Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of xylanase supplementation on the apparent metabolisable energy and ileal amino acid digestibility in a diet containing wheat and oats, and on the performance of three strains of broiler chickens

A commercial xylanase product was assessed for its effects on the performance of, and apparent metabolisable energy (AME) and ileal amino acid digestibility in, 3 commercial broiler strains (Strain A, B, and C) fed on a diet containing wheat (407 g/kg) and oats (78 g/kg). Exogenous xylanase improved weight gains (P = 0.07) and feed/gain (P < 0.04) of broilers, irrespective of genotype. Performance parameters significantly differed among the broiler strains. Strains A and C consumed more (P < 0.04) feed, and grew faster (P < 0.01) and more efficiently (P = 0.07) than Strain B. Enzyme supplementation resulted in 2.8% improvement (P < 0.05) in the AME of the wheat-based diet. The AME tended to be higher (P = 0.09) with Strain A (13.46 MJ/kg dry matter) and Strain C (13.57 MJ/kg dry matter) than with Strain B (13.10 MJ/kg dry matter). The apparent ileal digestibility of all amino acids was 1–2 percentage units higher in birds fed on the enzyme-supplemented diet than in those fed on the unsupplemented diet (controls), but the differences were significant (P < 0.05) only for threonine, methionine, isoleucine, arginine, aspartic acid, serine, and glutamic acid. Highly significant (P < 0.001) strain effects were observed for apparent ileal digestibility of all amino acids, with Strain A recording the highest (0.807–0.945) and Strain B the lowest (0.710–0.912). Mean ileal digestibility coefficients of the 15 amino acids in wheat-based diets for Strains A, B, and C were 0.858, 0.791, and 0.828, respectively. Ileal digesta viscosity was low, and was not affected by dietary enzyme, suggesting that other factors were responsible for the observed improvements in bird performance.
A New Dartless Species of Cahuillus (Pulmonata: Helminthoglyptidae) from the Mojave Desert, California with a Reassignment of Eremarionta rowelli unifasciata

Abstract. A new species of the helminthoglyptid genus Cahuillus Roth, 1996 from the Mojave Desert of southeastern California, is described as Cahuillus fultoni n.sp. It lacks the dart sac and associated mucus glands of the female system found in all other members of Cahuillus including Eremarionta rowelli unifasciata (Willett, 1930), which is herein reassigned to this genus and elevated to species status as Cahuillus unifasciata. Sequence comparisons support the new species as distinct from other available taxa, based on combined analysis of 16S and COI mitochondrial gene regions for Cahuillus fultoni and four of the nominal taxa of Cahuillus or Eremarionta Pilsbry, 1913 within the Mojave. Although a relevant species, Cahuillus greggi (Miller, 1981), remains unsampled, the estimated phylogeny supports a sister species relationship between C. unifasciata and C. fultoni.
Quantitative fluorescence methods for studying cellular protein networks, with applications to the yeast galactose pathway

Biology in the past two decades has shifted away from qualitative observation towards quantitative data, and away from reductionism towards viewing the phenomena under study as systems. Developments in fluorescent reporters, experimental instrumentation, and computational power have been integral to this change. A key feature of this transformation has been a substantial increase in the use of mathematical models to explore and verify our understanding of complicated biological mechanisms. This thesis looks at three different aspects of the systems modelling approach: data acquisition, model creation and evaluation, and measurement of parameter values. The system under study for the first two parts is the GAL pathway of the yeast Saccharomyces cerevisiae, a well-known model for genetic regulation. Despite this pathway being relative simple and well studied, various questions remain about the details of its regulatory mechanism. In the first part, I describe methodology for acquiring dynamic protein expression data. I use the green fluorescent protein (GFP) as a reporter and make measurements from cell populations growing in a microplate reader. Of particular interest is a technique I introduce for removing the autofluorescence that contaminates the GFP fluorescence signal. My technique makes it possible to detect expression even from very weakly expressed proteins. In the second part, I have developed a basic, deterministic model of the GAL pathway, which I then fit to dynamic protein expression data. I use the model to demonstrate that based on available data, the current understanding of the GAL pathway does capture a wide range of GAL system behaviours. I also identify and explore the GAL network's sensitivity to the relative levels of inducer and repressor proteins and discuss future directions for experiments and model development. In the third part, I present theoretical work that addresses the challenge of measuring protein-protein interactions in vivo from Forster resonance energy transfer (FRET) fluorescence data. I designed a computational tool that uses a Bayesian statistical framework to infer the dissociation constant and FRET efficiency from FRET data. One key advantage of this approach is that it produces probability distributions for these parameters of interest, revealing the uncertainty in the estimates obtained. I also demonstrate the experimental conditions, such as variations in levels of FRET donors and acceptors, that are necessary for the inference of the dissociation constant and FRET efficiency to be possible. %%%%Au cours des deux dernieres decennies, la biologie est passee d'une science reductionniste fondee sur l'observation qualitative a une science quantitative traitant les phenomenes biologiques comme des systemes. Le developpement de genes rapporteurs fluorescents, d'instruments experimentaux sophistiques et de la puissance de calcul des ordinateurs ont ete des elements garants de cette transformation. Plus particulierement, un element cle de cette transformation a ete l'utilisation…
New Floridatragulines (Mammalia, Camelidae) from the Early Miocene Las Cascadas Formation, Panama

