Miracle-dz/UniFAR-FTUs huggingface dataset:
Rediscovery of the Timor Bush Warbler Locustella timorensis on Alor and Timor, Wallacea: clarifying taxonomic affinities, defining habitat and survey recommendations

The Timor Bush Warbler Locustella timorensis was first collected by Georg Stein on Mount Mutis, West Timor in 1932, but there have been no confirmed field observations since. Here we report on the discovery of a new population of bush warbler on Alor (9 September 2009), which prompted a search for, and subsequent rediscovery, of the nominate Timor Bush Warbler (20 December 2009) in Timor-Leste. We also undertook the first bush warbler searches in the mountains on Atauro Island, and the first ornithological exploration of the mountains of Pantar and Wetar islands. On Alor, at least 13 male bush warblers were heard singing from shrub and grass beneath woodland and forest edge at 859–1,250 m. On Timor, at least 40 males were heard during December, April and July from tall grassland below Mount Ramelau (1,720–2,100 m), Timor-Leste. The song structure of the Alor and Timor birds is similar, and close to Javan Bush Warbler L. montis of Java and Bali, as well as to recordings of Russet Bush Warbler L. mandelli of mainland Asia and Benguet Bush Warbler L. seebohmi from the Philippines. The song of the Alor bird is substantially higher pitched (mean min/max 3,233–4,980 kHz) than the Timor bird (2,928–4,761 kHz) and both are substantially higher pitched than Javan birds. Recordings of Russet Bush Warbler from mainland Asia are higher pitched than songs of all insular taxa, and the song of Benguet Bush Warbler is of a similar pitch to the Timor bird. Recent molecular studies have found that divergences between Javan Bush Warbler and the Russet Bush Warbler are slight, and the high degree of song similarity of the Alor and Timor populations to Javan Bush Warbler places them close to the Benguet Bush Warbler complex. The Timor Bush Warbler is recognised as ‘Near Threatened’ by IUCN, but this will require re-evaluation. On Alor, suitable habitat is extensive and under little threat, but grassland in the uplands of West and East Timor is intensively grazed and regularly burnt. Further field surveys are needed on both Timor and Alor to capture birds, clarify taxonomic relationships using molecular approaches, and further define habitat use and conservation status. Bush warblers were not recorded from Pantar, Atauro and Wetar islands.
Orbilia laevimarginata sp. nov. and its asexual morph

O. laevimarginata is here described as a new species, and also its asexual morph could not be assigned to an existing taxon. Anamorphic strains were obtained from three teleomorph specimens which were collected at different sites and dates. The anamorph is characterized by cylindric-ellipsoid to oblong conidia, mainly 1-septate, growing either singly or mostly from 2–10 denticles in a capitate arrangement on the tip of conidiophores. These morphological characters are similar to those of the nematophagous anamorph genus Arthrobotrys , but the present isolates lack the ability to produce any trapping devices when contacting with nematodes. Phylogenetic analysis inferred from ITS rDNA sequences on different groups within Orbilia showed that the isolates of O. laevimarginata clustered together in a clade separate from Orbilia crenatomarginata (= Hyalinia crystallina ). The two species are close to O. scolecospora and an undescribed species, which all have a crenulate to dentate apothecial margin composed of solid glassy processes. The group clustered distant from those species identified within the nematode-trapping anamorph genera Arthrobotrys , Dactylellina and Drechslerella , but also distant from the non-predacious anamorph genus Dactylella . By combining morphological and phylogenetic analysis, we conclude that the three isolates belong to a single undescribed holomorph species. The morphological differences among the three isolated anamorphic strains, and phylogenetic divergence of nematode-trapping fungi and related species are discussed.
Vertical profile and temporal variation of chlorophyll in maize canopy: Quantitative "crop vigor" indicator by means of reflectance-based techniques

Chlorophyll (Chl) content is among the most important crop biophysical characteristics. Chlorophyll can be related to photosynthetic capacity, thus, productivity, developmental stage, and canopy stresses. Th e objective of this study was to quantify and characterize the temporal variation of Chl content in the vertical profi le of maize (Zea mays L.) canopies by means of a refl ectance-based, nondestructive methodology. A recently developed technique that relates leaf refl ectance with leaf pigment content has been used for accurate leaf Chl estimation. Th e technique employs refl ectance in two spectral bands: in the red edge (720–730 nm) and in the near infrared (770–800 nm). More than 2000 maize leaves were measured for refl ectance and total and green area during a growing season. A bell-shaped curve showed a very good fi t for the vertical distribution of Chl content regardless of crop growth stage. Th e parameters and coeffi cients of the bell-shape function were found to be very useful to interpret temporal changes in the vertical profi le of each variable. Comparisons among Chl, leaf area index (LAI) and green LAI showed that Chl content was more sensitive to changes in the physiological status of maize than other biophysical characteristics. Th e quantifi cation of Chl content in canopy should be seen as a useful tool to complement the information on green LAI or LAI. Its applicability will help to improve the understanding of the crop ecophysiology, productivity, the radiation use effi ciency and the interplant competition.
Implementing YOLO algorithm for real time object detection on embedded system

