Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of a Circulating Tumor-Derived DNA Blood Test for Detection of Methylated BCAT1 and IKZF1 DNA.

BACKGROUND Colvera™ is a test that detects circulating tumor-derived DNA in patients with colorectal cancer by assaying for the presence of methylated BCAT1 and IKZF1 in blood. This study describes the analytical and clinical performance characteristics of the test. METHODS Validation was performed in accordance with ISO15189 and National Pathology Accreditation Advisory Council requirements. Spiked samples including 264 plasma and 120 buffer samples were randomized, divided into 8 batches of 48 samples, and processed over 8 days using 2 equipment lines (each line consisting of a QIAsymphony SP/AS, QIACube HT, and LC480); 2 reagent batches; and 2 operators to determine limit of detection, selectivity/specificity, precision, reproducibility, ruggedness, and susceptibility to commonly known interfering substances. Clinical performance was validated by assaying 222 archived plasma samples from subjects (n = 26 with cancer) enrolled in a previous prospective trial. RESULTS The limit of detection for Colvera was 12.6 pg/mL (95% CI, 8.6-23.9 pg/mL), which equates to 2 diploid genome copies per milliliter plasma. No statistically significant difference was determined between testing days (n = 8), instrumentation, operators, or reagent batches in precision studies for the methylation-specific assays. The assay performance was unaffected by 9 commonly known interference substances, variations in bisulfite conversion, or quantitative PCR settings (cycling temperatures, incubation times, and oligonucleotide concentrations). For this clinical cohort, sensitivity and specificity estimates for Colvera were 73.1% (19 of 26; 95% CI, 52.2-88.4) and 89.3% (175 of 196; 95% CI, 84.1-93.2), respectively. CONCLUSION Colvera is a robust test and suitable for detection of circulating tumor-derived DNA by measuring levels of methylated BCAT1 and IKZF1 in human blood plasma.
A Preliminary Study on the Distribution Pattern, Feeding Behavior and Invasiveness of the Exotic Fish, Chitala ornata (Clown Knife Fish) in the Sub Water Ways of Attanagalu Oya

Increasing threat from the introduced invasive species has been identified as one of the major risk factors for the extinction of freshwater fishes. There are number of identified freshwater alien species which have become invasive within Sri Lankan natural waters. However, there is a dearth of information regarding many of these alien invasive species. Therefore, this research project focused on elucidation of distribution pattern, food and feeding habitats and invasiveness of Chitala ornata, an alien invasive freshwater fish species in potentially new site of infestation in the Attanagalu oya and its tributaries over a period of three months as a preliminary study. Key objectives of the study were, to find out the present distribution of C. ornata in Attanagalu Oya and its tributaries, to evaluate the food and feeding habits of C. ornata through gut analysis and to find out the presence of other invasive/introduced species in the area. Over the study peroid, 50 individuals of C. ornata ranging from 21cm to >80cm were collected using hook and line fishing gear and captured fish were deep-frozen immediately after capturing to avoid the deterioration of the food items within the fish gut. Fish gut analyses have been carried out under laboratory conditions. Morphological measures, frequency of occurrence and Index of fullness were calculated. The results indicated that C. ornata has established in the Attanagalu oya basin in areas such as Ekala and Kotugoda. Gut content analysis indicated that C. ornata feeds on significant number of native fish species. Five major prey fish species, consisting 58 Hirikanaya (Labeo dussumeri), 35 Rathu waral katu kuriya (Puntius kelumi), 23 Iri ankutta (Mystuss vittatus), 13 Walapoththa (Ompok bimaculatus) and 16 Illeya (Megalops cyprinoides) were found to make up the diet of 28 adults and 05 juveniles of C. ornata. The average Index of fullness was 378.19. Frequencies of occurrence are 0.606, 0.485, 0.424, 0.121 and 0.242 respectively for L.dussumeri, P. kelumi, M. vittatus, O. bimaculatus and M. cyprinoides. Out of these five species P. kelumi is listed as an endangered endemic species. Other than fishes, one shrimp species, molluscs and fish eggs were also recorded as their food items. Further, other exotic species such as Tank cleaner (Pterygoplichthys spp.) and giant gourami (Osphronemus goramy) were also recorded in the Attanagalu oya. It was concluded that immediate steps should be taken to manage this potentially harmful Alien invasive species in the Attanagalu Oya basin. Keywords: Invasive, Exotic, Fresh water, Chitala, Attanagalu oya
Promoter identification and effect on activation of NF-κB of porcine ISG58