ABSTRACT Early Miocene floridatraguline camels are characterized by having an elongate snout, shallow and narrow symphysial area, and relatively primitive dentitions. Their fossil record is restricted to subtropical assemblages including the Hemingfordian Thomas Farm Local Fauna (L. F.) in Florida, the Zoyotal L. F. in Mexico, and the Arikareean Castolon L. F. in Texas. Here we describe the first floridatraguline camels from the early Miocene Las Cascadas Formation, Panama Canal area, Central America. We describe two new species that are similar to Aguascalientia wilsoni from the Zoyotal L. F. in having (1) a primitive lower dental formula, (2) brachydont teeth, (3) an unusually elongate jaw with caniniform c1 and p1 that are well separated by a diastema, (4) a long and narrow mandibular symphysis, (5) lower molars with small intercolumnar pillars, (6) an m3 hypoconulid divided by lingual and labial selenes, and (7) no diastema between p2 and p3. Aguascalientia panamaensis, sp. nov., and Aguascalientia minuta, sp. nov., are represented by partial lower dentitions and isolated upper molars. Both new species are distinct from A. wilsoni in having (1) p1 and c1 similar in size, (2) less inflected paraconids on lower premolars, and (3) less reduced premolars. Interpreted primitive characters are similar to a small, unnamed camel from the earliest Miocene Buda L. F. of Florida (middle late Arikareean NALMA). The Las Cascadas fossil assemblage probably constitutes a distinctive Arikareean (Ar3–Ar4) faunal province characterized by the arrival of northern immigrants into a small continental basin connected with North American continental terrains.
Changes in Myofibrillar Protein and Collagen Content of Mechanically Deboned Chicken Meat Due to Washing and Screening

Abstract Mechanically deboned chicken meat (MDCM) was subjected to an aqueous washing process with a . 5% sodium bicarbonate solution. A screen sieving (.85-mm mesh) separation procedure was incorporated, and two fractions of the washed meat were obtained. One fraction of the washed meat captured by the screen yielded 18.7% of original MDCM on a dry weight basis, and contained 2.8 times more myofibrillar protein and 3.0 times more connective tissue than that of the unwashed MDCM when expressed on a dry weight basis. The fraction of washed meat that passed through the screen sieve device yielded 20.7% of original MDCM on a dry weight basis, and contained 9.2 times more myofibrillar protein than unwashed MDCM. Furthermore, it had 3.0 times less connective tissue than the unwashed MDCM when expressed on a dry weight basis. Thus, the subsequent washed meat fraction would have a composition closely analogous to that of fish surimi.
Impact of shading and chlormequat chloride on Lantana specific leaf area and mineral content.

