Miracle-dz/UniFAR-FTUs huggingface dataset:
Note on using nuclear 28S rDNA for sequencing ancient and strongly degraded insect DNA

A protocol using insect specimens or parts thereof allows for sequencing of sections of nuclear 28S rDNA. In the present note it is demonstrated that this protocol can readily be applied to strongly degraded DNA (ancient, fixed or contaminated). Primers that are specifically designed to discriminate against human DNA but also other non‐arthropod species are tested on a range of species covering all insect groups (59 insect species from all 33 orders). Additionally, the samples represent a selection of various, mostly DNA‐degrading, preservation methods, including the most common fixatives used for morphological investigations and for long‐term storage in collections. Successful amplification was possible for all tested samples including ca. 200 year‐old dried museum specimens as well as for over 4000 year‐old fossil insects embedded in copal. When the NCBI database contained information on the tested species an unambiguous taxonomic discrimination was possible. This approach is based on a standardized protocol that guarantees easy application. This note presents primer pairs for 28S rDNA that can be a useful tool for ancient DNA (aDNA) research.
Fractional Configurational Analysis And a solution to the Manhattan problem

Configurational analysis has been a very robust and successful tool to the understanding how space and occupation interact. There has been little work to date that tries to refine the core procedure of configuration to see if it is possible to improve on current correlations or remedy problems. This paper attempts to show that such an exploration is potentially rewarding by identifying a new method of fractional configurational analysis. One variant of this fractional configuration is explored which takes angle into account. This new fractional configuration appears to result it a reduction of the centralising effects common to large infinite radius axial-line maps. Future extensions of this work are then discussed.
Hypoxic areas, density-dependence and food limitation drive the body condition of a heavily exploited marine fish predator

Investigating the factors regulating fish condition is crucial in ecology and the management of exploited fish populations. The body condition of cod (Gadus morhua) in the Baltic Sea has dramatically decreased during the past two decades, with large implications for the fishery relying on this resource. Here, we statistically investigated the potential drivers of the Baltic cod condition during the past 40 years using newly compiled fishery-independent biological data and hydrological observations. We evidenced a combination of different factors operating before and after the ecological regime shift that occurred in the Baltic Sea in the early 1990s. The changes in cod condition related to feeding opportunities, driven either by density-dependence or food limitation, along the whole period investigated and to the fivefold increase in the extent of hypoxic areas in the most recent 20 years. Hypoxic areas can act on cod condition through different mechanisms related directly to species physiology, or indirectly to behaviour and trophic interactions. Our analyses found statistical evidence for an effect of the hypoxia-induced habitat compression on cod condition possibly operating via crowding and density-dependent processes. These results furnish novel insights into the population dynamics of Baltic Sea cod that can aid the management of this currently threatened population.
Allometric Equations for Tropical Seasonal Deciduous Forests in Cambodia: A Method of Estimating Belowground Tree Biomass with Reduced Sampling Loss of Roots

There is an urgent need to estimate the biomass of tropical seasonal forests in central Indochina, which have suffered from deforestation and degradation. However, allometric equations specific to such forests are limited. In this study, we destructively sampled 28 trees in a deciduous forest in Kratie Province, Cambodia, and developed new allometric equations for estimating the tree-level biomass of aboveground woody parts (trunk + branches), leaves, total aboveground parts (trunk + branches + leaves), and that of belowground parts (BGB). The sampling of belowground parts is usually very laborious and time-consuming, and entails inevitable root loss during excavation. Thus, it is difficult to accurately quantify tree-level BGB, especially for large trees. We used a new sampling method (called the mound method) to reduce the sampling loss of BGB. The percentage of BGB sampling loss (ratio of sampling loss estimated by the mound method to total BGB) averaged 28.9%. Our models estimated the stand-level biomass of a deciduous dipterocarp forest in Kratie to be 81.9 ± 45.1 Mg ha -1 . The allometric equations and tree-level biomass data presented here will support activities related to REDD+. Discipline
Epiploic Appendagitis Masquerading as Acute Appendicitis: A Report of Two Cases

