcuts. Here, we recorded magnetoencephalography from humans as they navigated a virtual desert island riven by shifting lava flows. The task probed their ability to take efficient detours and shortcuts to remembered goals. We report modulation in event-related fields and theta power as participants identified real shortcuts and differentiated these from false shortcuts that led along suboptimal paths. Additionally, we found that a decrease in alpha power preceded ‘back-tracking’ where participants spontaneously turned back along a previous path. These findings help advance our understanding of the fine-grained temporal dynamics of human brain activity during navigation and support the development of models of brain networks that support navigation.
A Framework for Predicting Design Failures in Engineered Genetic Codes

Extreme engineering of an organism’s genetic code could impart true genetic incompatibility, even blocking effects of horizontal gene transfer and viral infection. Recent experiments exploring this possibility demonstrate that such radical genome engineering achievements are plausible. However, it is unclear when the modifications will compromise the fitness of an organism. Efforts to reformat an entire genome are difficult and expensive; computational methods predicting fruitful experimental trajectories could play a pivotal role in advancing such efforts. We present a framework for building in silico models to assist genome-scale engineering. Genetic code engineering requires choosing from many possible codon-usage schemes, to find a design that is viable and effective. We use machine learning to identify which alternative codon-usage schemes are likely to result in no observed viable cells. Our data-driven approach employs observations of how modifying codon usage in individual genes impacted observed viability in E. coli, revealing salient features for early identification of problematic genetic code designs. We achieved an average area under the receiver operating characteristic of 0.72 on out-ofsample data. Author Summary As machine learning and artificial intelligence play an increasingly central role in science and engineering, it will be important to establish standardized techniques that facilitate the dialogue between experimentation and modeling. Biological experimental techniques are concurrently evolving at a rapid pace, providing unique opportunities to collect high-quality, novel information that was previously unobtainable. This work navigates the landscape of this vast, new territory, identifies interesting landmarks for exploration and posits new approaches towards advancing our research efforts in these areas. In this work, we show that, using a small dataset of 47 observations and rigorous nested cross validation techniques, we can build a model that makes better-than-random predictions of how codon usage changes in essential genes influence viability in E. coli. These predictions can be used to inform experimental trajectories in both genetic code and codon optimization experiments. We discuss ways to improve this model, iteratively, by performing high value experiments that decrease uncertainty in predictions and extrapolation error. Finally, we present novel visualization methods to aid in developing intuitions for how re-coding impacts groups of genes. These methods are also useful tools in building important insights into how well machine learning algorithms can generalize to new data.
The genetic mating system in the glass frog Hyalinobatrachium valerioi (Centrolenidae), a species with male parental care

Hyalinobatrachium valerioi ist eine Froschart, die in den Neotropen beheimatet ist. Beobachten kann man sie fast ausschlieslich wahrend der Regenzeit entlang von Bachen, wenn Mannchen auf Blattern der Ufervegetation rufen um Weibchen anzulocken. Wenn sie dabei erfolgreich waren, werden im Mittel 29 Eier auf die Unterseite eines Blattes abgelegt. Das Weibchen verlasst den Standort kurz nach der Eiablage, doch die Mannchen sind sehr standortstreu. Sie bleiben bei ihren Gelegen und bewachen diese, bis die Larven geschlupft und in das darunterliegende Fliesgewasser gefallen sind. Die Mannchen werben wahrend des Bewachens weiter um Weibchen und konnen somit bis zu sieben Gelege gleichzeitig bewachen. Es existieren einzelne Beobachtungsstudien uber das Fortpflanzungsverhalten dieser Froschart, doch uber individuelles Fortpflanzungsverhalten und Paarungsmuster war bisher nichts bekannt. In dieser Studie wurde durch die Integration von Beobachtungsdaten in molekularbiologische Elternschaftsanalysen das Paarungssystem von Hyalinobatrachium valerioi bestimmt. Es ist die erste molekularbiologische Elternschaftsstudie an Glasfroschen und PCR-Primer und -Protokolle wurden neu entwickelt. Wahrend des Untersuchungszeitraumes von 101 Tagen (Aug-Nov 2012) haben wir eine Population von H. valerioi im Areal der Forschungsstation La Gamba, im Sudwesten Costa Ricas, kontinuierliche beobachtet und beprobt. Wir konnten Gewebeproben von 93 Mannchen, 48 Weibchen und 374 Larven aus 193 Gelegen sammeln und einzelne Individuen an bis zu insgesamt 49 Tagen beobachten. Fur die untersuchte Population konnten wir ein polygynandrisches Paarungssystem feststellen. Die untersuchten Parameter zeigen ein ahnliches Potenzials fur sexuelle Selektion in beiden Geschlechtern und deuten auserdem darauf hin, dass Weibchen nicht wahlerisch sind und ein geringes Mas an Konkurrenz zwischen den Mannchen herrscht.
Carbon dynamics, potential and cost of carbon sequestration in double rice cropping system in semi arid southern India