Object detection deals with classifying and locating multiples objects in images and videos by using a specific type of artificial neural networks known as Convolutional Neural Networks. One of the networks that have gained recognition in this area of computer vision is YOLO, an algorithm that is a collection of multiple techniques used to improve performance both in terms of speed and precision to detect objects in images. Mostly, YOLO is known for being fast in comparison to other state-of-the-art object detectors which all use GPUs for training and detection. Unfortunately, GPUs are expensive and not accessible to everyone thus limiting the number of potential applications that can be implemented. In that sense, this work is focused on implementing YOLO for detection on an embedded system such as the Raspberry Pi. Although this device is computationally constrained, it represented a great chance to see if this feat was possible as the Raspberry Pi is a more accessible low cost alternative. The work covers a small description on object detection and convolutional neural networks with a more detailed overview of the techniques, applications and challenges of YOLO. It also presents details on the training parameters considered to improved YOLO’s precision and the tests performed on the Raspberry Pi using videos.
Occurrence and molecular characterization of Aspergillus species in beach sand

A total of 103 Aspergillus isolates were obtained from beach sand samples collected along Batu Ferringhi beach, Penang Island. Ten species of Aspergillus were identified and the most common species was A. tubingensis (33%) followed by A. aculeatus (21.4%), A. flavus (20.4%), A. niger (9.7%), A. terreus (6.80%), A. fumigatus (2.91%), A. ibericus (1.94%), A. sydowii (1.94%), A. carbonarius (0.98%) and A. tamarii (0.98%). Maximum likelihood tree of combined dataset of ITS regions and β-tubulin sequences showed that the same species were grouped in the same clade. The present study indicated that beach sand harbor a variety of Aspergillus species and the occurrence of Aspergillus in the sand might pose health concern in case of long term exposure as some species such as A. fumigatus, A. flavus, A. niger and A. terreus are potentially pathogenic especially to immune compromised individual. The present study also contribute to the knowledge on the diversity of Aspergillus species in the beach environment as well as contribute knowledge on the taxonomic relationship of Aspergillus species in Malaysia.
5′-Nucleotidases and their new roles in NAD+ and phosphate metabolism

5′-Nucleotidase (EC 3.1.3.5) designates a set of enzymes, which catalyze the hydrolysis of ribonucleoside and deoxyribonucleoside monophosphates into the corresponding nucleosides plus orthophosphate. 5′-Nucleotidases are classified according to subcellular localization, nucleobase specificity and their ability to hydrolyze deoxynucleoside monophosphate substrates. Membrane-bound 5′-nucleotidases are ectoenzymes principally involved in salvage of extracellular nucleosides, and often display a preference toward adenosine monophosphate, thereby modulating signal transduction cascades involving purinergic receptors. Cytosolic 5′-nucleotidases are members of the haloacid dehalogenase superfamily of enzymes, which are two-domain proteins containing a modified Rossman fold as the core and a variable cap structure. Extracellular and intracellular 5′-nucleotidase activities participate in purine and pyrimidine salvage to support balanced synthesis of nucleotides, which is critical for maintaining high fidelity DNA replication. While the production of ribonucleosides from ribonucleotides by 5′-nucleotidases remains the most well studied function, it appears that the physiological functions of these activities are more broad. Indeed, Sdt1, previously termed a pyrimidine-specific 5′-nucleotidase, and Isn1, previously termed an inosine monophosphate (IMP)-specific 5′-nucleotidase, have recently been implicated in catabolic processes in nicotinamide adenine dinucleotide (NAD+) metabolism, and are regulated by the NAD+ precursor vitamin nicotinic acid, glucose and phosphate availability in the medium. In addition, Usha, Pho5, Sdt1 and Phm8 are phosphate starvation-induced 5′-nucleotidases with diverse substrate specificities that liberate phosphate under phosphate starvation conditions. Here we review 5′-nucleotidase enzyme structure, catalytic mechanism and substrate specificity and focus on new biological roles for these enzymes in nucleotide, NAD+ and phosphate metabolism.
Multi-Scale Modeling in Bolted Interfaces

