Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalized Independent Component Analysis Over Finite Alphabets

Independent component analysis (ICA) is a statistical method for transforming an observable multi-dimensional random vector into components that are as statistically independent as possible from each other. Usually, the ICA framework assumes a model according to which the observations are generated (such as a linear transformation with additive noise). ICA over finite fields is a special case of ICA in which both the observations and the independent components are over a finite alphabet. In this paper, we consider a generalization of this framework in which an observation vector is decomposed to its independent components (as much as possible) with no prior assumption on the way it was generated. This generalization is also known as Barlow's minimal redundancy representation problem and is considered an open problem. We propose several theorems and show that this hard problem can be accurately solved with a branch and bound search tree algorithm, or tightly approximated with a series of linear problems. Our contribution provides the first efficient set of solutions to Barlow's problem. The minimal redundancy representation (also known as factorial code) has many applications, mainly in the fields of neural networks and deep learning. The binary ICA is also shown to have applications in several domains, including medical diagnosis, multi-cluster assignment, network tomography, and internet resource management. In this paper, we show that this formulation further applies to multiple disciplines in source coding, such as predictive coding, distributed source coding, and coding of large alphabet sources.
Capacidad promotora del crecimiento en cebada (Hordeum vulgare) y potencial antagónico de Rhizobium leguminosarum y Rhizobium etli

La agricultura sustentable plantea mejorar la eficiencia de la fijacion del nitrogeno mediante el uso de plantas (leguminosas) y bacterias (rizobio) competitivas, capaces de ser usadas en biofertilizacionn, biorremediacion y fitorremediacion y de esta manera extender las ventajas de la simbiosis a otros cultivos. En tal sentido, las investigaciones se han orientado al estudio del rizobio como promotor del crecimiento de plantas leguminosas y no leguminosas, proceso conocido como capacidad PGPR (Plant Growth Promoting Rhizobacteria). El presente estudio se ejecuto con el objetivo de evaluar 19 cepas de Rhizobium leguminosarum y Rhizobium etli , considerando su capacidad promotora de crecimiento en cebada ( Hordeum vulgare ) y su potencial antagonico con Alternaria solani y Fusarium sp . La evaluacion de la capacidad promotora se realizo en condiciones de invernadero y el potencial antagonico in vitro . El 89% de las cepas de Rhizobium evaluadas estimulo el crecimiento de las plantas de cebada, incrementando la materia seca total entre 8 a 37%. Se observo que el 63% de las cepas de rizobio mostraron potencial antagonico con A. solani y el 84% con Fusarium sp . , con porcentajes de inhibicion hasta de 49% y de 43% respectivamente. Se verifico que algunas cepas de R. leguminosarum y R. etli pueden promover el crecimiento de plantas de cebada y controlar hongos fitopatogenos como A. solani y Fusarium sp . en condiciones in vitro .
The Genetics of Some Morphs and Varieties of Cepaea nemoralis (L.)

The following segregants of shell colour are described: pale brown, faint brown, faint pink, yellow-white. Faint pink is dominant to dark and pale yellow and recessive to pale pink. Murray’s finding that the hyalozonate gene when homozygous pales shell colour as well as removing the lip and banding pigment is confirmed; faint pink or yellow-white shells homozygous for hyalozonate may be genetically faint pink or pale pink. Deep pink hyalozonates exist and transmit their phenotype to their offspring; in these the paling effect is not noticeable. Shells with no bands but a strip of fascialbate opaque material in the position for bordering the middle band are genetically mid-banded. The condition is due to a multifactorial suppression of the pigmented band. Spread-banded is described in the five-banded form as well as the m id-banded; the strong linkage between it and shell colour previously suggested is confirmed, but crossovers are recorded. White lip (with normally pigmented bands) is recessive to normal lip, linked to the locus for shell-colour, and allelic to hyalozonate. The normal lip/white lip heterozygote appears to be palelipped, but the degree of pallor is modified by the presence of yellow or pink shell colour. White lip, when homozygous, may reduce the intensity of shell colour in some cases, as does hyalozonate. Hyalozonate is shown to be linked to the banding locus, which itself is strongly linked to that for shell colour. Orange-banded is complementary to hyalozonate, not allelic to it as is the very similar form lurida described by Murray in Cepaea hortensis . A form of the var. punctata producing only traces of bands and occasionally a definite punctate band is described, which is linked to the shell colour locus and dominant to normal bands. This and the form figured by Lang and by Taylor with well-developed punctate bands (the segregation of which from normal bands is confirmed) may well be alleles. A segregation of medium grey to very pale body is described, with medium grey dominant to pale. It appears to be unlinked to shell colour, banding and mid-banded.
A Comparative Study on the Modulatory Effects of Inhibition in the Mammalian and Avian Sound Localization Circuits