ABSTRACT Interferon (IFN)-stimulated gene (ISG) 56 family (composed of ISG54, ISG56, ISG58, and ISG60) plays important roles in defense against viral infection in mammalian cells. Numerous studies have been conducted on ISG54, ISG56, and ISG60; however, little is known on ISG58. In the present study, the upstream sequence of porcine ISG58 gene was first characterized as functional promoter by luciferase reporter assay, and then two directly adjacent IFN-stimulated response elements (ISREs), one at −206 to −194 (ISRE-I) and a second one, directly upstream of this element at −219 to −207 bp (ISRE-II), were identified using the bioinformatics method. The subsequent site-directed deletion and transient transfection experiments showed the candidate ISREs are functional. ISRE-I works better than ISRE-II and synergistic cooperation exists between two ISREs. Additionally, the effect of porcine ISG58 on activation of NF-κB was analyzed using the dual-luciferase reporter assay. The results will contribute to revealing the role of ISG58 in immune response.
Handbook of European freshwater fishes

This reference work covering 546 native and 33 introduced species is a very important contribution on the biodiversity of freshwater fish species in Europe. Much of the information presented is drawn from original research conducted over 8 years in 24 European countries. This document includes: key to genera and species; diagnoses for all species; methods for identification; habitat, biology and ecology; native, extirpated and introduced distribution; conservation status, validated through IUCN procedures; up-to-date taxonomy and nomenclature, with modern methods and concepts; and more than 870 bibliographic references.
Barriers to globally invasive species are weakening across the Antarctic

Biological invasions are a substantial threat to Antarctic biodiversity and a priority conservation policy focus for Antarctic Treaty Parties and the sovereign states of surrounding islands. Key to their strategies is prevention, including assessment of establishment risk for alien species. Despite establishment of some of the worst globally invasive species across the Antarctic region, assessments of establishment potential of these species are non‐existent. Here, we address this deficit and determine whether these invasive species constitute a significant conservation threat to the broader Antarctic region both now and in response to future regional climate change.
Mechanism of the adjuvant activity of the synthetic mycobacterial cord factor analog Trehalose-6,6-dibehenate (TDB)

The mechanism behind the adjuvant activity of the mycobacterial cord factor TDM and its synthetic analog TDB as a component of the new adjuvant system CAF01 was investigated and compared to the TLR9 ligand CpG. In vitro, TDB and TDM potently activate antigen-presenting cells via a Myd88 and TLR independent, but FcRg-Syk-Card9 dependent signaling pathway. Microarray analysis indicated that in macrophages, TDB induced genome-wide transcriptional responses similar to the Dectin-1 ligand Curdlan that were distinct from the pattern of CpG-induced activation and completely Card9 dependent. By using a TB vaccination model, it was shown that TDB induces the development of an antigen-specific Th-1/Th-17 response in a Card9 dependent way. Card9 was furthermore identified to be essential for the induction of protective immunity to challenge with TB. In contrast to the in vitro studies, the adaptor protein Myd88 was shown to be essentially required for TDB adjuvanticity in vivo. The precise role of Myd88 in the adjuvant effect of TDB is still unclear.
Diversidade local e influência da sazonalidade sobre taxocenoses de anfíbios e répteis na Reserva Extrativista Chico Mendes, Acre, Brasil