The thesis develops a framework for modeling the dynamics of bolted structures in a multi-scale manner. Understanding that most of the challenges faced by the joints community is around the reconciliation of contact response with physical parameters of the system, the current work is an attempt for this reconciliation using properties identified from interfacial scans of the structure. The basic idea of statistical averaging as conducted in rough contact studies is used here for achieving this in a segmentby-segment fashion. Thus, the response characterization may be done in a manner that represents the micro-level asperity distributions while also preserving a mesolevel understanding of possible local variations. Since all of these are used, through the framework, for macro-level simulations of the dynamics, the approach links the micro-, meso-, and the macro-length scales (in that order). For the dynamical simulations, a modified modal quasi-static approach is proposed, which is capable of representing amplitude-dependent nonlinear modal characteristics of nonlinear dynamical systems with linear limit cases. Since the fully stuck and the fully slipped cases may be taken as the limit cases, this is well applicable for the cases with frictional contacts. The results for the modified approach are compared with the responses characterized from other timeand frequency-domain approaches for a simple example in order to validate its efficacy. Finally, the approach is applied for a three bolt lap-joint benchmark (the so-called “Brake-Reuß-Beam”). Since the characterization of the interface is conducted in a
Historical museum collections and contemporary population studies implicate roads and introduced predatory bullfrogs in the decline of western pond turtles

The western pond turtle (WPT), recently separated into two paripatrically distributed species (Emys pallida and Emys marmorata), is experiencing significant reductions in its range and population size. In addition to habitat loss, two potential causes of decline are female-biased road mortality and high juvenile mortality from non-native predatory bullfrogs (Rana catesbeiana). However, quantitative analyses of these threats have never been conducted for either species of WPT. We used a combination of historical museum samples and published and unpublished field studies shared with us through personal communications with WPT field researchers (B. Shaffer, P. Scott, R. Fisher, C. Brown, R. Dagit, L. Patterson, T. Engstrom, 2019, personal communications) to quantify the effect of roads and bullfrogs on WPT populations along the west coast of the United States. Both species of WPT shift toward increasingly male biased museum collections over the last century, a trend consistent with increasing, female-biased road mortality. Recent WPT population studies revealed that road density and proximity were significantly associated with increasingly male-biased sex ratios, further suggesting female-biased road mortality. The mean body size of museum collections of E. marmorata, but not E. pallida, has increased over the last 100 years, consistent with reduced recruitment and aging populations that could be driven by invasive predators. Contemporary WPT population sites that co-occur with bullfrogs had significantly greater average body sizes than population sites without bullfrogs, suggesting strong bullfrog predation on small WPT hatchlings and juveniles. Overall, our findings indicate that both species of WPT face demographic challenges which would have been difficult to document without the use of both historical data from natural history collections and contemporary demographic field data. Although correlational, our analyses suggest that female-biased road mortality and predation on small turtles by non-native bullfrogs are occurring, and that conservation strategies reducing both may be important for WPT recovery.
Cloning and sequencing of Cystatin C (CST3) from Human's Tissues

Background: Cystatines have regulative and preventive roles on Cysteine Proteases which existing in all biologic fluids of the human body. The protein-coding genes in humans and mice are located on chromosomes 20. The purpose of the present study is cloning and sequencing of hman Cystatin Gene of human normal tissues isolated from Iranian samples for future expression and production of recombinant protein to design of ELISA kit for cystatin detection in patients as a substitute for current creatinin. Methods: In this research, total RNA was extracted from human cord, thyroid, breast and blood tissues and then cDNA was synthesized by RT-PCR method. The resulted fragment was cloned in pET28a vector and transformed into the E.coli DE3-BL21 and finally DNA sequence of the gene was revealed by sequencing and compared with the reference sequence. Result: Amplification of cDNA from different tissue revealed that best result came from new born cord sample comparing to other human tissues like kidney. Cloned gene was verified by restriction digestion, PCR and sequencing. Conclusion: Analysis of sequence from cloned gene revealed that there is only single deletion before primer location with 99% alignment to the reference gene. Amino acid analysis shows that protein is correct and can be used for expression and design of Elisa kit.
Genotype-Species Interactions in Neighbourhoods of Forest Tree Communities

Abstract Studies on plant communities of various annual species suggest that there are particular biotic interactions among individuals from different species which could be the basis for long-term species coexistence. In the course of a large survey on species-genetic diversity relationships in several forest tree communities, it was found that statistically significant differences exist among isozyme genotype frequencies of conspecific tree groups, which differ only by species identity of their neighbours. Based on a specific measure, the association of the neighbouring species with the genotypes of the target species or that of the genotypes with the neighbouring species was quantified. Since only AAT and HEK of the five analysed enzyme systems differed in their genotype frequencies among several tree groups of the same target species, a potential involvement of their enzymatic function in the observed differences was discussed. The results of this study demonstrate a fine-scale genetic differentiation within single tree species of forest communities, which may be the result of biotic interactions between the genetic structure of a species and the species composition of its community. This observation also suggests the importance of intraspecific genetic variation for interspecific adaptation.
Conservation implications of using an imitation carnivore to assess rarely used refuges as critical habitat features in an alpine ungulate

