Miracle-dz/UniFAR-FTUs huggingface dataset:
Territoriality, Reproductive Behavior, and Parental Care in Gray Triggerfish, Balistes capriscus, from the Northern Gulf of Mexico

We documented spawning behaviors in gray triggerfish, Balistes capriscus (Gmelin, 1789), in June and July 2004-2007 on artificial reefs in the northern Gulf of Mexico, including territoriality, nest building, harem spawning, and parental care. Males were significantly larger than females and could be distinguished from females by size and dark charcoal coloration during the spawning season. Pre-fertilization dominant males were observed building and maintaining one to 13 demersal nests at particular reef sites, aggressively defending the immediate area surrounding the nests against other male gray triggerfish and other fishes, while attracting one to five females to spawn. Pre-fertilization females were observed frequently visiting and inspecting the newly constructed nest. Post-fertilization females stayed continuously on the nest guarding the eggs, and displayed a contrasting white and black color pattern, while fanning and blowing the eggs. Post-fertilization males continued to defend a territory immediately around the nest, visiting the female on the nest, and chasing other fish away. Actual spawning behavior was observed where a male and female tightly circled each other within the nest, with fertilized eggs produced immediately after this circling. Active nests with a guarding female and male were observed 28 times on 18 different reef sites. Mean number of eggs per spawning event was 772,415 from 13 active nests each with a guarding female. Observations of aggressive male behavior and sex ratios of single dominant male and up to five spawning-condition females indicate that gray triggerfish display harem spawning behavior.
UV‐B EFFECTS ON TERRESTRIAL PLANTS

The potential impacts of an increase in solar UV‐B radiation reaching the Earth's surface due to stratospheric ozone depletion have been investigated by several research groups during the last 15 years. Much of this research has centered on the effects of plant growth and physiology under artificial UV‐B irradiation supplied to plants in growth chambers or greenhouses. Since these artificial sources do not precisely match the solar spectrum and due to the wavelength dependency of photobiol‐ogical processes, weighting functions, based on action spectra for specific responses, have been developed to assess the biological effectiveness of the irradiation sources and of predicted ozone depletion. Recent experiments have also utilized artificially produced ozone cuvettes to filter natural solar radiation and simulate an environment of reduced UV‐B for comparative purposes.
Molecular systematics of the New Zealand Pachycladon (Brassicaceae) complex: Generic circumscription and relationships to Arabidopsis sens. lat. and Arabis sens. lat.

Abstract Nuclear ribosomal DNA ITS sequence data were used to assess the relationships of Cheesemania, Ischnocarpus, and Pachycladon to each other and to other genera in the Brassicaceae. Phylogenetic analyses are congruent with other studies that infer the Pachycladon complex (including Pachycladon, Cheesemania, and Ischnocarpus) is monophyletic. The complex occurs within an Arabidopsoid clade that includes Arabidopsis and the recently recognised segregate genera Beringia, Crucihimalaya, Olimarabidopsis, and Pseudoarabidopsis, and the Arabis segregates Boechera and Turritis. The Pachycladon complex is sister to Beringia and Crucihimalaya, and forms a distinct New Zealand lineage. Molecular clock estimates suggest the Pachycladon complex diverged from its nearest relatives between 1.0 and 3.5 million years ago. The close relationship of Cheesemania, Ischnocarpus, and Pachycladon is reflected in low (<2.6%) sequence divergence values, high bootstrap support (98%), and the lack of a well‐resolved topology in the phylogenetic trees. Morphological characters and data from previous studies of intergeneric hybrids and DNA Amplified Fragment Length Polymorphisms, support the recircumscription of Pachycladon to include species placed in Cheesemania and Ischnocarpus. New combinations are made in Pachycladon for species previously placed in Cheesemania and Ischnocarpus. A new name, P. cheesemanii, is presented for Ischnocarpus novae‐zelandiae as that species epithet is preoccupied in Pachycladon.
Genetic Relationships Among Chum Salmon Populations in Southeast Alaska and Northern British Columbia

