Miracle-dz/UniFAR-FTUs huggingface dataset:
Mosaic Evolution of Subterranean Mammals: Regression, Progression, and Global Convergence

Life underground has evolved among different groups of mammals all over the globe. It is an extraordinary environment - with relatively constant temperature, few opportunities to meet organisms other than the immediate family, and a completely different sensory environment. Locomotion, communication, food-finding, navigation, circadian rhythms, and indeed the whole of the animals' physiology may be specialized to cope with underground life. From burrowing to blindness, magnetic communication to the weird bee-like eusociality of naked mole rats, specialization has been extreme - and, in turn, has led to speciation in a whole range of new contexts. That the subterranean way of life occurs in different species of mammals across the globe has provided scientists with one of nature's best studied global evolutionary demonstrations of adaptive radiation and speciation. The revolution in molecular biology that has occurred over the last ten years has massively expanded these horizons, allowing scientists to explore, map, and clone the genes underlying the basis of adaptation and speciation and translate their fascinating structural and functional evolution into genes and genomic language. This book draws together the burgeoning literature about all aspects of the biology of subterranean mammals. Beginning with their evolutionary history and the processes that led to the subterranean way of life, the author goes on to review ecology, behaviour, and physiology within the context of the highly stressful subterranean context, consider the specializations that have evolved in response, and then to compare the 11 families of extant subterranean mammals. The extraordinary circumstances surrounding subterranean mammals present a unique, global, 'natural experiment' in evolution that has implications throughout biology. As such this comprehensive survey will stand as an invaluable reference in years to come.
Variability studies in fennel (Foeniculum vulgare Mill.).

Analysis of variability carried out for nine characters in 25 diverse genotypes of fennel (Foeniculum vulgare) revealed high genotypic and phenotypic coefficient of variations for seed yield plant-1, weight of grains umbel-1, number of umbels plant-1, number of branches plant-1, number of umbellet umbel-1 and plant height. Heritability estimates were high for test weight, weight of grains umbel-1, seed yield plant-1, number of umbel plant-1, plant height and number of umbelletes umbel-1. Higher genetic advance as per percentage of mean was recorded for seed yield plant-1, weight of grains umbel-1, number of umbels plant-1, number of branches plant-1, number of umbelletes umbel-1, plant height and test weight. The plant height, days to 50% flowering, number of branches plant-1, number of umbels plant-1, number of umbellets umbel-1 and weight of grains umbel-1 exhibited positive and significant correlation with seed yield. Path coefficient analysis revealed that days to maturity had highest direct effect on seed yield followed by days to 50% flowering and number of umbels plant-1. Therefore, greater emphasis should be given on these characters while selecting for higher yield and related traits.
Students' Argumentation Skills: Does It Need Strengthening?

Physics learning is directed at ways of thinking and submitting scientific statements. Students' understanding of how to think and propose scientific statements change better as argumentation skills are strengthened. The purpose of this study was to analyse the construction of the decomposition of quality argumentation production in strengthening argumentation skills using the argued skills assessment instrument. The method used in this research is descriptive survey method. The subjects of this study were high school students in Bandar Lampung City Region, amounting to 50 class XI students and had obtained Archimedes principle material. Data was collected using reasoned multiple choice tests and interviews. The specific role of the argumentation skill assessment instrument in this study shows that: the structure or complexity of the argument strengthened 51.7%; fill in the argument 27.3% and the nature of the statement of reason 24.0%. The results of this study allow researchers to develop learning strategies to strengthen argumentation skills and improve learning environment technology to promote and support more productive arguments in the
Evaluation of two species of entomopathogenic fungi against white grub, Holotrichia consanguinea (Blanchard) infesting potato in Maharashtra, India.

