Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid Response of Bird Communities to Small-Scale Reforestation in Indonesian Borneo

The island of Borneo suffers from one of the highest deforestation rates in the world, primarily due to agriculture, logging, and other human activities. This habitat loss may be partly mitigated by reforestation programs in degraded landscapes, especially anthropogenic grasslands that have little conservation or economic value. By monitoring native bird communities, we evaluated the success of two small (<20 ha) community reforestation projects in Gunung Palung National Park in Indonesian Borneo. Birds responded rapidly following reforestation, with species richness doubling over 7 years at one site, and increasing by 29% in just 3 years at the other. Final tallies (63–70 species per site) were comparable to those obtained in older secondary forests elsewhere in Borneo. Anthropogenic fire is the primary threat to reforestation success, but intensive fire prevention allows bird communities to recover from temporary setbacks. Absence of fire was thus the most important factor in recovery, and we detected no effect of replanted area on bird species richness. Our results suggest that by engaging local communities and ensuring long-term maintenance, even small reforestation sites in Borneo can provide immediate benefits for native biodiversity.
Population Dynamics of Whitefly, Bemisia tabaci (Gennadius) and its Management on Tomato

Population dynamics of whitefly, Bemisia tabaci and its management through use of insecticides profenophos @ 500 g a.i. ha, imidacloprid @ 20 g a.i. ha, cypermethrin @ 25 g a.i. ha, indoxacarb @ 50 g a.i. ha, profenophos (40 %) + cypermethrin (4%) @ 440 g a.i. ha, neem seed kernel extract (NSKE) 5 %, neem oil 2 %, tobacco decoction 5 % and yam bean seed extract (YBSE) 5 % in tomato variety ‘Avinash – 2’ was studied at Vegetable Research Farm of Dr. Rajendra Prasad Central Agricultural University, Pusa during Rabi 2016-17. Peak population (42.4 per three leaves) of whitefly was observed on 70 day after transplanting. Temperature (max. and min.) and sunshine (hrs) had a negative significant correlation, while morning and evening relative humidity had a positive significant correlation but wind speed had nonsignificant positive correlation. The correlation coefficient (r) was computed for max. Temperature (-0.481), min. temperature (-0.483), morning relative humidity (0.514), evening relative humidity (0.483), wind speed (0.007) and sunshine hrs (-0.641), respectively. The weather parameters were found to contribute around 55.70 per cent impact on population of Bemisia tabaci when acted together (R The mean per cent reduction in whitefly population over control after first, fifth and seventh day of 1 = 0.5570). , 2 and 3 spray of insecticides was maximum in imidacloprid @ 20 g a.i. ha (47.41 %, 81.03 % and 88.14 %, respectively) followed by profenophos 40 % + cypermethrin 4% @ 440 g a.i. ha (42.20, 77.38 and 85.93 %, respectively). All the insecticidal treatments proved profitable over control and increase in yield varied from the maximum of 90 q ha in imidacloprid (20 g a.i. ha) to the minimum of 48 q ha in tobacco decoction 5 %. The benefit cost ratio was highest in imidacloprid @ 20 g a.i. ha (22.69: 1) followed by cypermethrin @ 25 g a.i. ha (17.21:1) and lowest in YBSE 5% (1.53: 1).
Ecology and field biology of two dominant Camponotus ants (Hymenoptera: Formicidae) in the Brazilian savannah

Camponotus renggeri and C. rufipes are very abundant in Brazilian cerrado savannah, where they feed extensively on liquid rewards and commonly associate with plants bearing extrafloral nectaries and honeydew-producing insects. Here, we provide a qualitative and quantitative field account on the natural history and ecology of these two ant species. The study was carried out in a cerrado reserve in south-eastern Brazil across a rainy/hot season (summer) and a dry/cold season (winter). The ants were found in two vegetation physiognomies: all nests of C. rufipes were located in the cerrado sensu stricto (scrub of shrubs and trees, 3–8 m tall), whereas C. renggeri occurred mostly in the cerradão (forest with more or less merging canopy, 10–12 m tall). Both species nested in fallen or erect dead trunks, as well as underground. In addition, C. rufipes built nests using dead plant material arranged or not around shrub bases. Colonies of C. rufipes were generally more populous than those of C. renggeri, and both species had colonies with more than one dealated queen. Both species were active mainly at night and foraged for resources near their nests, mainly extrafloral nectar and hemipteran honeydew (aphids and mealybugs). The average size of the home ranges of C. renggeri in cerrado sensu stricto and cerradão varied from ≈ 2.8 to 4.0 m2 and apparently were not affected by season. In C. rufipes, however, foraging grounds in cerrado sensu stricto showed a twofold increase from dry/cold (≈ 4.5 m2) to rainy/hot season (≈ 9.8 m2). Our study highlights the importance of natural history data to understand the foraging ecology and role of these ants in cerrado savannah.
Systematic Studies on Sea Cucumbers of the Family Stichopodidae (Echinodermata:Holothuroidea)