The creation of high quality plants and their maintenance depends, primarily, on proper fertilization, deriving mainly from the knowledge of their nutrient requirements (NR). Spray-applied chlormequat chloride (CCC), at the concentrations of 3000 and 6000 mg L -1 , has been reported to contribute to the production of attractively flowering Lantana camara L. subsp. camara (lantana) plants. However, no information is available about the NR of the se plants. The effects of the aforementioned CCC concentrations plus 0 mg L -1 (control) on specific leaf area (SLA) and leaf potassium (K), phosphorus (P), calcium (Ca), iron (Fe) and manganese (Mn) contents of lantana s were examined under the 0% and 66% shading levels. Chlormequat chloride (3000 and 6000 mg L -1 ) decreased, generally, SLA of lantanas compared to control, at both shadings. Increased SLA values were estimated with increased shading. Phosphorus content increased with the increased CCC concentrations at 66% shading level. Phosphorus and Fe contents increased while Ca and Mn decreased with the increasing shading. The results of our study may contribute to the planning of a fertilization program for CCC-treated Lantana plants, a promising genus in landscaping in many countries around the world.
Systematics of Some Reindeer Lichens (Cladonia Subg. Cladina) in the Southern Hemisphere

Abstract Cladonia arbuscula subsp. squarrosa (Wallr.) Ruoss and C. stygia (Fr.) Ruoss are reported for the first time from the Southern Hemisphere. Populations of C. arbuscula in New Zealand and Australia are recognized as subsp. stictica Ruoss, subsp. nov., usually containing stictic acid, norstictic acid (first report in subg. Cladina), and sometimes also the fumarprotocetraric acid complex. C. laevigata (Vainio) Gyelnik is reinstated in Cladonia subg. Cladina sect. Tenues, while C. stygia is considered to belong to sect. Crustaceae rather than to sect. Tenues. C. confusa R. Sant. is morphologically highly variable, although chemically uniform, usually containing usnic acid and perlatolic acid. An usnic acid-deficient chemodeme is reported as new to New Zealand.
Development of ''substrate-trapping'' mutants to identify physiological substrates of protein tyrosine phosphatases

Theidentification of substrates of protein ty- rosine phosphatases (PTPs) is an essential step toward a com- pleteunderstandingofthephysiologicalfunctionofmembersof this enzyme family. PTPs are defined by a conserved catalytic domain harboring 27 invariant residues. From a mutagenesis study of these invariant residues that was guided by our knowl- edge of the crystal structure of PTP1B, we have discovered a mutationoftheinvariantcatalyticacid(Asp-181inPTP1B)that converts an extremely active enzyme into a ''substrate trap. '' ExpressionofthisD181AmutantofPTP1BinCOSand293cells resultsinanenzymethatcompeteswithendogenousPTP1Bfor substrates and promotes the accumulation of phosphotyrosine primarilyontheepidermalgrowthfactor(EGF)receptoraswell as on proteins of 120, 80, and 70 kDa. The association between the D181A mutant of PTP1B and these substrates was suffi- ciently stable to allow isolation of the complex by immunopre- cipitation.Aspredictedforaninteractionbetweenthesubstrate- binding site of PTP1B and its substrates, the complex is dis- rupted by vanadate and, for the EGF receptor, the interaction absolutelyrequiresreceptorautophosphorylation.Furthermore, fromimmunofluorescencestudies,theD181AmutantofPTP1B appearedtoretaintheendogenousEGFreceptorinan intracel- lular complex. These results suggest that the EGF receptor is a bona fide substrate for PTP1B in vivo and that one important function of PTP1B is to prevent the inappropriate, ligand- independent,activationofnewlysynthesizedEGFreceptorinthe endoplasmicreticulum.Thisessentialcatalyticaspartateresidue is present in all PTPs and has structurally equivalent counter- partsinthedual-specificityphosphatasesandthelowmolecular weight PTPs. Therefore we anticipate that this method may be widely applicable to facilitate the identification of substrates of other members of this enzyme family.
Improving the Quality of Distribution Models for Conservation by Addressing Shortcomings in the Field Collection of Training Data