The efficacy of two entomopathogenic fungi, Metarhizium anisopliae and Beauveria bassiana, against white grub, Holotrichia consanguinea infesting potato crop was studied under laboratory and field conditions. The estimated LC 50 of M. anisopliae and B. bassiana towards third instar larvae of H. consanguinea were 5.76 x 10 5 and 7.50 x 10 5 conidia ml -1 , respectively. The LT 50 of M. anisopliae and B. bassiana at the concentration of 8 x 10 5 conidia ml -1 against third instar larvae of H. consanguinea were 4.88 and 6.73 days, respectively. In field experiments, M. anisopliae @ 2 x 10 12 conidia ha -1 was found to be effective with an average efficacy of 46.74%, while it was 41.32% in phorate 10G @ 25kg ha -1 . The maximum mycosis was recorded with the use of M. anisopliae (44.44%). The tuber infestation was statistically lowest (6.91%) and yield of marketable tubers highest (27.6t ha -1 ) with the use of M. anisopliae as against 27.85% and 17.8t ha -1 in untreated plot, respectively.
Gut morphology of developing Malaysian river catfish Mystus nemurus (Cuvier and Valenciennes) larvae

This study was conducted to monitor ontogenetic changes in the gut morphology of Malaysian river catfish, Mystus nemurus during larval development. Fish larvae were reared in three 1 ton fiberglass tanks. During the study, the larvae were fed on Artemia nauplii at 5 organisms ml feeding-1 from the start of exogenous feeding (4 DAH). The morphological development of the gut in M. nemurus larvae was observed using a profile projector and a light microscope for a 21 days period. At hatching and during the yolk absorption period, the gut was a simple, straight, undifferentiated tube throughout its length. By 4-5 DAH, the gut differentiated to the esophagus, stomach, and intestine which coincided to the commencement of exogenous feeding. Strong (GL = 0.3179TL-0.1412, R2 = 0.9284) relationship was found between gut length (GL) and total length (TL) of fish.
The Pathogenesis of Clostridium difficile infection

Clostridium difficile is a major problem as the aetiological agent of antibiotic associated diarrhoea. The mechanism by which the bacterium colonises the gut is poorly understood, but undoubtedly involves a myriad of components present on the bacterial surface. The aims of this study were to further define roles for selected surface proteins using a knockout approach, to evaluate the feasibility of surface protein based immunotherapeutics and to obtain structural information using X-ray crystallography. Mutants of cell wall-binding domain (PFam04122) containing proteins CD1036, CD2735, CD2784, Cwp66, CD2791, Cwp84, CD2795 and the flagella cap (FliD) were created. Mutants were characterised with regard to growth, sporulation, toxin production, adhesion in vitro, and, for the Cwp84 mutant, using the in vivo hamster model. The surface-located cysteine protease, Cwp84, was found to play a key role in maturation of the C. difficile S-layer, yet the Cwp84 mutant still caused disease with a similar pathology to the wildtype. Culture supernatant levels of toxin A were increased in CD2735, Cwp66, CD2791, CD2795 and particularly in Cwp84 and FliD 24 hr cultures, while CD2735, Cwp66, CD2791, CD2795 mutants also showed reduced adherence to Caco-2 cells compared to the wild-type. Passively administered immunotherapy, generated to low pH surface protein extracts of the C. difficile R20291 strain, did not protect hamsters from challenge with the cognate strain. Structural studies were undertaken on the surface proteins CD2791, Cwp66 and CD2767. Crystallisation conditions were identified for a recombinant N-terminal domain of CD2767 and an X-ray data set collected to 2 A, although the structure was not solved by molecular replacement. Together these results further our knowledge of C. difficile surface proteins, although further work is required to identify which surface proteins play key roles in vivo during infection.
Linking trait similarity to interspecific spatial associations in a moist tropical forest