Apesar da elevada riqueza de anfibios e repteis conhecida para a porcao Sul-Ocidental da Amazonia brasileira, o conhecimento sobre estes dois grupos ainda e pontual e poucos estudos avaliaram as variacoes temporais na ocorrencia e abundância das especies. Os objetivos deste estudo foram descrever as taxocenoses de anfibios e repteis em uma localidade da reserva extrativista Chico Mendes, verificar quais variaveis climaticas influenciam as flutuacoes temporais na riqueza e abundância e identificar as principais especies de anfibios e repteis que sao influenciadas por estas variaveis. A area de estudo esta localizada na regiao do Seringal Etelvi, porcao sudoeste da Reserva Extrativista Chico Mendes, municipio de Brasileia, estado do Acre. A coleta de dados ocorreu entre outubro de 2011 e setembro de 2012, num total de 48 dias de amostragem com os metodos de procura limitada por tempo e armadilhas de interceptacao e queda. Foram registrados 978 especimes de 31 especies de anfibios e 54 de repteis. Maior riqueza e abundância de anfibios ocorreram durante o periodo chuvoso, ambas correlacionadas positivamente com todas as variaveis selecionadas. Apenas a abundância de repteis foi maior durante o periodo chuvoso, nao havendo correlacao da riqueza e abundância com as variaveis climaticas selecionadas. Tres anfibios ( Rhinella marina (Linnaeus, 1758) , Adenomera hylaedactyla (Cope, 1868) e Allobates femoralis (Boulenger, 1884 “1883”)) e dois repteis ( Kentropyx penviceps Cope, 1868 e Norops fuscoauratus (D’Orbigny, 1837)) tiveram suas abundâncias mensais correlacionadas com variaveis climaticas. Foi possivel verificar o aumento da riqueza e abundância de anfibios e repteis durante periodos em que a disponibilidade de recursos e favoravel para muitas especies. A utilizacao das especies dominantes mostrou que as especies podem responder de formas diferentes as variacoes climaticas, enquanto algumas sao sensiveis as flutuacoes, outras parecem nao responder facilmente ou nao reduzir suas abundâncias em periodos teoricamente desfavoraveis.
An Integrative Investigation of Convergent Bipedal Locomotion in Desert Rodents

Bipedalism is commonly assumed to be an adaptive convergence because it has evolved independently three times in small desert rodents. However, the functional benefits of bipedality in this ecosystem have long been unclear. In this thesis I integrate phylogenetics, functional morphology, biomechanics, information theory, and behavior to investigate whether and how bipedality increases fitness in desert ecosystems, and whether bipedal rodents convergently evolved to have the role in their respective ecosystems. Based on the diversity of extant dipodid rodents, I begin by statistically reconstructing the pattern of morphological evolution in jerboas. I find that the strongest indicator of bipedality is metatarsal to humerus length, and that changes in this ratio are associated with increased rates of speciation, supporting a punctuated equilibrium pattern of evolution in this clade. Furthermore, the distinct patterns of morphological evolution suggest that a complex suite of genetic and developmental mechanisms governs the acquisition of bipedality in jerboas. I then use an inverse dynamics approach to characterize the biomechanics of bipedal hopping in a derived jerboa. I find that the dynamics of jerboa hopping are generated predominantly by muscular contractions, rather than tendon–based elastic energy storage and return between strides. Therefore hopping in small rodents favors rapid production and absorption of forces, rather than sustained bouts of steady–state locomotion. By reviewing predator–prey studies in biomechanics, ecology, and evolution I hypothesize that ricochetal locomotion enhances the ability of small rodents to evade predators that hunt via ballistic interception. I then develop Information Theoretic techniques to measure the unpredictability of escape trajectories in sympatric bipedal and quadrupedal rodents. As expected, bipedal rodents use significantly more unpredictable escape trajectories, likely enhancing predator evasion ability
Studies on Compatibility of Fungal Aalkaline Protease with Commercially Available Detergents

In the present endeavour, a total of 27 mold isolates were obtained from 10 soil samples by serial dilution agar plate technique and all these fungal isolates were screened for production of alkaline protease on casein agar plates. The most promising isolate was identified on the basis of cultural and microscopically characteristics as Aspergillus niger. Various cultural parameters such as substrate concentrations, enzyme concentrations, pH and temperature were observed for the optimization of production of alkaline protease. Optimum enzyme activity was observed at 1% substrate concentration, 10% enzyme concentration, at temperature 50 °C and at pH 8.5. In presence of casein, alkaline protease of Aspergillus niger retained 66-86% activity in the presence of commercially available detergents such as Tide, Surf excel, Wheel, Rin and Nirma, indicating its suitability for application in detergent industry. The lab-scale study on protease production by Aspergillus niger might give the basic information of further development for large scale production.
Passive restoration following ungulate removal in a highly disturbed tropical wet forest devoid of native seed dispersers