Epiploic appendagitis (EA) is a rare clinical entity caused by an inflammatory/ischemic process involving the serosal outpouchings of the colon. Its clinical presentation of acute, localised, lower abdominal pain often mimics more common conditions like diverticulitis or appendicitis. The diagnosis of EA is challenging due to the lack of pathognomic clinical features. The definitive diagnosis primarily relies on cross-sectional imaging modalities like abdominal ultrasound or computed tomography (CT). Being a benign and self-limiting condition, it can be managed conservatively with analgesic and anti-inflammatory drugs. We present two cases to highlight EA as an important differential diagnosis for cases of acute lower abdominal pain, crucial to prevent unnecessary antibiotic therapy and surgical interventions.
Observations on the Breeding Biology of Passerines in a Seasonally Flooded Savanna in Venezuela

AasraKr. -The breeding biology of passerines was studied in a seasonally inundated savanna in the llanos of western Venezuela. A total of 4 12 nests of 36 species were located, and other evidence of breeding activity was observed for 13 additional species. Most species bred principally in the early half of the wet season, sometimes starting very late in the dry season. Other species bred throughout the wet season, although generally with a gradual decline in the latter half. A few species bred principally or entirely in the latter half of the wet season. Ground-nesting species bred principally, and often exclusively, at the beginning and end ofthe wet season, avoiding the main part of the rains. The Shiny Cowbird (Molothrus bonariensis) was a brood parasite on four species, with two important host species, the Pied Water-Tyrant (Fluvicola pica) and the White-headed Marsh-Tyrant (Arundinicola leucocephalu). The first known nest of the River Tyrannulet (Serpophuga hypoleucu) and the first known breeding north of the Amazon River for the transequatorial migrant Yellow-browed Tyrant (Sutrupa icterophrys) are described. Natural history information is presented for the little-known White-naped Xenopsaris (Xenopsuris albinucha), and for the Yellow-browed Sparrow (Ammodramus aurifons) and the Grassland Sparrow (A. humeralis) in one of the few known areas of sympatry. Received 20 May 1988, accepted 15 Sept. 1988. The savannas (llanos) in Colombia and Venezuela cover an area of approximately half a million km2, constituting the largest uninterrupted surface of neotropical savanna north of the equator (Sarmiento 1984). The llanos constitute approximately a third of the surface of Venezuela, and dominate the landscape in the plains that surround the Orinoco River. The Venezuelan llanos have two dominant types: Trachypogon savannas (which are nearly treeless in the east and semi-wooded in the central llanos and the Andean Piedmont), and the seasonally flooded savannas in the west (Fig. 1) (Ramia 1967). The passerine avifauna of the llanos, especially of the flooded savannas, is imperfectly known. Basic distribution and ecological information is included in Meyer de Schauensee (1964) and Hilty and Brown (1986) for Colombia, and in Phelps and Phelps (19X$1963) and Meyer de Schauensee and Phelps (1978) for Venezuela. Species lists, with varying amounts of additional information, have been provided for the Colombian llanos by Olivares (1974), Barreto (198 l), and Fumiss (unpubl. data), and for the eastern and central Venezuelan llanos by Berlepsch and Hartert (1902) ’ Dept. Environmental, Population, and Organismic Biology, Univ. Colorado, Boulder, Colorado 8030902334.
Suplementasi Minyak Ikan Lemuru dan Niacin terhadap Kolesterol dan Trigliserida Serum Darah Kambing Lokal