Aim Community assembly theory predicts that niche differentiation promotes the spatial clustering of functionally dissimilar species, whereas habitat filtering has the converse effect. We used these predictions to assess the relative effects of habitat filtering and niche differentiation on recruit community assembly over spatial (5- and 30-m neighbourhoods) and temporal (20-yr) scales in the Forest Dynamics Plot at Barro Colorado Island. Location Barro Colorado Island, Panama. Methods We integrated data on the spatial patterns of ≥1 cm DBH (diameter at 1.3 m above ground) recruits with data on seven functional traits for 64 species. First, we quantified the interspecific association patterns of all species pairs i and j using the K-function Kij(r) and the nearest-neighbour distribution function Dij(r). Second, for those pairs with significant spatial associations, we calculated an index of interspecific spatial association using the results of these two summary statistics. Finally, we examined the relationship between interspecific spatial association and trait similarity using simple and partial Mantel tests. Results In all censuses, almost one-half of species pairs had no spatial associations, but for pairs that were significantly spatially associated, positive relationships between trait similarity and spatial association occurred in 5-m and 30-m neighbourhoods, whereas significant negative relationships only appeared in 5-m neighbourhoods. This suggests that habitat filtering was more important than niche differentiation in assembling recruit communities at 5- and 30-m scales. Habitat filtering mainly acted upon traits related to topographic habitat preferences and dispersal mode, whereas spatial association was inversely related to similarity in terms of wood specific gravity and shade tolerance. Conclusions Our findings suggest that both stochastic and deterministic processes operate in species-rich ecological communities, but the role of habitat filtering and niche differentiation as determinants of community assembly vary over spatial and temporal scales. Species co-occurrence was driven by habitat filtering at small and large scales, but also by a combination of niche differentiation and weaker-competitor exclusion effects at small scales. Temporal variations in the importance of habitat filtering and niche differentiation could be related to the occurrence of disturbances such as tree falls. Our results emphasize the role of trait-based processes in plant community assembly.
Evidence for Two Subgroups of CD4−CD8− NKT Cells with Distinct TCRαβ Repertoires and Differential Distribution in Lymphoid Tissues1

NKT cells are a subset of T lymphocytes that is mainly restricted by the nonclassical MHC class I molecule, CD1d, and that includes several subpopulations, in particular CD4+ and CD4−CD8− (DN) cells. In the mouse, differential distribution of these subpopulations as well as heterogeneity in the expression of various markers as a function of tissue localization have been reported. We have thus undertaken a detailed study of the DN NKT cell subpopulation. With a highly sensitive semiquantitative RT-PCR technique, its TCR repertoire was characterized in various tissues. We found that mouse DN NKT cells are a variable mixture of two subgroups, one bearing the invariant Vα14 chain paired to rearranged Vβ2, Vβ7, Vβ8. 1, Vβ8. 2, or Vβ8. 3 β-chains and the other exhibiting unskewed α- and β-chains. The proportion of these subgroups varies from about 100:0 in thymus, 80:20 in liver, and 50:50 in spleen to 20:80% in bone marrow, respectively. Finally, further heterogeneity in the tissue-derived DN NKT cells was discovered by sequencing extensively Vβ8. 2-Jβ2. 5 rearrangements in individual mice. Despite a few recurrences in TCR sequences, we found that each population exhibits its own and broad TCRβ diversity.
PENGARUH KEBIJAKAN PENDANAAN DAN MODAL KERJA TERHADAP PROFITABILITAS USAHA MIKRO KECIL DAN MENENGAH DI KECAMATAN BANAWA

This research aims to know and analyze the effects of financing policy and working capital simultaneously on small medium enterprise profitability in Banawa District; to know and analyze the effect of financing policy on small medium enterprise profitability in Banawa District; to know and analyze the effect of working capital on small medium enterprise profitability in Banawa District. This study involves 172 small medium enterprise entrepreneurs in Banawa District, Donggala Regency Analysis method employed in this research is descriptive verificative using multiple linear regressions. The results show that financing policy and working capital simultaneously perform significant effect on small medium enterprise profitability in Banawa District, financing policy performs significant effect on small medium enterprise profitability in Banawa District working capital performs significant effect on small medium enterprise profitability in Banawa District
Production objectives and selection criterions of three endemic ruminant breeds in The Gambia and Senegal