Allozymes from 46 loci were analyzed from chum salmon (Oncorhynchus keta) collected at 61 locations in southeast Alaska and northern British Columbia. Of the 42 variable loci, 21 had a common allele frequency <0.95. We observed significant heterogeneity within and among six regional groups: central southeast Alaska, Prince of Wales Island area, southern southeast Alaska – northern British Columbia, north-central British Columbia, and two groups in the Queen Charlotte Islands. Genetic variation among regions was significantly greater than within regions. The three island groups were distinct from each other and from the mainland populations. Allele frequencies were stable over time in 14 of 15 locations sampled for more than 1 yr. The geographic basis for heterogeneity among regions is confounded in part by spawning-time differences. The Prince of Wales and Queen Charlotte populations spawn in the fall; the mainland populations spawn mainly in the summer, although some overlap exists. Overall, most genetic.
Vibrational spectra of lactic acid and lactates

The Raman and IR spectra of lactic acid and sodium lactate in aqueous solution and methyl lactate as a pure liquid were recorded from 3600 to 100 cm -1 . Vibrational assignments are proposed for the three compounds. The effects of hydrogen bnoding on the δOH vibrations of the hydroxyl alcohol groupwere studied and the results suggest both inter- and intra-molecolar hydrogen-bonded association
OneG-Vali: a computational tool for detecting, estimating and validating cryptic intermediates of proteins under native conditions

Understanding structural excursions of proteins under native conditions at residue level resolutions is crucial to map energy landscapes of proteins and also to solve the ‘Levinthal paradox’ of protein folding. Native-state hydrogen–deuterium (NS H/D) exchange methods are powerful to structurally characterize cryptic intermediates (CIs) populating sparsely in the unfolding kinetics of proteins under conditions favoring folded conformations of the proteins. However, the methods are not applicable to proteins that are susceptible to denaturation or degradation or aggregation in the course of exchange experiments and also to proteins that are smaller in size (<10 kDa) in general. We have herein demonstrated a novel computational tool, OneG-Vali, which predicts the possible existence of cryptic intermediates of proteins in a qualitative and quantitative manner. And, the tool validates the prediction efficiency by comparing multistate unfolding curves defined by the tool with pseudo two-state unfolding curves of the proteins determined by macroscopic methods. In addition, the OneG-Vali facilitates accounting for the effect of cis–trans proline isomerization on estimating the population of CIs defined by the tool and also by experimental methods. The prediction accuracy of the tool is validated using proteins such as cytochrome c, apocytochrome b562, the third domain of PDZ and T4 lysozyme. The OneG-Vali is implemented using CGI-Perl and it can be freely accessed and instantly used at http://sblab.sastra. edu/oneg-vali.html.
Glycogen synthase kinase‐3β: homologous regulation of cell surface insulin receptor level via controlling insulin receptor mRNA stability in adrenal chromaffin cells

In cultured bovine adrenal chromaffin cells, 48 h‐treatment with 20 mmol/L LiCl, 1 mmol/L valproic acid, 30 μmol/L SB216763, 30 μmol/L SB415286, or 100 nmol/L insulin, a condition that inhibits constitutive active glycogen synthase kinase‐3 (GSK‐3), decreased cell surface 125I‐insulin binding capacity by ∼39%, without altering the Kd value; LiCl, SB216763 or insulin decreased insulin receptor (IR) and IR precursor levels, attenuating insulin‐induced Tyr‐autophosphorylation of IR. LiCl increased inhibitory Ser9‐phosphorylation of GSK‐3β at 6 h, decreasing 125I‐insulin binding at 24 h. SB216763‐induced 125I‐insulin binding reduction (IC50 = 3 μmol/L) was preceded by β‐catenin level increase by SB216763 (EC50 = 11 μmol/L), a hallmark of GSK‐3 inhibition. Insulin‐induced rapid (> 1 min) Ser9‐phosphorylation of GSK‐3β ( Nemoto et al. 2006 ) was followed by ∼48% decrease of IR level. LiCl did not stimulate endocytosis, nor proteolysis of IR. LiCl destabilized IR mRNA (t1/2 = 9.3 vs. 6.5 h), decreasing IR mRNA level by ∼47%, without altering IR gene transcription. Decreases of 125I‐insulin binding and IR level, as well as increased Ser9‐phosphorylation of GSK‐3β were restored to the control levels by washing the test compound‐treated cells. Thus, GSK‐3β regulates IR level via controlling IR mRNA stability.
Comparison of methods for regression interval mapping in QTL analysis with non-normal traits