ABSTRAK Penelitian ini bertujuan untuk mengevaluasi pengaruh penggunaan minyak ikan lemuru dan niacin terhadap kandungan kolesterol (kolesterol total, K-LDL dan K-HDL) dan trigliserida serum darah kambing lokal. Penelitian menggunakan Rancangan Acak Lengkap dengan 2 faktor perlakuan. Faktor pertama adalah taraf pemberian minyak ikan lemuru (0%, 1% dan 2 %) dan faktor kedua pemberian niacin 0 ppm dan 400 ppm, tiap kombinasi perlakuan diulang 4 kali. Kambing lokal yang digunakan sebanyak 24 ekor dengan umur sekitar 6 bulan dan berjenis kelamin jantan. Pakan yang diberikan berupa konsentrat dengan kandungan protein 14% sebanyak 1% dari bobot badan dalam bentuk bahan kering.Sedangkan pakan hijauan yang diberikan sebanyak minimal 10% dari bobot ternak. Pengamatan dilakukan selama 2 bulan dengan masa adaptasi lebih kurang 2 minggu. Kandang yang dipergunakan adalah kandang panggung dengan system individual dengan ukuran 1.5 x 2 m/ 4 ekor. Variabel yang diambil meliputi: Kadar kolesterol total, kadar LDL ( Low Density Lipid) dan HDL (Hight density Lipid) serum darah dan trigliserida. Hasil penelitian menunjukkan bahwa tidak terdapat interaksi (P>0,05) antara minyak ikan lemuru dan niacin pada kandungan kolesterol, LDL dan HDL dalam serum darah kambing. Namun terhadap kandungan trigliserida menunjukkan interaksi (P<0,05). Perlakuan lemuru 2% secara nyata (P<0,05) menurunkan kadar kolesterol darah kambing (97.92 mg/dl) dan kadar HDL serum menjadi 29.25 mg/dl. Sedangkan kadar LDL pada perlakuan pemberian minyak ikan lemuru 2% secara nyata (P<0,05) mengalami penurunan ( 44.95 mg/dl). Demikian juga halnya dengan perlakuan pemberian niacin 400 ppm secara nyata (P<0,05) menyebabkan kolesterol turun (109.46 mg/dl), LDL turun ( 61.62 mg/dl). Sedangkan kandungan trigliserida dipengaruhi secara nyata (P<0,05) oleh pemberian minyak ikan lemuru dan Niacin, kombinasi perlakuan minyak ikan lemuru 2% dan Niacin 400 ppm mampu menurunkan kadar Trigliserida serum darah menjadi 99.46 mg/dl. Kata kunci: Niacin, Minyak ikan lemuru, Kolesterol, HDL, LDL, Trigliserida.
Abiotic factors affecting the foraging activity and potential displacement of native ants by the invasive African big-headed ant Pheidole megacephala (Fabricius, 1793) (Hymenoptera: Formicidae)

The African big-headed ant, Pheidole megacephala, is a widespread invasive species that threatens native ecosystems and has been implicated in the decline of native ants. Although the consequences of P. megacephala invasion have been relatively well studied, the mechanisms responsible for success remain unclear. We examined the survival of P. megacephala under differing thermal conditions in the laboratory, as well as daily and seasonal variation in foraging activity in disturbed urban bushland. In two comparable sets of laboratory experiments, high temperatures had a strong negative effect on worker survival of P. megacephala, particularly under low moisture conditions. In contrast, common native species of Iridomyrmex had significantly greater survival at high temperatures. Foraging activity of P. megacephala at baits was directly related to variation in soil surface temperatures. In addition, proportional bait occupancy by P. megacephala was higher during warm seasons (early autumn) than during cool seasons (early spring), and in autumn, bait occupancy was higher in the cool morning than in the warmer afternoon (all these effects were moderated by significant variation among sites). In contrast, native ants dominated baits under warmer afternoon conditions, with almost no cooccurrence of native ants with P. megacephala. This study suggests that daily and seasonal variation in abiotic conditions can modify the dynamics of P. megacephala foraging interactions with native ants, thereby affecting local community dynamics.
Applications of Mathematical Optimization Methods to Digital Communications and Signal Processing

Applications of Mathematical Optimization Methods to Digital Communications and Signal Processing Spencer Giddens Department of Mathematics, BYU Master of Science Mathematical optimization is applicable to nearly every scientific discipline. This thesis specifically focuses on optimization applications to digital communications and signal processing. Within the digital communications framework, the channel encoder attempts to encode a message from a source (the sender) in such a way that the channel decoder can utilize the encoding to correct errors in the message caused by the transmission over the channel. Low-density parity-check (LDPC) codes are an especially popular code for this purpose. Following the channel encoder in the digital communications framework, the modulator converts the encoded message bits to a physical waveform, which is sent over the channel and converted back to bits at the demodulator. The modulator and demodulator present special challenges for what is known as the two-antenna problem. The main results of this work are two algorithms related to the development of optimization methods for LDPC codes and the two-antenna problem. Current methods for optimization of LDPC codes analyze the degree distribution pair asymptotically as block length approaches infinity. This effectively ignores the discrete nature of the space of valid degree distribution pairs for LDPC codes of finite block length. While large codes are likely to conform reasonably well to the infinite block length analysis, shorter codes have no such guarantee. Chapter 2 more thoroughly introduces LDPC codes, and Chapter 3 presents and analyzes an algorithm for completely enumerating the space of all valid degree distribution pairs for a given block length, code rate, maximum variable node degree, and maximum check node degree. This algorithm is then demonstrated on an example LDPC code of finite block length. Finally, we discuss how the result of this algorithm can be utilized by discrete optimization routines to form novel methods for the optimization of small block length LDPC codes. In order to solve the two-antenna problem, which is introduced in greater detail in Chapter 2, it is necessary to obtain reliable estimates of the timing offset and channel gains caused by the transmission of the signal through the channel. The timing offset estimator can be formulated as an optimization problem, and an optimization method used to solve it was previously developed. However, this optimization method does not utilize gradient information, and as a result is inefficient. Chapter 4 presents and analyzes an improved gradient-based optimization method that solves the two-antenna problem much more efficiently.
PERTURBATION OF A STATIONARY SOLUTION OF A NONLINEAR CONSERVATIVE SYSTEM UNDER RESONANCE CONDITIONS