Studying the dynamics of soil organic carbon (SOC) is important for understanding the mechanistic pathways of C stabilization into different SOC pools. An attempt was, therefore, made to assess the impact of double rice cropping system with different levels of fertilizers and in combination with organics on C sequestration and its stabilization in an Inceptisol using a 14-year old experiment at Jagtial under semi-arid climate in India. Total organic carbon (TOC) allocated into different pools in order of very labile > less labile > non labile > labile, constituting about 41.4, 20.6, 19.3 and 18.7%, respectively. In comparison with control, system receiving farmyard manure (FYM-10 Mg ha-1 season-1) alone showed greater C build up (40.5%) followed by 100% NPK+FYM (120:60:40 kg N,P,K ha-1+5 Mg FYM ha-1season-1)(16.2%). In fact, a net depletion of carbon stock was observed with 50% NPK (-1.2 Mg ha-1) and control (-1.8 Mg ha-1) treatments. Only 28.9% of C applied through FYM was stabilized as SOC. A minimal input of 2.34 Mg C ha-1 y-1 is needed to maintain SOC level. Treatments with organics showed a higher carbon management index, and microbial biomass and other labile pools of SOC. Results also indicated that100% NPK+FYM could maintain yield sustainability with a lower cost of carbon sequestration.
Novel Resilience Phenotypes from a Natural Disease Challenge Model for Wean-to-Finish Pigs

1 Iowa State University, Department of Animal Science, 50011, Ames, IA, United States aputz@iastate.edu (Corresponding Author) 2 University of Saskatchewan, Large Animal Clinical Sciences, SK S7N 5B4, Saskatoon, Canada 3 University of Alberta, Department of Agricultural, Life, and Environmental Sciences, AB T6G 2R3, Alberta, Canada 4 PigGen Canada, Guelph, Ontario, Canada 5 Centre de développement du porc du Québec inc. (CDPQ), QC G1V 4M6, Quebec, Canada 6 Livestock Gentec Centre, University of Alberta, Department of Agricultural, Food, and Nutritional Science, AB T6G 2C8, Edmonton, Alberta, Canada
Inhibiting foodborne pathogens Vibrio parahaemolyticus and Listeria monocytogenes using extracts from traditional medicine: Chinese gallnut, pomegranate peel, Baikal skullcap root and forsythia fruit

Abstract Foodborne illnesses have been a heavy burden in the United States and globally. Many medicinal herbs have been cultivated in the US and many of which contain antimicrobial compounds with the potential to be used for food preservation. Methanol/water extracts of pomegranate peel (“PP”, Punica Granatum L.), Chinese gallnut (“CG”, Galla chinensis), Forsythia fruit (“FF”, Forsythia suspensa) and Baikal skullcap root (“BS”, Scutellaria baicalensis) were tested for antimicrobial activity using the agar diffusion assay on tryptic soy agar (TSA) and microdilution assay in tryptic soy broth (TSB). CG and PP extracts showed good to excellent inhibitory effect against Vibrio parahaemolyticus and Listeria monocytogenes in both assays, with a minimum inhibitory concentration (MIC) range from 0.04 to 5 mg/mL. BS had moderate inhibitory effects against V. parahaemolyticus with an MIC of 5 mg/mL in TSB, and against L. monocytogenes with an MIC of 20 mg/mL on TSA. CG was analyzed using LC-MS and fractionated using HPLC. The major components were identified as gallic acid, digallic acid, methyl gallate, and gallotannins (oligo-galloyl-D-glucose, nGG, n = 1~10). Six fractions (I - VI) were collected and their antibacterial activities were tested against L. monocytogenes, and V. parahaemolyticus both on TSA and in TSB. On TSA, fraction III, IV and V inhibited V. parahaemolyticus but no fraction inhibited L. monocytogenes. In TSB, all fractions inhibited V. parahaemolyticus and fractions II - V inhibited L. monocytogenes. Future studies are needed to investigate the effects of medicinal plants on food products.
EFFECTS OF ORGANOCHLORINE PESTICIDE RESIDUES ON HEMATOLOGICAL PARAMETERS IN LIBYAN AGRICULTURAL WORKERS