We compare the powers of three methods for the QTL analysis of non-normally distributed traits. We describe the nonparametric and the logistic regression approaches recently proposed in the literature and study the properties of the standard regression interval mapping method when the trait is not normally distributed. It is shown that the standard approach is robust against non-normality and behaves quite well for both continuous and discrete characters. The loss of power compared with the nonparametric or the logistic approach is generally minor. Moreover, the least squares estimation procedure of the regression interval mapping is not affected by departure from normality. The use of other approaches could be restricted to extreme cases where the trait distribution is very skewed.
Typology Revisited: Historical Taxa of the Bean Goose - Pink-Footed Goose Complex

Ruokonen M. & Aarvak T. 2011. Typology revisited: historical taxa of the bean goose — pink-footed goose complex. Ardea 99: 103–112. Taxonomic practices change over time and this affects the number of taxonomical units recognized. In late 19th and early 20th centuries the number of species increased as a consequence of typological thinking, i.e. classifying all aberrant individuals to a separate species. During this period, several species or subspecies of the bean goose complex were described, and currently their status is either considered not valid or is not agreed upon. We studied individuals from five of the historical taxa, Anser neglectus, A. mentalis, A. oatesi, A. fabalis johanseni and A. fabalis curtus, by using mitochondrial DNA and morphological measurements to clarify their taxonomical status. Overall, we did not find support for additional taxa other than those currently recognized.
Food resources of shredders and other benthic macroinvertebrates in relation to shading conditions in tropical Hong Kong streams

Summary 1. Gut content analyses (GCA) of benthic macroinvertebrates, supplemented by carbon and nitrogen stable isotope analyses (SIA), were used to determine the relative contribution of leaf litter and autochthonous food sources to consumer biomass in five shaded and five unshaded streams in tropical Hong Kong. 2. Only four obligate shredders and two facultative shredders were identified out of 58 morphospecies dissected. Non-shredder taxa consumed little (<23% food eaten) coarse particulate organic matter (CPOM) in spite of its abundance in streams, and GCA revealed that fine particulate organic matter was the major food (25–99%) of most primary consumers. 3. Stable isotope analysis results were in general agreement with the findings of GCA, and confirmed that three of the four obligate shredders had a high dependence (55–78% of assimilated carbon) on CPOM. 4. Autochthonous energy sources were important in all streams: non-shredding primary consumers examined, which accounted for 72% of total macroinvertebrate abundance in shaded streams, derived (on average) 61% of their biomass from autochthonous foods; the equivalent values for unshaded streams were 72% (abundance) and 71% (biomass).
DEVELOPMENT OF MULTIPLEX PCR BASED ASSAY FOR THE CONCURRENT DETECTION OF PATHOGENIC MICROORGANISMS

Objective: Salmonella enterica is an important enteric pathogen which causes gastroenteritis and enteric fever in humans and is widely spread in nature. Outbreaks of Salmonella infections are frequently reported in both developed and developing countries, as this pathogen spreads very rapidly by means of water and the food chain. Methods: A multiplex PCR (mPCR) assay was developed for the detection of multiple Salmonella serotypes in different kind of food products. To increase specificity of this molecular method, three sets of oligonucleotide primer were used to detect the most prevalent salmonella species. Different primer pairs were used for the optimization of the multiplex PCR. The primer pair, ST FW and ST RV, was specific to Salmonella typhi and targeted a randomly selected sequence of 600bp. The primer pair SPFW and SPRV specific to Salmonella paratyphi for a sequence of 800 bp in length. Likewise, the primers pairs SEFW and SERV were designed to amplify a sequence of about 1000bp from S. enterica . Results: The Salmonella strains tested in this study were Salmonella typhi , Salmonella enterica and Salmonella Paratyphi . The STFW/STRV primer pair amplified 600bp DNA fragments when the DNA templates from Salmonella typhi , Salmonella enteritidis , Salmonella enterica and Salmonella paratyphi were tested. Conclusion: The DNA template of Salmonella paratyphi specifically amplified 800-bp fragments. Likewise, the DNA template for Salmonella enterica amplified 1000-bp fragment. This technique can be used routinely for the rapid detection of Salmonella spp. in food materials at low level of contamination with an enrichment time that depends in complexity of the food product. Keywords: Multiplex PCR, Salmonella, Optimization of PCR
Actions of GnRH Agonists on Gonadotrope Physiology