This work develops a method of perturbation of a stationary solution of a nonlinear conservative system. In the reference solution the frequencies depend on the momenta, that is, the fundamental frequencies of the reference solution are amplitude dependent and for some values of the momenta are linearly dependent. The basic assumption is that the Hamiltonian of the system can be expanded in terms of an n-dimensional convergent Fourier Series with the usual property that the magnitude of the coefficients decreases quadratically with the increase in frequency of the angular variables associated. The Hamiltonian is reduced to a simple form by means of a number of canonical transformations. The method is applied to a nonlinear oscillator and to the motion of a geostationary artificial satellite.
Cell Signaling Mechanisms of Sperm Motility in Aquatic Species

Initiation and activation of sperm motility are prerequisite processes for the contact and fusion of male and female gametes at fertilization. The phenomena are under the regulation of cAMP and Ca 2+ in vertebrates and invertebrates. Mammalian sperm requires Ca 2+ and cAMP for the activation of sperm motility. Cell signaling for the initiation and activation of sperm motility in the ascidians and salmonid fishes has drawn much attention. In the ascidians, the sperm-activating and attracting factors from unfertilized egg require extracellular Ca 2+ for activating sperm motility and eliciting chemotactic behavior toward the egg. On the other hand, the cAMP-dependent phosphorylation of protein is essential for the initiation of sperm motility in salmonid fishes. A decrease of the environmental K + concentration surrounding the spawned sperm causes K + efflux and Ca 2+ influx through the specific K + channel and dihydropyridine-sensitive L-/T-type Ca 2+ channel, respectively, thereby leading to the membrane hyperpolarization. The membrane hyperpolarization induces synthesis of cAMP, which triggers further cell signaling processes, such as cAMP-dependent protein phosphorylation, to initiate sperm motility in salmonid fishes. This article reviews the studies on the physiological mechanisms of sperm motility and its cell signaling in aquatic species.
Character diversification and patterns of evolution in early vascular plants

Available data on the stratigraphic ranges of latest Silurian and Devonian vascular plant macro-fossils (sporophytes) and spores provide insights into the tempo and mode of early tracheophyte evolution. Patterns of diversification, origination, and extinction conform in general to the predictions of Sepkoski's kinetic model of diversification. Rates of generic origination and extinction vary not only through time but also between organ systems for a single time interval. This fact, coupled with data on longevity and turnover and comparative morphological observations, can be used to document mosaic evolution in early vascular plant history. Mosaic evolution is an important theme in plant evolution; indeed, what we recognize as macroevolutionary events often correlate with brief periods of pronounced mosaicism. Such evolutionary patterns reflect the developmental biology of tracheophytes in which individual organs often have life spans that are considerably shorter than the life of the whole plant. Under these conditions, individual organs or organ systems can respond to different sets of evolutionary pressures. The major period of early vascular plant diversification occurred during the late Early and early Middle Devonian Period, 30 Myr or more after the origin of the group. Such lags in diversification are not uncommon in the fossil record. Sometimes they reflect extrinsic controls on diversification, but in other cases they appear to be a consequence of intrinsic rates of origination and extinction.
Effect of Terminalia Arjuna against Arsenic-Induced Renal Toxicity in Mice