Understanding relationships between animals and their habitat is a central goal in ecology with important implications for conservation. Misidentified habitat requirements can have serious repercussions because land protection or reintroductions might occur in less than optimal habitat. Studies of resource selection have greatly facilitated an understanding of ecological relationships but can be improved when vital yet infrequently utilized habitat features are more fully described. A critical element for many prey species is escape terrain or some other form of refuge to avoid predation. Mountain goats (Oreamnos americanus) are well known for their use of cliffs to avoid predation, but a survey of the literature revealed at least twelve different approximations of goat escape terrain, ranging from > 25° to > 50° slopes. Here, we seek to (1) enhance estimates of mountain goat escape terrain and antipredator behavior, and (2) highlight the limitations of the assumption that the time an animal spends in an area is proportional to importance. To improve estimates of goat escape terrain, we conducted field work across two years (2014–15) in Glacier National Park, Montana USA and manipulated apparent predation risk by exposing mountain goats to a threatening simulated grizzly bear (Ursus arctos) treatment and a non-threatening ungulate (control) treatment. Mountain goats moved in response to the simulated bear but not in response to the simulated ungulate, with shorter latencies to move for subjects in larger groups and at shorter distances to the simulated threat. Through a used-unused resource selection function we tested 22 landscape variables to describe the use of escape terrain. Proximity to slopes greater than 60° best explained the locations to which mountain goats fled after exposure to the simulated bear, and the average slope of these escape locations was 56.5° (±14.1 S.D.). Our results suggest that mountain goat escape terrain be considered at slopes of 60° as a minimum because our simulated threat did not include pursuit of goats and, thus, slopes of 60° are likely underestimates of actual escape terrain. Additionally, because direct interactions between carnivores and goats seldom occur, serious escape terrain is infrequently used. Past estimates of escape may have miscalculated the slopes which goats select for in response to predation risk. Based on experimental approaches in the wild, we suggest that anti-predator behavior should be included in studies of resource selection when the goal is to consider habitat as a predictor for conservation success. Finally, we discuss evidence suggesting a past mountain goat introduction failed due to lack of adequate escape terrain and subsequent recolonization of a predator.
CURCUMIN, GARCINOL AND DIETARY N-3 FATTY ACIDS, LOWER THE RELEASE OF LYSOSOMAL ENZYMES IN RAT PERITONEAL MACROPHAGES.

Male Wistar rats (12rats/group) were fed a diet containing 8 wt % coconut oil or groundnut oil or cod-liver oil for a total period of 8 weeks. The diets were also supplemented with 2 wt % groundnut oil for providing essential fatty acids. During the last 2 weeks, 6 rats form each group were additionally given curcumin (30 mg/kg body wt/day) or garcinol (5 mg/kg body wt/day) in 1 ml groundnut oil. The peritoneal macrophages from rats fed cod-liver oil diet secreted lower levels of lysosomal enzymes collagenase, elastase and hyaluronidase as compared to those from rats fed coconut oil or groundnut oil diets. Curcumin and garcinol significantly lowered the secretion of these lysosomal enzymes from macrophages in animals given coconut oil or groundnut oil diet. These studies indicated that dietary cod-liver oil (rich in n-3 fatty acids), and spice principles curcumin and garcinol can lower the secretory functions of macrophages in a beneficial manner. (Mol Cell Biochem 203:153–161, 2000)
Detection of Conjugative Plasmid Encoded Ampicillin and Tetracycline Resistant in Klebsiella pneumonia

Klebsiella pneumonia were isolated and identified on the basis of morphology, growth, and biochemical characteristics. All the isolates offered different resistance patterns against antibiotics including Ampicillin, Cefotaxime, Erythromycin, tetracycline and Chloramphenicol. Transformation and conjugation techniques were used for plasmid transfer studies. The conjugation experiment showed that ≈ 51kbp conjugative plasmid conferring resistance to tetracycline and ampicillins were successfully transferred to the recipient cells E. coli MM294. The rest of the plasmid borne markers was non-conjugative/nontransferable. Conjugative plasmids carry a tremendous potential to disseminate resistance markers to distant recipient cells. The protocol is reliable enough to be used for large-scale visualization of native plasmids and we have used it to visualize and isolate DNA from hundreds of multidrug resistance plasmids.