iv ACKNOWLEDGMENTS There are many, many people that have contributed to this document and my career at Lehigh. The following acknowledgements are not a complete list, but for the sake of brevity I cannot thank everyone individually. I would first like to thank my wife for supporting me unconditionally in my doctoral endeavor and tolerating unpleasant employment so that we could live comfortably. I am incredibly lucky to be married to such a beautiful and caring person. I love you. I would next like to acknowledge the hard work and patience of my advisor Dr. R. Michael Burger. Mike, you have taught me how to be a scientist. Your critical feedback has improved my scientific work in innumerable ways. Your support and compassion over the course of my time at Lehigh will never be forgotten. Thank you for always urging me to be the best I could be. I would also like to thank the members of my dissertation committee, Dr. your advice and analytical eye has had a major influence on my research. Matthias, your questions and conversations have really made me feel that my research was interesting and important. Julie, I am indebted to you for agreeing to join my committee given the short notice. Thank you for your vital input. The entire department of biological sciences deserves acknowledgement. This includes all of the groups such as the graduate committee who endowed me with two fellowships during my research, the faculty who have all helped train me through their coursework and seminars, and the administrators who have answered the same questions repeatedly over my career here. This department has been a very fostering environment. I thank my family and friends for all of their love and support. Many of you have helped me to maintain my sanity during this process by lending an ear or offering a beer. To my mother and father, thank you for always encouraging me and never stifling my inquisitions or ambitions. I am grateful for all of the sacrifices you made so I could further my education. I would also like to thank everyone for their generous contributions to the Heather Oehling MDS foundation. Special thanks to Kandi Kulp (Schrader) and Jen Snekser for organizing the benefit and thanks to all of the celebrity bartenders for volunteering their time. Helping my wife return to health while continuing my graduate studies was the most …
Essential Oil of Arial Parts of Adiantum capillus-veneris : Chemical Composition and Antioxidant Activity

Background: Adiantum capillus-veneris (Adiantaceae) is the only species of Adiantum genus growing in Iran. As a well-known plant in Iranian Traditional Medicine, to our knowledge, there has not been any report on essential oil constituents of this species as well as antioxidant activity evaluation of any plant belonging to Adiantum genus. Objectives: This study aimed to determine phytoconstituents of A. capillus-veneris volatile oil and its antioxidant activity. Materials and Methods: Essential oil obtained from arial parts of Adiantum capillus-veneris was analyzed by GC-Mass and its antioxidant activity was assessed by DPPH assay. Results: Analyses of yellow colored essential oil yielded 88.22% of total oil with 67 components. Among identified phytochemicals, carvone was the main component (31.58%). Moreover, percentage of carvacrol (13.75%), Hexadecanoic acid (5.88%), Thymol (4.05%), Hexahydrofarnesyl acetone (3.16%) and n-nonanal (2.99%) were more than other identified constituents. RC50 of this volatile oil was 0.039 mg/mL. Conclusions: Antioxidant activity of this essential oil could be somehow attributed to high contents of carvone, carvacrol and thymol. The volatile oil of this plant could have the potential of other biological activities, so further experimental investigations are recommended on this essential oil.
Distribution, biology, ecology and management of potato tuber moth, Phthorimaea operculella (Zeller) (Lepidoptera: Gelechiidae): A review

Abstract Among the major insect pests of potato, the potato tuber moth Phthorimaea operculella (Zeller) is important in both field and storage. The biology of the pest, studies of spatial distribution, sampling technique, effect of density dependent and Independent factors, losses caused and economic threshold levels are reviewed. Various management strategies such as agronomic practices, biological and chemical control are discussed. Attempts to identify the potential components of management of potato tuber moth are made.
Notes relating to the floras of Norfolk and Lord Howe Islands, I.