Abstract: Conservation biology can benefit greatly from models that relate species' distributions to their environments. The foundation of successful modeling is a high‐quality set of field data, and distribution models have specialized data requirements. The role of a distribution model may be primarily predictive or, alternatively, may emphasize relationships between an organism and its habitat. For the latter application, the environmental variables recorded should have direct, biological relationships with the organism. Interacting species may be valuable predictors and can improve understanding of distribution patterns. Sampling should cover the full range of environmental conditions within the study region, with samples stratified across major environmental gradients to ensure thorough coverage. Failure to sample correctly can lead to erroneous organism‐environment relationships, affecting predictive ability and interpretation. Sampling ideally should examine a series of spatial scales, increasing the understanding of organism‐environment relationships, identifying the most effective scales for predictive modeling and complementing the spatial hierarchies often used in conservation planning. Consideration of statistical issues could benefit most studies. The ratio of sample sites to environmental variables considered should ideally exceed a ratio of 10:1 to improve the analytical power and reliability of subsequent modeling. Presence and/or absence models may suffer bias if training data detect the study organism at an atypical proportion of sites. We considered different strategies for spatial autocorrelation and recommend it be included wherever possible for the benefits in biological realism, predictive accuracy, and model versatility. Finally, we stress the importance of collecting independent evaluation data and suggest that, as with the training data, a systematic approach be used to ensure broad environmental coverage, rather than relying on a random selection of test sites.
Borrelia burgdorferi sp. nov.: Etiologic Agent of Lyme Disease

A review of reports on the genetic and phenotypic characteristics of strains of the spirochete which causes Lyme disease revealed that these organisms are representative of a new species of Borrelia. We propose the name Borrelia burgdorferi for this species. The type strain of B. burgdorferi is strain B31 (= ATCC 35210). In two separate studies the guanine-plus-cytosine content of the deoxyribonucleic acid of the type strain was determined to be 29.0 to 30.5 mol% (thermal denaturation method).
Phytosociology and gradient analysis of a subalpine treed fen in Rocky Mountain National Park, Colorado

The vegetation of a subalpine fen in Colorado was studied. Insight was sought into the community structure and factors influencing species distribution of a vegetation type heretofore undescribed in the southern Rocky Mountains. A vegetational gradient was evaluated using detrended correspondence analysis (DCA). Four types of vegetation were subjectively defined; these same types were distinguished by the DCA. DCA further revealed marked differences in the vegetation occurring on peat hummocks versus in hollows. Species composition was related to environment using canonical correspondence analysis (CCA). Water-table depth, hummock height, shading, groundwater temperature, and conductivity were significantly correlated with species distribution, accounting for 51% of the total species variance. Univariate regression was used to examine how tree density varied with environment. The above factors, except for shading and conductivity, were also significantly correlated with tree density. It is suggested that .
Fcγ receptors are crucial for the expression of acquired resistance to virulent Salmonella enterica serovar Typhimurium in vivo but are not required for the induction of humoral or T‐cell‐mediated immunity

Antibodies play an important role in immunity to Salmonella enterica. Here we evaluated the requirement for Fcγ receptors in host resistance to S. enterica using an in vivo model of systemic infection. We show that mice lacking FcγRI, II and III can control and clear a primary infection with S. enterica micro‐organisms of low virulence, but are impaired in the expression of vaccine‐induced acquired immunity to oral challenge with virulent bacteria. We also show that, in vivo, FcγRI, II, III−/− mice were able to mount efficient T‐helper 1 type T‐cell responses and antibody responses specific for S. enterica. The work indicates that targeting S. enterica to FcγR is needed for the expression of vaccine‐induced acquired immunity, but is not essential for the engenderment of T‐ and B‐cell immunity to the bacterium in vivo.
The Effect of Roost Environment on Roost Selection by Non-Reproductive and Dispersing Asian Parti-Coloured Bats Vespertilio sinensis

Abstract. Roosting of Asian parti-coloured bats (Vespertilio sinensis) in man-made structures is frequently results in conflict with humans. Therefore, to determine optimal alternative roosts, we studied roost preference of this species by testing the effects of roost temperature, surrounding environment and the distance from the nearest nursery colony on roost selection by V. sinensis in manipulative field experiments. We installed white (cooler) and black (warmer) bat boxes at shaded and sun-exposed sites. Although no nursery colonies were formed in the bat boxes, a few individuals (1–5) roosted during the lactation period, while many individuals (≥20) roosted during the post-lactation period. During lactation, bats used both white and black boxes, but preferred using the boxes placed at the shaded sites over those placed at the sun-exposed sites. On the other hand, during the post-lactation period, almost all individuals used the white boxes rather than the black boxes. However, adult females preferred the shaded sites while young females preferred the sun-exposed sites. In conclusion, V. sinensis exhibited seasonal changes in roost selection, implying that several types of bat boxes in different environments need to be installed as alternative roosts. In the future, other types of bat boxes should be tested as alternative nursery roosts.
Mitochondrial DNA variation in two samples of northern pike, Esox lucius L.