of Doctoral Dissertation Degree requested Doctor of Science Applicant’s name Woo Sau Pinn Title of Doctoral Dissertation Systematic Studies on Sea Cucumbers of the Family Stichopodidae (Echinodermata: Holothuroidea) (シカクナマコ科(棘皮動物:海鼠類)の体系学的研究) Sea cucumbers in the family Stichopodidae are predominantly distributed in a wide range of depths, both in the tropics as well as the temperate waters. Despite their ecological and economic importance, the systematic and phylogenetic position of this family remains problematic and unresolved. Therefore, this dissertation presents a collection of some studies done on the systematics of the family Stichopodidae with the aim to further understand the relationships and systematics of the family. Resulting from these studies, one new genus, one new species, two new species combinations, and one resurrected species name are proposed in this dissertation. A taxonomic study of species in the genus Stichopus was done using specimens collected from the Straits of Malacca. Five species, including one new species, were reported. The new species, Stichopus fusiformiossa, has unusual fusiform ossicles in the tentacles, which are not found in the other species of the genus. Pseudo-tables and large perforated plates are newly recorded for Stichopus herrmanni and Stichopus vastus, respectively. The taxonomic status of the genus Apostichopus has been in a constant change due to the confusions arising from the existence of four nominal taxa, three colour morphs, and two valid species. A revision of this genus was done using the type specimens, as well as additional specimens from Japan, to clarify the taxonomic status by detailed ossicle analysis. Scanning electron micrographs of complete ossicle assemblages from dorsal body, papillae, tentacles, tube feet and cloaca are reported for the first time. This resulted in redescription of this genus with two member species including one resurrected species name (A. armatus). Both A. japonicus and A. armatus can be differentiated by the character of either smooth or spinous rim of the reduced table ossicle in dorsal body. Lastly, a new genus is proposed in this dissertation to accommodate two species already described from Australia that were previously placed in the genus Stichopus. The erection of the new genus, Notostichopus, is based on morphology, phylogenetic, genetic distance, and geographical distribution. Notostichopus is characterized by the absence of rosette ossicles, and table ossicles only have a single or no crossbeam in dorsal body. This genus is represented by two species revised here (Notostichopus ludwigi and N. ellipes), distributed in the shallow, subtropical and temperate waters of Australia. Following the outcome of this dissertation, the family Stichopodidae at present consists of a total of 10 genera and 34 described species after incorporating changes proposed by these studies.
Genetic variability and correlation analysis of various traits in chickpea genotypes (Cicer arietinum L.) under rainfed condition in western Uttar Pradesh

The present studies were conducted to the estimation of correlation for quantitative traits in chickpea (Cicer arietinum L.) in the field of the department of Genetics and Plant Breeding, Janta Vedic College, Baraut Baghput (U.P.) during the crop season 2003 to 2004 under rainfed condition. The present investigation revealed that the maximum days to maturity (151) were recorded in BG 1107 and Pusa 1063, whereas three genotypes (Pusa 209, BG 2002 and Pusa 1090) took minimum days (136) to mature. There was a great variation in biological yield among genotypes that ranged from 19.43 g to 36.83 g. Number of branches ranged from 9.37 to 15.33. Number of pods plant-1 varied from 45.53 to 68 and BG 1105 exhibited maximum number of pods (68). The variation for 100-seed weight ranged from 17.05 g to 32.31 g. The highest seed yield plant-1 was recorded for genotype BG 2002 (12.68 g), Pusa 362 (12.73g) and AT-2-1184 showed minimum seed yield (7.83 g). High heritability estimates were observed for number of branches (88.12), protein content (78.65), number of pods per plants, harvest index plant height and biological yield. High heritability coupled with high genetic advance for number of branches per plant, harvest index, pods per plant, 100-seed weight and biological yield. High heritability with low genetic advance was observed for protein content plant height. Seed yield per plant showed positive and significant phenotypic correlation with number of branches, number of pods per plant, biological yield per plant, 100-seed weight and harvest index. Cluster I, VII, III and VI, respectively possessed 12, 10, 6 and 5 genotypes. Means of various traits for each character showed that genotypes with maximum number of branches, pods per plant, 100-seed weight biological yield and seed yield per plant were placed together in cluster II. Genotypes with maximum harvest index were placed in cluster VI and genotypes with maximum days to maturity were placed in cluster VII.
Mechanisms of Salmonella pathogenesis in animal models