Miscellaneous floristic and taxonomic notes. The following new species are described from Lord Howe Is. : Coprosma inopinata I. Hutton & P. S. Green (Rubiaceae), Euphorbia psammogeton P. S. Green (Euphorbiaceae)-also from Queensland and New South Wales, and Macropiper hooglandii I. Hutton & P. S. Green (Piperaceae). Olearia elliptica subsp. praetermissa P. S. Green is described, and Trophis scandens (Lour.) Hook. & Am. subsp. megacarpa (P. S. Green) P. S. Green, comb. nov. established, from Lord Howe I. Marsdenia tubulosa F. Muell. (Asclepiadaceae) from Lord Howe Is. , as well as Euphorbia norfolkensis Boiss. and E. obliqua Endl. (Euphorbiaceae) from Norfolk Is. , are reestablished. Nicotianaforsteri Roem. & Schult. is shown to be the correct name for N. debneyi Domin (Solanaceae) and Pseuderanthemum pelagicum (Seem.) P. S. Green, comb. nov. that for P. grandiflorum Domin (Acanthaceae), of Vanuatu, formerly thought to be from Lord Howe Is. Alyxia gynopogon Roem. & Schult. (Gynopogon alyxia Forst. f., A. squamulosa C. Moore & F. Muell. Apocynaceae) and Scaevola taccada (Gaertn.) Roxb. (Goodeniaceae) are lectotypified. The identity of Euphorbia sparrmanii Boiss. is investigated and the record of Acronychia laevis J. R. & G. Forst. from Lord Howe Is. rejected.
Netcage Rearing of the Asian Seabass Lates calcarifer (Bloch) in Brackishwater Pond: The Technical and Economic Efficiency of Using High Protein Diets in Fingerling Production

Intensification in the grow-out culture of high-value fish requires a large quantity of quality fingerlings. Fingerling production is a component of fish farming that comprises nursery and grow-out culture, and may be a commercial enterprise option for fish farmers with limited pond area. The nursery rearing of the Asian seabass Lates calcarifer (Bloch) was conducted in netcages inside a brackishwater pond. The fish were fed with two isocaloric, high-protein diets formulated at the Southeast Asian Fisheries Development Center (SEAFDEC/AQD) and a control treatment: diets A (40.40% crude protein, CP) and B (46.17% CP), and trashfish (TF) as control. Hatchery-bred seabass early juveniles of two size groups (S1, 4.0 ± 0.2 g; S2, 2.40 ± 0.03 g) were stocked at 75–100 fish per m3 and given diets A or B at 6–10% of average body weight (ABW) d-1, or TF at apparent satiation. Seabass given the formulated diets attained the desired size (≥ 20–40 g) after 45 d but not the fish fed with trashfish. Size and treatments showed significant effects on final ABW, although no significant interaction between these factors was shown to affect body weight. As expected, S1 fish attained a significantly higher ABW (30.7 ± 18 g) compared with S2 fish (20.7 ± 11 g) regardless of diet treatment. Seabass fed with trashfish exhibited significantly lower final ABW (6.6 ±1.6 g) than those fed Diet A (33.4 ± 6.5 g) or Diet B (37.1 ± 9.4 g). Fish size did not have any significant effect on specific growth rate (SGR), but diet treatments did. SGR was significantly better when either Diet A (5.2 ± 0.30) or B (5.4 ± 0.20) was used compared with the SGR of seabass fed with trashfish (1.7 ± 0.5). Although size and treatment did not show significant interaction on fish survival, the use of bigger seabass resulted in higher survival (89 ± 11%) compared with smaller seabass (80 ± 11%). Regardless of size, similar survival was attained in seabass fed Diet A (89 ± 6%) or B (95 ± 5%), significantly higher than that in seabass given trashfish (72 ± 6%). An interaction between size at stocking and diet treatment significantly affected protein efficiency ratio (PER). When S1 fish was used, diets A and B gave similar PER. However, when S2 fish was used, diet A gave significantly higher PER (2.49 ± 0.02) among the treatments (P Key Words: Asian seabass, cannibalism, fingerling production, fish shelters, isocaloric high protein diet, Lates calcarifer Bloch, ‘shooter’ fish Abbreviations: ABL – average body length, ABW – average body weight, BL – body length, CP – crude protein, DO – dissolved oxygen, FCR – feed conversion ratio, NFE – nitrogen free extract, PER – protein efficiency ratio, ppt – parts per thousand, SEAFDEC/AQD – Southeast Asian Fisheries Development Center, Aquaculture Department, SGR – specific growth rate, TF – trashfish
Linkage of plant trait space to successional age and species richness in boreal forest understorey vegetation