Arsenic is an established toxin to both renal and neuronal system. It induces oxidative stress through free radical formation within the renal system. Clinical effects of arsenic toxicity depend on chronicity. Acute renal damages are very common patho- physiological disturbances that are caused by arsenic. The present study is conducted to evaluate the protective role of the aqueous extract of Termnalia arjuna bark. T. arjuna is an important plant of Indian origin that is widely used against kidney disorders (renal failures). Antioxidant level in the kidney is estimated by the activity of antioxidative enzymes like superoxide dismutase (SOD), glutathione-s-transferase (GST), glutathione reductase (GR) reduced glutathione (GSH) and thiobarbutaric acid reactive substances (TBARS). Mice were first treated with the aqueous extract of T. arjuna (100 mg/kg body weight) for two week and then subjected to arsenic trioxide toxicity (5 mg/kg body weight). The results shows a remarkable rise in TBARS level along with the significant diminution of GSH, SOD, GST, GR levels in the kidney tissues. The results were further analyzed for the antioxidant activity. The aqueous extract of T. arjuna possesses a strong free radical scavenging activity. The results suggested that the T. arjuna extracts can protect kidney tissues against arsenic-induced oxidative stress probably by increasing antioxidative defense activities.
Effects of cytochalasin B on the morphogenesis of explanted early chick embryos.

: Effects of cytochalasin B (CB) on chick embryos explanted at stages 4-5 and cultured for 24 hours were studied. CB (2-4 mug/ml) inhibited blastodermal expansion and neural tube closure in over 90% of the embryos. Somite formation was inhibited only where neural tissue was very degenerate. The development of other structures was usually unaffected. Cellular degeneration occurred in severely affected neuroepithelium, but cells at various phases of mitosis were found throughout its thickness, suggesting that interkinetic nuclear migration had been inhibited. Electron microscopic studies of the flattened neural tube showed that CB disrupted microfilaments and reduced the number of cytoplasmic extensions, but had no apparent effect on microtubules and other organelles. These effects were reversible. Futhermore, dimethyl sulfoxide, at 0.2-0.4% (concentrations present in 2-4 mug/ml CB medium), had no adverse effect, indicating that the observed abnormalities were direct consequences of CB treatment.
Effect of the Inclusion of Organic Copper, Manganese, And Zinc in The Diet of Layers on Mineral Excretion, Egg Production, and Eggshell Quality

This study aimed at evaluating the replacement of inorganic copper, manganese, and zinc sources by organic sources in the diet of laying hens during the second laying cycle in trace mineral excretion, egg production, and eggshell quality. Two hundred and fifty 100-week-old Dekalb hens were distributed according to a completely randomized design into five treatments with five replicates of ten birds each. The control treatment consisted of a basal diet with all trace minerals in the inorganic form. The other treatments consisted of a basal diet with a mixture of the minerals copper, manganese, and zinc in the organic form with concentrations of 100%, 90%, 80%, and 70% of the levels of inclusion of inorganic mineral sources in the control treatment. Trace mineral excretion was determined in five layers per treatment by the method of total excreta collection. Excreta trace mineral contents were determined by atomic absorption spectrophotometry. Egg production and eggshell quality were determined by the mass of the eggs and the egg specific gravity, respectively. For all trace minerals examined, the dietary supplementation with organic sources reduced trace mineral excretion compared with the control group, even at 70% inclusion level, without compromising egg production or eggshell quality. The replacement of the inorganic trace mineral sources by organics source effectively reduced the excretion of copper, manganese, and zinc by laying hens in the second laying cycle.
VARIATIONAL BOUNDS FOR MULTIPHASE ANISOTROPIC ELASTIC COMPOSITES WITH SPHERICAL, CYLINDRICAL AND SPHEROIDS GEOMETRIC SHAPE OF INCLUSIONS

Using the spherical and deviator decomposition of the polarization and strain tensors, a general algorithm for the calculation of variational bounds for any type of anisotropic linear elastic composite as a function of the properties of the comparison body is presented. This procedure is applied in order to obtain analytical expressions of bounds for multiphase, linear elastic composites with spherical, cylindrical and spheroids geometric shapes of the inclusions. Numerical calculations and some comparisons with other models and experimental data are shown.