ABSTRACT Animal models play an important role in understanding the mechanisms of bacterial pathogenesis. Here we review the recent studies of Salmonella infection in various animal models. Although mice are a classic animal model for Salmonella, mice do not normally get diarrhea, raising the question of how well the model represents normal human infection. However, pre-treatment of mice with oral streptomycin, which apparently reduces the normal microbiota, leads to an inflammatory diarrheal response upon oral infection with Salmonella. This has led to a re-evaluation of the role of various Salmonella virulence factors in colonization of the intestine and induction of diarrhea. Indeed, it is now clear that Salmonella purposefully induces inflammation, which leads to the production of both carbon sources and terminal electron acceptors by the host that allow Salmonella to outgrow the normal intestinal microbiota. Overall use of this modified mouse model provides a more nuanced understanding of Salmonella intestinal infection in the context of the microbiota with implications for the ability to predict human risk.
Tracking Individual Differences in Perception by TMS-EEG Intrinsic Effective Connectivity

Non-invasive human electroencephalography (EEG) coupled with transcranial magnetic stimulation (TMS) is currently used to measure coarse stimulus-response relationships in brain physiology during behavior. However, with key modifications, the TMS-EEG technique holds even greater promise for monitoring fine-scale neural signatures of human behavior. Here, we demonstrate that a novel TMS-EEG co-registration technique can dynamically monitor individual human variation in perception based solely on EEG resting-state intrinsic effective connectivity probed by TMS-based phase resetting of ongoing activity. We used a bistable stimulus task, where the percept is perceived as either horizontal or vertical apparent motion, to record gamma band interhemispheric integration of information. Fine-grained inter-individual behavioral differences in horizontal motion bias could be measured by tracking resting-state gamma-band effective connectivity from right hMT+ to left hMT+. Thus, our method of triggering intrinsic resting-state effective connectivity in oscillatory dynamics can monitor individual differences in perception via the long-range integration of information. This technique will be useful for the manipulative dissection of individual-scale human cognition mediated by neural dynamics and may also expand neurofeedback approaches.
Emergence of mosaic plasmids harboring Tn1546-ermB element in Staphylococcus aureus isolates

Antimicrobial resistance in Staphylococcus aureus is a major problem and the acquisition of resistance genes may occur by horizontal gene transfer (HGT). The transposon, an important means of HGT, is recognized as a mobile genetic element that can integrate in plasmids, replicate and transfer to other strains. We have previously reported a novel structure of the Enterococcus faecium-originated Tn1546-ermB element in S. aureus. The emergence of the Tn1546-like element is an emerging problem that requires continuous monitoring. In the present study, we expand the examination of Tn1546-ermB element to ermB-positive methicillin-susceptible S. aureus (MSSA) (n = 116) and ermB-positive methicillin-resistant S. aureus (MRSA) (n = 253) during a 16-year period, from 2000 to 2015. PCR mapping showed that 10 MSSA and 10 MRSA carried the Tn1546-ermB element. The 10 MSSA belonged to three sequence types (ST), ST7 (n = 6), ST5 (n = 3), and ST59 (n = 1), and the 10 MRSA belonged to two STs, ST188 (n = 8) and ST965 (n = 2). Since only clonal complex 5 (including ST5, ST85, ST231, and ST371) MRSA, ST8 MRSA and ST5 MSSA have been previously reported to carry Tn1546 plasmids, this is the first report describing the presence of the Tn1546-ermB element in ST7/5/59 MSSA and ST188/965 MRSA. Plasmid sequencing revealed that the Tn1546-ermB element was harbored by five different mosaic plasmids. In addition to resistance genes, some plasmids also harbored toxin genes.
Thermal constraints of energy assimilation on geographical ranges among lungless salamanders of North America