Livestock plays a major role in the livelihood of poor rural communities, being the source of tangible and intangible benefits. The objective of this study was to analyse the production objectives and selection criteria for cattle (N’Dama) and small ruminants (Djallonke sheep and West African Dwarf goat) in The Gambia and Senegal. A Participatory Rural Appraisal (PRA) survey was conducted in 18 villages in both countries. A total of 412 livestock owners and contract herders participated in the survey. The results showed that benefits such as manure production, income, savings and insurance, were the most important reasons for keeping ruminants. Furthermore, cows were important for milk sale and domestic milk consumption, and bulls were kept for draught. Intangible benefits, such as ceremonial and dowry were some of the main reasons for keeping small ruminants. In The Gambia body size was the most important selection criterion for all species. Trypanosomiasis resistance was essential when selecting cattle. Other important selection criterion traits were milk yield in cows, growth in bulls, and fertility and disease resistance in goats. In Senegal, cattle selection was based mainly on morphological characteristics, i.e. body size, conformation and growth. Trypanosomiasis resistance in cattle was rated lower than in The Gambia. In both countries, body size, fertility and growth were the main traits when selecting small ruminants. Generally, most of the farmer’s production objectives were in harmony with the selection criteria. However, a number of differences were noted. In The Gambia sheep were selected for milk yield, but this was not an essential production objective. In addition, milk yield was an important selection criterion for cows but not for bulls. Inbreeding was the least important selection criterion in both countries. This divergence in production objectives with selection criteria, and the negative effects of inbreeding need to be addressed in breeding programmes in order to conserve, improve and sustainably utilise these three endemic ruminant species.
Inactivation of Escherichia coli by high pressure.

This chapter examines the effects of lethal pressures above 100 MPa on cellular structure and function of Escherichia coli and attempts to distinguish between events that may be associated with loss of viability and those that are not. This is summarized in a provisional model of the mechanisms of inactivation in E. coli based on our current understanding. The confirmatory tests for identifying events as being lethal may be carried out with cells which show different degrees of resistance to pressure, e.g., in different physiological states, treated in particular media, or subjected to different pressure intensities. Researchers investigated the response of stationary-phase cells of a pressure-resistant strain of E. coli O157:H7, EC-88, to a sublethal pressure of 100 MPa for 15 min. More than 100 genes were up-regulated or downregulated following pressure treatment, but in only 36 of these was the change regarded as significant. The major functional categories affected were (i) stress responses, (ii) thioldisulfide redox system, (iii) iron-sulfur cluster assembly, (iv) spontaneous mutation, and (v) several miscellaneous genes. An important conclusion from this study was that high pressure adversely affects the cell’s redox homeostasis. The role of protein denaturation, including cytoplasmic and membrane proteins, in cell death remains to be determined, as does the role of chaperones in protecting against pressure damage. The interrelationships between the various manifestations of pressure-induced damage, both direct and indirect, and cell death will be a fascinating topic of study for the future.
QTL affecting milk protein percent also affect milk yield and protein yield.

INTRODUCTION We recently completed a total scan of the bovine genome for QTL affecting milk protein percent, using selective DNA pooling of milk samples in a half-sib daughter design (Darvasi and Soller, 1994 ; Mosig et al., 2001). In this procedure, determination of linkage between a genetic marker and a QTL is based on the distribution of sire marker alleles among pooled DNA samples of the extreme high and low phenotypic groups of the daughter population. In the case of microsatellite markers, estimating allele frequencies in pooled DNA samples requires correction for “shadow” bands (Lipkin et al., 1998). In the present study, the same procedures were used to examine pleiotropic effects on milk yield (M) and protein yield (K) (kg/yr), of the markers found to be associated with QTL affecting milk protein percent (P).
Analysis of suppressive soils and development of biological control methods for Phytophthora root rot of avocado.

Phytophthora root rot (PRR) of avocado (Persea americana), caused by Phytophthora cinnamomi, is a serious problem in California despite current approaches to disease control that include chemical fungicides, resistant rootstocks, and cultural methods. The current trend toward increasing restrictions on the use of chemical pesticides threatens to eliminate any benefits these materials may provide. This research project was initiated in response to the need for effective alternative approaches to control PRR that will shift the emphasis away from chemical fungicides. Our approach was to identify sites in which replants or older avocado trees were growing well despite the presence of P. cinnamomi in these or neighboring groves. Soils from these suspected "PRRsuppressive" sites were investigated as possible sources for biological control agents. Some of these soils have suppressed PRR in greenhouse experiments. Microorganisms isolated from these soils have reduced disease of test plants caused by P. cinnamomi in our greenhouse tests.
Caracterización bromatológica de Tithonia diversifolia (Hemsl.) A. Gray en dos etapas de su ciclo fisiológico