Objectives: Agricultural workers are at risk of exposure to occupational hazardous such as pesticides. Bio monitoring of effects in agricultural workers is necessary to assess the individual risk of handling pesticides. Settings: The study was conducted in the hematological unit at the Analytical Medical Laboratory at El-Beida Hospital, Libya. Subjects and Methods: This study was designed to study the hematological parameters effects of the pesticide pollution among Libyan agricultural workers at Aljebal Alakhtar, Libya. A total of 45 blood samples were collected from male agriculture workers who have been exposed to pesticides in crop fields for a long period time on Aljebal Alakhtar, while 25 blood samples have been taken from the group of people in meanwhile who were not dealing with pesticides (control). The hematocrit value (HCT), hemoglobin content, red blood cells count (RBCs) and mean corpuscular volume (MCV) concentration with increased white blood cells counts (WBCs), mean erythrocyte hemoglobin concentration (MCHC), mean corpuscular hemoglobin (MCH), lymphocytes and neutrophils levels were performed on Selectra E fully automatic hematological analyzer. The samples were analyzed for organochlorine pesticide residues by using gas chromatography-electron capture detector (GC-ECD). All the data from Libyan agricultural workers and age-matched controls from different experiments were analyzed and compared using Student’s t-test. The results were expressed as mean ± SD. The significant test was applied at p value < 0.05. Results: The study indicated also detected four (p,p`-DDT, o,p`-DDT, o,p`-DDE and p,p`-DDD) of the 16 organochlorine compounds tested for in the whole blood samples were detected in all analyzed samples. The mean total p,p`-DDT, o,p-DDT, o,p`-DDE and p,p`-DDD levels in blood samples were 0.169 ± 0.001, 0.129 ± 0.003, 0.328 ± 0.007 and 0.510 ± 0.01 ppm, respectively. Assessment of hematological parameters revealed that the RBCs, hemoglobin, HCT, MCV. MCH, MCHC and neutrophils levels were significantly lower in workers than in controls, while WBCs and lymphocytes levels were significantly higher in workers. Conclusions: These biomarkers seem to be indicative of adverse effects of pesticides in agricultural workers, confirming their use for routine monitoring of effects.
The Efficacy of High-Protein Tropical Forages as Alternative Protein Sourcesfor Chickens: A Review

Smallholders of poultry production systems in developing countries are commonly found in rural, resource-poor areas, and often face food insecurity. The main constraints for smallholders in poultry production in rural, resource-poor areas are the shortage of available commercial dietary protein and the high cost of commercial diets. The beneficial effects of legume and forage cultivation are economic, through providing protein for animals, and ecological, such as soil amendment, nitrogen fixation, and stripping control which participate to increase cropping efficiency. The potential nutritive value of a wide range of forages and grain legumes is presented and discussed. The impacts of dietary protein, fiber, and secondary metabolites in plant content, as as well as their consequences on feed efficiency, animal performance, and digestion processes are enclosed in this review. Lastly, approaches to reduce the anti-nutritional factors of the secondary metabolites of plants are explained.
Effects of dietary supplemental chromium methionine, zinc oxide, and ascorbic acid on performance, egg quality traits, and blood parameters of laying hens subjected to heat stress

ABSTRACT Based on a 2 × 2 × 2 factorial, the effects of three dietary supplemental including chromium methionine (Cr) (0 and 400 μg/kg diet), zinc oxide (Zn) (0 and 30 mg/kg diet), and vitamin C (VitC) (0 and 250 mg/kg diet) on egg production (EP) and mass (EM) and egg traits in heat-stressed (HS) Lohmann LSL-Lite laying hens from 30 to 45 weeks of age were evaluated. The house temperature was kept at 18°C (weeks 30–40 of age) and then increased to 32°C (weeks 41–45 of age). Dietary treatments had no significant effects on EP, egg weight, EM, and feed conversation ratio before and after exposure to heat stress (P > 0.05). Decreased feed intake intake was observed in group of VitC during exposing to HS (P < 0.05). Dietary supplemental Cr decreased serum glucose concentration before HS (P < 0.05). A combination of Cr and VitC increased serum glucose concentration before and during HS (P < 0.05). Decreased serum concentration of Zn was detected in hens fed the diets with VitC, Cr, or Zn (P < 0.05). Increased serum concentration of Cr was observed in hens fed the diets supplemented with Cr (P < 0.05).
Inference of species histories in the presence of gene flow