The mitochondrial genotype of northern pike, Esox lucius L. , was characterized by restriction analysis performed over the entire mtDNA molecule (33 fish) and over a µ1. 4-kb PCR-amplified segment of a mitochondrial non-coding control region (six fish). Out of eight restriction endonucleases used in the present study of the entire mitochondrial genome, the Nco I and Pst I enzymes produced variant fragment patterns which allowed identification of three mitochondrial genotypes. Low mtDNA diversity was shown by estimates of pairwise nucleotide substitution values (d; mean 6 SE 5 0.49 6 0.43%), haplotype diversity (h 5 0.16) and the nucleotide diversity index (π 5 0.06%). The present authors developed a PCR protocol for mitochondrial DNA non-coding control region to search for more variation. Whereas the PCR assays revealed distinct length variation in this mtDNA segment, restriction analysis performed with three additional restriction enzymes showed no variability which could be attributed to a gain or loss of a particular restriction site. Although the mtDNA analysis proved ineffective in genetic discrimination between the two northern pike samples studied, fish with rare mtDNA genotypes could be used for conducting experimental genome engineering or stocking studies with this species.
Allelopathy of 68 Iranian Wheat Genotypes Released between 1939 and 2009

Allelopathic potential of wheat plant and genotypic variation among cultivars has been observed in several studies. In order to recognize and screen allelopathic potential of wheat genotypes against Amaranthus retroflexus, Hordeum spontaneum and Avena fatua, a glasshouse experiment was conducted, using 68 wheat genotypes. Root and shoot water extracts of wheat genotypes were prepared from fourth leaf stage wheat plants. Weeds root length was measured after germination in Petri dishes exposed to wheat extracts. The results showed considerable variation in inhibitory potential of wheat genotypes. Shoot extracts had higher allelopthic effects than root extract. The highest inhibitory effects were observed in the cultivars Rasool, Mahdavi, Navid, Karaj1, Adl1, Gaspard, Gascogen, Bam, Arvand, Baiat and Azadi, but high variation in weed responses were observed. In conclusion, some wheat genotypes had more allelopathic potential so they could be built into weed management programs.
Establishment and Characterization of an Epstein-Barr Virus-negative Lymphoma B-Cell Line from a Patient with a Diffuse Large Cell Lymphoma

Cell line (LNPL) was established from a tumor biopsy of a nasopharyngeal “histiocytic” lymphoma composed of large noncleaved B-cells. LNPL expressed immunoglobulin M κ surface immunoglobulin, as did the original tumor. LNPL also expressed la antigen but lacked Epstein-Barr virus nuclear antigen. It exhibited a translocation between chromosomes 8 and 14 which has been described in certain other malignant lymphoproliferative disorders. An autologous T-cell line lacked the translocation between chromosomes 8 and 14. LNPL is being used as an immunogen to produce monoclonal antibodies in our laboratory. Such cell lines may facilitate identification of lymphoma-associated surface antigens.
Measuring Fleet Capacity and Capacity Utilization

Fishing capacity measures the capability to catch fish. Capacity utilization is the actual effectiveness in catching fish; the ratio of catch to capacity. The factors comprising a fleet's capacity are the number and size of vessels, the technical efficiency of those vessels, and the time commitment of fishermen. Knowing the capacity utilization of a fleet is critical for evaluating management alternatives. This is true regardless of whether fisheries are managed with fleet controls or with individual controls. We illustrate the measurement of capacity utilization with the Oregon bottom trawl fishery, in which fleet capacity quadrupled between 1976 and 1982. From 1982 to 1985 capacity declined 30% due to economic problems in the industry and vessels finding better opportunities elsewhere. Capacity measurement is necessary to assess management-induced changes in controlled fisheries. Controlling capacity requires addressing all the elements associated with capacity growth. Examination of the components of f.