Understanding biogeographical patterns of variation in distributional ranges of lungless salamanders in North America by examining the relationship between geography, temperature and range. We examined how these patterns fit with Rapoport's rule, that species distributional ranges increase with increasing elevation and latitude. We also examined a possible physiological mechanism behind Rapoport's rule, the climate variability hypothesis (CVH).
The effect of friabilin on wheat grain hardness: a review

A wheat marketing system established the primary classification of hexaploid wheat based on the endosperm texture, i.e. hardness or softness of the grain. Hardness affects a range of characters including the milling (tempering, milling yield, flour particle size, shape and density of flour particles), baking and end-use properties. Wheat grain hardness is largely controlled by genetic factors but it can also be affected by the en - vironmental and other factors. The endosperm texture is primarily associated with the Hardness (Ha) locus on the short arm of chromosome 5D. It is regulated by friabilin. This 15 kDa starch surface protein complex is present in larger amounts in soft wheats compared to hard ones and consists of three major polypeptides: puroindoline a (Pina), puroindoline b ( Pinb) and grain softness protein 1 ( Gsp-1). The soft grain texture in wheat is a result of both puroindoline genes being in the wild type active form and bound to starch. When one of the puroindolines is either absent or altered by mutation, then the result is a hard texture. Gene sequence variation and mutation of both puroindoline genes account for the majority of variation in the wheat grain texture. The latter may serve as the potential for improvement of milling and baking wheat quality. However, many wheat varieties have the intermediately (mixed) hard endosperm and there is a wide variation between soft and hard grain texture. Grain hardness is affected by a number of factors beyond genetics including N management, tillage system, pest infestations, environment (location of growth, temperature and rainfall during the growing season) and their interactions, and factors such as moisture, gliadin composition, and content of lipids, starch and pentosans.
Visual Observation to Identify Sexes in Subspecies of Adult Black Skimmers (Rynchops niger)

Abstract. Identifying sexes in birds from visual observations could be a useful and inexpensive method. While sexual dichromatism and ornaments are readily used by observers, sexual size dimorphism can also be used to identify sexes in some bird species. This study assessed the applicability of visual observation of size differences to identify sexes in adult Black Skimmers (Rynchops niger). Black Skimmers do not have sexual dichromatism; however, Black Skimmer males are skeletally larger (6.7–31.7% depending on trait) and 33.3–37.5% heavier than females. The study focused on two subspecies: Amazonian (R. n. cinerascens) and South American (R. n. intercedens) Black Skimmers. Sex identified by visually observing size differences was consistent with the sex identified at specimen preparation from examining gonads (RGLMM = 0.996 ± 0.004). The identification of sexes from photographs using visual observation of size had a very high within- (RGLMM = 0.995 ± 0.001) and between- (RGLMM = 0.984 ± 0.002) observer repeatability. Non-invasive methods for identifying sex by visual observation may allow enhanced use of data from photographic datasets, citizen science projects, and surveys using direct observation or images.
Discovery and functional analyses of Hessian fly effector-encoding genes