When populations become isolated, members of these populations can diverge genetically over time. This leads to genetic differences between individuals of these populations that increase over time if the isolation persists. This process can be counteracted when genes are exchanged between populations. In order to study the speciation processes when gene flow is present, isolation-with-migration methods have been developed. These methods typically assume that the ranked topology of the species history is already known. However, this is often not the case and the species tree is therefore of interest itself. To infer it is currently only possible when assuming no gene flow. This assumption can lead to wrongly inferred speciation times and species tree topologies. Building on a recently introduced structured coalescent approach, we introduce a new method that allows inference of the species tree while explicitly modelling the flow of genes between coexisting species. By using Markov chain Monte Carlo sampling, we co-infer the species tree alongside evolutionary parameters of interest. By using simulations, we show that our newly introduced approach is able to reliably infer the species trees and parameters of the isolation-with-migration model from genetic sequence data. We then infer the species history of six great ape species including gene flow after population isolation. By using this dataset, we are able to show that our new methods is able to infer the correct species tree not only on simulated but also on a real data set where the species history has already been well studied. In line with previous results, we find some support for some gene flow between bonobos and common chimpanzees.
Le Machine Learning : numérique non supervisé et symbolique peu supervisé, une chance pour l’analyse sémantique automatique des langues peu dotées

Résumé : Les données non structurées dominent l’univers de la production et de la publication des données, et en représentent, d’après plusieurs études, plus de 80%. Ce type de contenus, constitue la partie riche et précieuse en termes de données, d’informations et de connaissances ; donc nécessaire à intégrer et à prendre en considération dans les processus d’analyses et d’exploitations des données. L’analyse des données non structurées reste une discipline difficile, car elle repose sur de nombreux (pré-)traitements numériques (formalisation, normalisation, corpus, annotations, etc.) de la langue naturelle, faisant souvent défaut, surtout dans le cas des langues peu dotées. Dans cet article nous présentons une approche, bien adaptée aux cas où on ne dispose pas ou que de peu de données traitées. Elle est basée sur des méthodes d’apprentissages numériques non supervisés indépendants de la langue et symboliques peu supervisés, permettant d’exploiter directement des données brutes ou seulement des petites quantités de données traitées, comme base d’apprentissage pour l’interprétation des données. En l’appliquant à un cas concret d’une langue peu dotée, nous avons pu, montrer l’utilité et surtout l’opportunité que ces technologies pourraient constituer pour contourner les problèmes dont souffre ce type de langues, facilitant ainsi leur accès dans le monde de l’analyse sémantique automatique des données non structurées. Cette étude a été validée à travers des expérimentations confirmant de bons résultats pour l’approche. Mots clés : Machine Learning, apprentissages non/peu supervisés, contextes, relations sémantiques, modèles des données, ressources langagières, LSA, LDA, langues peu dotées.
Effect of Replacing Canola Meal for Fish Meal on the Growth, Digestive Enzyme Activity, and Amino Acids, of Ovate Pompano, Trachinotus ovatus

Ovate Pompano (Trachinotus ovatus) is one of the most highly valued aquaculture species due to its commercial value, rapid growth, high quality flesh, and suitability for cage culture. Ovate Pompano were fed diets containing graded levels of canola meal to replace the fish meal. Six diets containing 45% crude protein and 12% crude lipid were fed to the fish during the 8-week feeding trial. Weight gain of the fish was negatively related to canola meal ratio in the diets. Protein efficiency and feed conversion ratio were inversely related to the canola meal inclusion in the diets. The crude lipid of the fish was positively related to the dietary canola meal, while an inverse trend was found in the crude protein of the fish. Protease activity and amylase activity showed a similar trend to the crude protein, while the lipase activity showed an inverse trend. No significant differences were observed in the moisture, ash, or fillet yield of the fish among dietary treatments. The “delicious amino acid ” i.e. those eliciting Umami flavor (UEAA), e.g. glutamic acid and others, essential amino acid, and total amino acid content of the fish were inversely related to the canola meal ratio in the diets. The results of the experiment indicated that canola meal can replace 18.17 % fish meal without affecting growth. Higher substitution levels of canola meal produced adverse influences on growth, digestive enzyme activity, and amino acid content of Ovate pompano. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il. To read papers free of charge, please register online at registration
Characterisation and evolution of globin-like genes in phylum Cnidaria

Globins, such as hemoglobin, are a well-studied gene and protein family, but there is limited research on non-vertebrate lineages. This research has identified an extensive repertoire of globin genes in phylum Cnidaria, with a focus on sea anemones. This study has provided an excellent starting point to further our understanding of the evolutionary history and function of the globin gene and protein superfamily in ancient lineages.
Bacteriophages as surrogates of viral pathogens in wastewater treatment processes

Although wastewater reuse presents numerous benefits, wastewater-borne pathogens, especially human enteric viruses, may pose risks to human health. Wastewater treatment processes have been shown to remove bacterial pathogens more effectively than they do viral pathogens, and in aquatic environments, levels of traditional faecal indicator bacteria (FIB) do not appear to correlate consistently with levels of human viral pathogens. There is, therefore, a need for novel viral indicators of faecal pollution and novel surrogates of viral pathogens. Potential candidates for this role include enteric bacteriophages (phages), viruses capable of infecting enteric bacteria.