El objetivo del estudio fue caracterizar bromatologicamente algunos componentes esenciales del valor nutritivo de Tithonia diversifolia (Hemsl.) Grayen dos etapas del ciclo fisiologico (30 y 60 dias), en los periodos lluvioso (PLL) y poco lluvioso (PPLL). Se utilizo un diseno experimental completamente aleatorizado, con seis tratamientos derivados de la relacion entre las fracciones comestibles (hojas, tallos tiernos y hojas mas tallos tiernos) y los momentos del ciclo fisiologico de la planta. Los indicadores medidos fueron: la materia seca (MS), la proteina bruta (PB), la fibra bruta (FB), el calcio (Ca), el magnesio (Mg) y la ceniza. Para el analisis de varianza se utilizo el paquete estadistico SPSS version 15.0 para Windows. El follaje de tithonia presento variaciones en su calidad nutritiva. A los 30 dias se encontraron los mejores valores de PB (29,79% y 28,69%), Mg (0,094% y 0,210%) y ceniza (16,32% y 20,59%) para el PLL y el PPLL, respectivamente, con resultados similares entre las fracciones comestibles para las dos etapas del ciclo fisiologico, en los dos periodos evaluados. El contenido de FB en los tallos tiernos a los 60 dias fue el mas representativo en ambos periodos (5,29 y 5,27%, respectivamente). Integralmente, la fraccion hoja mas tallo tierno alcanzo los mejores valores de los indicadores medidos para ser utilizada en la alimentacion animal .
Inactivation of Copper, Zinc Superoxide Dismutase by the Lipid Peroxidation Products Malondialdehyde and 4-Hydroxynonenal

【Membrane lipid peroxidation processes yield reactive aldehydes that may react with copper,zinc superoxide dismutase (Cu,Zn SOD), one of the key antioxidant enzymes against oxidative stress. We investigated this possibility and found that exposing Cu,Zn SOD to malondialdehyde (MDA) or 4-hydroxynonenal (HNE) caused the loss of dismutase activity, cross-linking of peptides, and an increase in protein oxidation, reflected by the increased level of carbonyl groups. When Cu,Zn SOD that had been exposed to MDA or HNE was subsequently analyzed by amino acid analysis, histidine content was found to be significantly lost. Both MDA-and HNE-treated Cu,Zn SOD were resistant to proteolysis, which may imply that damaged proteins exist in vivo for a longer period of time than the native enzyme. The lipid peroxidation-mediated damage to Cu,Zn SOD may result in the perturbation of cellular antioxidant defense mechanisms, and subsequently lead to a pro-oxidant condition. 】
Statistical HLA type imputation from large and heterogeneous datasets

An individual's Human Leukocyte Antigen (HLA) type is an essential immunogenetic parameter, influencing susceptibility to a variety of autoimmune and infectious diseases, to certain types of cancer and the likelihood of adverse drug reactions. I present and evaluate two models for the accurate statistical determination of HLA types for single-population and multi-population studies, based on SNP genotypes. Importantly, SNP genotypes are already available for many studies, so that the application of the statistical methods presented here does not incur any extra cost besides computing time. HLA*IMP:01 is based on a parallelized and modified version of LDMhc (Leslie et al., 2008), enabling the processing of large reference panels and improving call rates. In a homogeneous single-population imputation scenario on a mainly British dataset, it achieves accuracies (posterior predictive values) and call rates >=88% at all classical HLA loci (HLA-A, HLA-B, HLA-C, HLA-DQA1, HLA-DQB1, HLA-DRB1) at 4-digit HLA type resolution. HLA*IMP:02 is specifically designed to deal with multi-population heterogeneous reference panels and based on a new algorithm to construct haplotype graph models that takes into account haplotype estimate uncertainty, allows for missing data and enables the inclusion of prior knowledge on linkage disequilibrium. It works as well as HLA*IMP:01 on homogeneous panels and substantially outperforms it in more heterogeneous scenarios. In a cross-European validation experiment, even without setting a call threshold, HLA*IMP:02 achieves an average accuracy of 96% at 4-digit resolution (>=91% for all loci, which is achieved at HLA-DRB1). HLA*IMP:02 can accurately predict structural variation (DRB paralogs), can (to an extent) detect errors in the reference panel and is highly tolerant of missing data. I demonstrate that a good match between imputation and reference panels in terms of principal components and reference panel size are essential determinants of high imputation accuracy under HLA*IMP:02.