In the early 1970s, the characterization of the decapeptide structure of gonadotropin-releasing hormone (GnRH) by the independent research teams of Guillemin and Schally led directly to the creation of pharmacologic analogues that could influence luteinizing hormone (LH) and follicle-stimulating hormone (FSH) in a readily reversible fashion in the presence or absence of gonadal steroids. GnRH agonists and antagonists soon evolved into important diagnostic and clinical tools that suppressed and/or stimulated gonadotropin secretion in numerous physiologic or pathologic states. GnRH agonists are generated by ethylamide modification at the carboxy-terminal glycine (position 10) and, more importantly, by substitution of D amino acids containing bulky hydrophobic side groups at position 6. The latter substitutions stabilize a spatial conformation necessary for activation of post-receptor mechanisms and block biodegradation through hydrolysis by endogenous peptidases. These modifications endow these compounds with greater affinities for the GnRH receptor, enhanced abilities to activate postreceptor mechanisms, and biologically effective half-lives that are dramatically increased above that of the native decapeptide. As a result, agonists such as Leuprolide (Abbott Labs), Buserilin (Hoechst), and Nafarelih (Syntex) stimulate gonadotropin release up to 200-fold more effectively than native GnRH. However, prolonged treatments with GnRH agonists have routinely eventuated in very low immunoreactive and even lower bioactive levels of LH and FSH in the circulation and the subsequent collapse of gonadal steroid output. Significantly, the Food and Drug Administration approved the use of these pharmacologic agents for the treatment of precocious puberty, endometriosis, and prostate cancer, pathologies that benefit from these suppressive actions on gonadotroph and gonadal function. In contrast, GnRH antagonists are characterized by modifications of the pyroglutamic and glycine amide termini (positions 1 and 10) or deletions and substitutions of hydrophobic D-amino acids at positions 2 and 3. GnRH antagonists actively bind to the GnRH receptor on the cell membrane of the gonadotroph but, unlike GnRH agonists, exert no physiologic effect on gonadotropin synthesis or secretion. As a result, these analogues compete with the native neurohormone for binding to the receptor and block fully most responses to GnRH. Such activity suggests that the amino terminal region is involved in the activation of the postreceptor mechanisms necessary for GnRH actions. Unfortunately, the bioactivity of many GnRH antagonists is low relative to GnRH and they also display histaminereleasing properties. However, such drawbacks are not characteristic of two newly developed antagonists: Antide (Serono) and Ganirelix (Syntex). Nonetheless, since there is no clinically available GnRH antagonist to replace GnRH agonists when gonadal suppression is desired, the following discussion will focus on topics relevant to our understanding of the actions of GnRH agonists to stimulate and suppress gonadotropin secretion.
CO2: Different interpretation of the same data

From the complex topic, fundamental and com-prehensible arguments are selected and pre-sented so that the effect of atmospheric CO2concentration on balance in troposphere can be clearly evaluated. Presentation of relative values as used in the last report of an accredited scien-tific authority, the Intergovernmental Panel on Climate Change (IPCC), leads to considerable overestimation of the real situation. We docu-ment that the outcomes from this report of IPCC are provably false. Using a simple calculation, it is possible to demonstrate that the elevating of CO2 concentration does not cause the global warming in a degree that is expected basing on the report.
A New Subspecies Trigonella coerulescens (Fabaceae), from Turkey

Trigonella coerulescens (Bieb.) Hal. subsp. kemerensis R.S. Göktürk subsp. nova (Fabaceae) is described from SW Anatolia, Turkey and illustrated. It grows on sandy seashores in Olimpos-Çıralı (Kemer) and Adrasan (Kumluca) beaches. It is closely related to subsp. coerulescens, an endemic taxon confined to Olimpos-Beydağlari National Park. Diagnostic morphological characters of subsp. kemerensis and subsp. coerulescens are discussed.
Leaf zinc and copper concentrations of mature pistachio trees in response to fertigation.