Determining the changes in within‐ and between‐species functional diversity in plant communities, and their contribution to overall species trait overlap, can enhance efforts at understanding mechanisms of species coexistence. However, little is known about how variation in species functional diversity influences variation in species trait overlap among contrasting environments. Here, we studied the understorey vegetation in a well‐characterized 5000‐year‐old chronosequence involving 30 forested islands that differ greatly in size, soil fertility and species diversity. Across this chronosequence, we expected consistent changes in both within‐ and between‐species functional diversity that would lead to decreasing overall species trait overlap with increasing successional age, species richness, understorey vegetation density and spatial heterogeneity of soil resources. For each island, we measured specific leaf area (SLA) of each of ten individuals of each plant species present. Using a variance decomposition method, we partitioned the total community functional diversity of SLA on each island into within‐ and between‐species functional diversity. Further, we estimated overall species trait overlap as the ratio of within‐species functional diversity to total functional diversity. Using regression analyses, we then explored relationships of within‐ and between‐species functional diversity, and of overall species trait overlap, with several environmental variables across the 30 islands. Consistent with our hypotheses, overall species trait overlap decreased with successional age due to a statistically significant decrease in within‐species functional diversity, and decreased with species richness due to a simultaneous decrease in within‐species functional diversity and increase in between‐species functional diversity. Against our predictions, overall species trait overlap increased in more competitive environments and did not change with increasing spatial heterogeneity of soil N or P. Synthesis. Our study suggests niche packing as a key mechanism for species coexistence in plant communities. Using SLA as an integrator of plant ecological strategy, we show that community successional age and species richness are significantly linked to trait space distribution of plant individuals of boreal forest understorey vegetation and therefore to local species coexistence. Our results also suggest that the trait space of dominant and subordinate species may respond differently to local environmental variables.
Exploring Variability in Reads from Next Generation RNA-Sequencing Data

Next generation RNA-sequencing (RNA-seq) technologies have revolutionized the study of the transcriptome, allowing for estimation of RNA levels in a given population of cells or even in individual cells. The levels of mRNAs are most commonly examined as they are generally a good proxy for gene expression, an important variable in many studies. Much less commonly studied are the levels of tRNA. We investigated whether information about the levels of tRNA present in Escherichia coli provide useful information with regards to amino acid levels in the context of a larger metabolic characterization study. To this end, we found very little correlation but did observe several distinct patterns in tRNA read coverage that may suggest ﬂaws in read mapping or sequencing techniques when dealing with this type of RNA. Further work should be pursued to determine whether these patterns are biologically relevant or simply an artifact of the current sequencing and processing techniques.
Phosphoinositide 3-Kinase and p85/Phosphoinositide 3-Kinase in Platelets

Platelets exposed to thrombin or thrombin receptor agonist peptide (SFLLRN) activate phospholipase C and protein kinase C (PKC), and accumulate 3-phosphorylated phosphoinositides (3-PPI) as a function of the activation and relocalization of two cytoskeletally-associated phosphoinositide 3-kinases (PI 3-K): p85/PI 3-K and PI 3-K. We now report that exposure of platelets to PKC-activating β-phorbol myristate acetate (βPMA) does not stimulate PI 3-K, but rather stimulates p85/PI 3-K, which associates with the cytoskeleton. Wortmannin is an inhibitor of both PI 3-Ks, known to act with more potency on p85/PI 3-K. βPMA-stimulated 3-PPI accumulation is more sensitive to wortmannin (IC = 1.3 nM) than is SFLLRN- or thrombin-stimulated 3-PPI accumulation (IC = 10 nM). The activity of p85/PI 3-K in immunoprecipitates or in cytoskeletal fractions is inhibited more potently by exposure of platelets to wortmannin than is the activity of PI 3-K. βPMA or SFLLRN promotes the conversion of platelet integrin αβ into a fibrinogen-binding form required for platelet aggregation. Activation of αβ in response to βPMA or SFLLRN is inhibited by wortmannin with an IC of 1 nM in each case. Wortmannin inhibits neither activation of αβ by ligand-induced binding site antibody (anti-LIBS6 Fab) nor anti-LIBS6 Fab-induced platelet aggregation in the presence of fibrinogen, indicating that this type of “outside-in” signaling by αβ is largely PI 3-K-independent. We conclude that p85/PI 3-K, in preference to PI 3-K, contributes to activation of αβ when the thrombin receptor or PKC is stimulated.
Self-Regulated Pax Gene Expression and Modulation by the TGFβ Superfamily