Navarro-Escalante, Lucio Ph.D., Purdue University, August 2016. Discovery and Functional Analyses of Hessian Fly E↵ector-Encoding Genes. Major Professor: Je↵rey J. Stuart. The Hessian fly wheat system is a well-known model of gene-for-gene interaction between host plants and parasitic insects. The Hessian fly uses secreted e↵ector proteins to control susceptible host plant physiology, transforming the plant cells in a nutritive tissue to support the developing insect larva. HF-resistant wheat cultivars employ resistance (R) proteins to perceive the insect avirulence e↵ectors (Avr) and display defensive immune responses. This study is focused in the discovery and functional analyses of insect e↵ector-encoding genes. Chapter one of this thesis o↵ers an introduction about the molecular basis of HF-wheat interactions. In Chapter two, I present the genetic mapping of HF Avr genes vH6, vHdic and vH5 using a genomewide strategy. Di↵erences in SNP-allele frequencies obtained from whole-genome pool sequencing positioned vH6 and vHdic on two di↵erent genomic regions in the long arm of chromosome X2. vH5 was mapped on ⇠1.3Mb of a proximal genomic region of chromosome A2 (Sca↵old A2.7). Gene expression analyses permitted to identify two vHdic candiate genes. In chapter three, I propose that HF SSGP71 family members encode e↵ectors that structurally resemble E3-ubiquitin-ligases. SSGP71 proteins contain putative F-box and leucine rich repeats (LRR) domains. Yeast 2-hybrid experiments showed that SSGP71 members interact with host plant Skp1-like proteins. In chapter four, I use bacterial T3SS-based delivery of proteins into plants to test candidate HF e↵ector-encoding genes. Candidate vH13 failed to induce plant immune responses in H13 -resistant wheat leaves when carried by Pseudomonas fluorescens. However, experiments with the plant pathogen Burkholderia glumae carrying candixii dates vH13 or vH16 suggest they might interfere with plant immunity in Nicotiana spp.
Life expectancy of wild ruminants in zoological institutions

Summary Increasing husbandry success is an important aim of zoological institutions, but evaluation procedures are rare. Here, data of the International Species Information System was used to calculate the relative life expectancy (rLE; life expectancy of a species expressed as proportion of the longevity record) of 78 ruminant species in captivity. This parameter reflects the husbandry success for individual species. A comparative analysis of rLE across species tested for biological characteristics that influence life expectancy in captivity. In adult females, rLE correlated positively with the percentage of grass in a species’ natural diet (χ2 = 8.28, p=0.004). This parameter describes the diet a species is adapted to. Thus, our results confirm the general experience of zoos that browsers have more nutrition-related problems than mixed feeders and grazers. Higher rLE was also achieved in adult males of monogamous species (χ2 = 9.92, p=0.007), suggesting intrinsic physiological stress in males adapted to defend harems even if not kept with competing males. Furthermore, life expectancy was significantly higher in both sexes of species that were managed by an international studbook (females: χ2 = 8.80, p=0.003, males: χ2 = 5.52, p=0.019), indicating a positive effect of ex situ conservation efforts. Considering these results in husbandry regimes of wild ruminants, husbandry success in zoos may be further improved. Lebenserwartung von Wildwiederkauern in zoologischen Institutionen In der vorliegenden Studie wurden Daten des “International Species Information Systems” verwendet, um die relative Lebenserwartung (rLE; durchschnittliche Lebenserwartung einer Art als Proportion des Altersrekords) von 78 Wiederkauerarten in Gefangenschaft zu ermitteln. Dieser Wert reflektiert den jeweiligen Haltungserfolg. Die vergleichende Analyse der rLE verschiedener Arten ermoglichte es, biologische Merkmale zu identifizieren, die einen Einfluss auf die Lebenserwartung haben. So korrelierte der rLE adulter Weibchen positiv mit dem Anteil an Gras in der naturlichen Asung einer Art (χ2 = 8.28, p=0.004). Dies bestatigt die Erfahrung aus der Zoohaltung, dass Laubaser im Vergleich zu Gras- und Mischasern mehr futterungsbedingte Probleme zeigen. Hohere rLE erreichten adulte Mannchen monogamer Arten (χ2 = 9.92, p=0.007). Dies weist darauf hin, dass Arten, die daran adaptiert sind, ein Harem oder ein Revier zu verteidigen, intrinsischem, physiologischen Stress ausgesetzt sind, selbst wenn sie nicht in Gesellschaft anderer Mannchen gehalten werden. Zudem war der rLE beider Geschlechter hoher bei Arten, fur die ein internationales Zuchtbuch gefuhrt wird (Weibchen: χ2 = 8.80, p=0.003, Mannchen: χ2 = 5.52, p=0.019). Dieses Ergebnis zeigt, dass sich ex-situ Zuchtprogramme auch positiv auf den Haltungserfolg einer Art auswirken. Sollten die Ergebnisse dieser Studie in den Haltungsregimen von Wildwiederkauern berucksichtigt werden, konnte deren Haltungserfolg weiter verbessert werden.