●ADDITIONAL INDEX WORDS. heavy metals, micronutrients, Pistacia vera, foliar fertilization SUMMARY. Mature ‘Kerman’ pistachio (Pistacia vera L.) trees, located on the west side of the San Joaquin Valley of California on an alkaline clay-loam soil, were fertigated in 1997 and 1998 with three combinations of zinc (Zn) and copper (Cu) sulfate. Seasonal applications of Zn and Cu were injected at three separate times starting in spring and ending in summer. Efficacy of the treatments were compared by measuring the concentration of Zn and Cu in leaf tissue. Fertigated treatments were compared to trees receiving no supplemental Zn or Cu and to trees receiving a single foliar treatment of Zn and Cu each year. Soil Zn and Cu concentrations increased in the fertigated plots. Plots receiving the highest rates of Zn and Cu showed the greatest increase. However, at the recommended August leaf sampling period, only the foliar treated pistachio trees showed a significant increase in leaf Zn and Cu. The results demonstrate that after two seasons, a foliar application of Zn and Cu in April, two to three weeks after flowering, increased leaf-tissue concentrations of Zn and Cu to sufficiency levels. These foliar applications were more effective than fertigating with Zn and Cu sulfate. A pplication of some fertilizer nutrients and soil amendments through low-volume irrigation systems has proven to be fast, convenient and economical in comparison to foliar applications with less soil compaction and reduced risk of phytotoxicity. Pistachios grown in soils in the Central Valley of California may manifest Zn and Cu micronutrient deficiencies in the absence of a routine micronutrient fertilization program. Currently, Zn is commonly applied in a single foliar application of up to 40 lb/acre (45 kg·ha ‐1 ) of elemental Zn after harvest or as a late dormant spray. Previous research (Brown et al., 1993, 1994) has shown that foliar Zn was absorbed and transported within the tree when applied after flowering during early leaf development. The quantity of nutrients applied at this time must be reduced when compared to late dormant or postharvest treat
Hypergravity Specifically Affects Anterior Head Formation in Early Xenopus Embryos

Xenopus embryos raised under conditions of hypergravity develop various abnormalities, including head defects such as microcephaly and cyclopis. However, it is unknown which region of the head is most sensitive to hypergravity, and whether regions behind the midbrain are affected by hypergravity. In this study, we investigated the effects of hypergravity on Xag , Xotx2 , En2 , Krox20 , and HoxB9 expression by whole-mount in situ hybridization. Double staining with Xag and Xotx2 revealed that Xotx2 expression was dramatically suppressed in embryos exposed to 5 G ; Xag expression was also affected, but to a lesser extent. Furthermore, En2 expression was also affected by hypergravity. A detailed examination by double staining with Xotx2 and En2 showed that although Xotx2 expression was strongly suppressed in embryos exposed to 5 G , the region expressing En2 was only slightly smaller. Lastly, Krox20 or HoxB9 expression was unaffected by hypergravity. These results suggest that formation of the anterior head region, including the eyes, forebrain, and midbrain, in Xenopus embryos is sensitive to hypergravity, while the posterior regions (i.e., behind the hindbrain) are unaffected by hypergravity. doi:
Differences in energy balance and energy efficiency between an old endangered and a modern Norwegian dairy cattle breed in a traditional indoor feeding system

Abstract The aim was to test possible differences in energy balance and energy efficiency between two dairy cattle breeds with different selection histories. The data were derived using the two Norwegian breeds Black Sided Trønder and Nordland Cattle (STN; N=9) and Norwegian Red (NRF; N=10), in the same herd through three consecutive indoor feeding seasons. STN milked 52% of energy corrected milk, weighed 78% of live weight and ate 65% of MJ metabolisable energy per day compared to NRF. There were no breed differences in energy balance or partial energy efficiency for lactation. NRF had higher gross energy efficiency (GEE) than STN. It was found that interaction between breed and lactation month for GEE indicating different curves for this trait during the lactation period.
Preliminary Studies on Furfural Production from Lignocellulosics

Abstract This study focused on the production of furfural from agricultural and industrial biomass residues by a hydrodistillation process. Corncobs, sugarcane bagasse, and eucalypt wood were treated with sulfuric, hydrochloric, and phosphoric acids as catalysts, with different acid concentrations (1.5 to 5.2 mol.L −1). In addition, the eucalypt liquor from the auto-hydrolysis, kraft-dissolving pulp production process was also investigated as a source of furfural, using sulfuric and hydrochloric acids as a catalyst (0.9 and 3.9 mol.L −1) . Furfural yields of 30.2, 25.8, and 13.9% were achieved for corncob, sugarcane bagasse, and eucalypt wood, respectively, on the basis of biomass dry weight. The efficiency of conversion from pentose to furfural using eucalypt liquor from the auto-hydrolysis kraft process was 71.5% using HCl 3.9 mol.L −1 . Due to the presence of a high amount of pentose, corncob produced the highest amount of furfural, followed by sugarcane bagasse and then eucalypt wood.