The mammalian Pax gene family encode a set of paired-domain transcription factors which play essential roles in regulating proliferation, differentiation, apoptosis, cell migration, and stem-cell maintenance. Pax gene expression is necessarily tightly controlled and is associated with the demarcation of boundaries during tissue development and specification. Auto- and inter-regulation are mechanisms frequently employed to achieve precise control of Pax expression domains in a variety of tissues including the eye, central nervous system, kidney, pancreas, skeletal system, muscle, tooth, and thymus. Furthermore, aberrant Pax expression is linked to several diseases and causally associated with certain tumors. An increasing number of studies also relate patterns of Pax expression to signaling by members of the TGFβ superfamily and, in some instances, this is due to disruption of Pax gene auto-regulation. Here, we review the current evidence highlighting functional and mechanistic overlap between TGFβ signaling and Pax-mediated gene transcription. We conclude that self-regulation of Pax gene expression coupled with modulation by the TGFβ superfamily represents a signaling axis that is frequently employed during development and disease to drive normal tissue growth, differentiation and homeostasis.
DNA barcoding and morphology reveal exceptional species diversity of Scoparia (Lepidoptera: Crambidae) from the Hailuogou Glacier area, China

The genus Scoparia from the Hailuogou Glacier area in the south-eastern fringe of the Tibetan Plateau of south-western China is studied, nine species are revealed by combining DNA barcoding (658 bp of the mitochondrial gene cytochrome c oxidase subunit I, COI) and morphology. Studies show that Scoparia species from the Hailuogou Glacier area are 37.5% as many as all the previously known congeners in China. Six species are described as new to science: Scoparia simplicissima Li sp. nov., Scoparia tribulosa Li sp. nov., Scoparia longispina Li sp. nov., Scoparia gibbosa Li sp. nov., Scoparia globosa Li sp. nov., and Scoparia annulata Li sp. nov. The female of Scoparia metaleucalis is described for the first time herein. All species are either diagnosed or described and illustrated, and a map of China showing the topography and localities where Scoparia species are recorded is also provided, including the species number of all the recorded localities. The results reveal the exceptional species diversity of Scoparia from the Hailuogou Glacier area, as well as demonstrate that the integration of DNA barcoding and morphological approaches is highly effective for indentifying scopariine moths in the Hailougou glacier area. All the studied specimens are deposited in the Insect Museum, Jiangxi Agricultural University, Nanchang, China. © 2014 The Linnean Society of London
Evaluation of NRC (2000) model energy requirement and DMI equation accuracy and precision for wintering beef cows in western Canada

Three years of winter feeding trials using 90 Angus cows (15 pens of six cows) fed typical western Canadian wintering diets formulated to stage of pregnancy were used to evaluate National Research Council (NRC 2000) energy requirement and dry matter intake (DMI) equation accuracy and precision. Data collection included pen DMI, individual cow weights, body condition scores, calving dates and weights, and daily environmental temperature. Diet energy density was estimated from nutrient analysis of composited weekly feed samples. Equation evaluations compared observed and predicted DMI and conceptus corrected average daily gain (ADG) for the second and third trimesters using regression, means comparison, concordance correlation coefficient (CCC), and total deviation index (TDI) methods. Across all 3 yr, second trimester DMI was over-predicted (P < 0.01) with low precision (CCC = 0.24, TDI90 = n/a) using actual environmental conditions, but not (P = 0.34) when assuming thermal neutral (TN) conditions, althoug.