Overabundant ungulate populations can alter forests. Concurrently, global declines of seed dispersers may threaten native forest structure and function. On an island largely devoid of native vertebrate seed dispersers, we monitored forest succession for 7 years following ungulate exclusion from a 5‐ha area and adjacent plots with ungulates still present. We observed succession from open scrub to forest and understory cover by non‐native plants declined. Two trees, native Hibiscus tiliaceus and non‐native Leucaena leucocephala, accounted for most forest regeneration, with the latter dominant. Neither species is dependent on animal dispersers nor was there strong evidence that plants dependent on dispersers migrated into the 5‐ha study area. Passive restoration following ungulate removal may facilitate restoration, but did not show promise for fully restoring native forest on Guam. Restoration of native forest plants in bird depopulated areas will likely require active outplanting of native seedlings, control of factors resulting in bird loss, and reintroduction of seed dispersers.
INVITRO ANTI-DIABETIC ACTIVITY OF ETHANOLIC EXTRACT IN ANDROGRAPHIS PANICULATA LEAVES

Plant research has been intensified worldwide in the recent times. A large number of medicinal plants and their purified constituents have immense therapeutic potentials and have been reported to exhibit antidiabetic activity of ethanolic extract Andrographis paniculata. In vitro anti-diabetic was investigated by using alpha amylase, alpha glucosidase, tyrosinase, glucose uptake in yeast cells, heamoglobin glycosylation, extracts on heamoglobin glycosylation, extracts at physiological glucose concentration. The preliminary phytochemical analysis is also carried out. The results of the present study clearly depicted that ethanolic extract of Andrographis paniculata has potent antidiabetic activity.
Rosemary as natural antioxidant to prevent oxidation in chicken burgers

Natural antioxidants offer alternatives approach to prevent the oxidative deterioration of foods. Such compounds found in plants have attracted considerable interest in preventing the auto-oxidation of fat and oil in foods (Fernández-Ginés et al., 2005; Mariutti et al., 2008). Antioxidant activities of herbs, spices, vegetables and other extracts has been linked to phenolic compounds, suggesting that the antioxidant action is similar to that of the synthetic additives (Asolini et al., 2006; Rêgo et al., 2011). Antioxidants act as scavengers of free radicals and oxygen, which reduce the progress of lipid peroxidation. However, it is need hinder the free radicals production at start of the reaction sequence or to interrupt the sequence at some point (Singleton et al., 1999).
Oscillatory Activity in the basal ganglia of Patients with Parkinson's Disease

Parkinson’s disease (PD) is a movement disorder that is of basal ganglia origin. It is characterized by a severe loss of dopaminergic input to the striatum and symptoms such as bradykinesia, rigidity and tremor. There is growing evidence that PD is associated with pathological synchronous oscillatory activity in the basal ganglia, which primarily occurs in the 11-30 Hz range, the so-called beta band. The aim of this project was to better understand the oscillatory activity recorded from the basal ganglia of PD patients and to elucidate the significance of this activity in PD. To do this, neuronal firing and local field potentials (LFPs) were recorded from the subthalamic nucleus (STN) and globus pallidus internus (GPi) of PD patients undergoing stereotactic neurosurgery for implantation of therapeutic deep brain stimulation electrodes. Beta oscillatory LFP activity in the STN and GPi was found to be coherent with, and reflect to a certain degree, rhythmic activity in a population of local neurons. I have demonstrated for the first time that the degree of beta oscillatory firing in the STN, which is maximal in the motor portion, correlates with the patients’ benefit from dopaminergic medications, but not with baseline motor deficits. My study has also established that beta oscillatory firing in the STN does not positively correlate with the patients’ tremor scores and that during periods of tremor patients tend to have less beta oscillatory firing and increased neuronal oscillatory firing at the tremor frequency. Temporal examination of the LFPs recorded during periods of intermittent resting tremor revealed that stronger tremor is associated with increased LFP power in the low gamma range (35-55 Hz) and there is a decrease in the ratio of beta to gamma coherence. Similarly, a change in balance between oscillatory activities was observed during levodopa-induced dyskinesias. Finally, when the oscillatory activity in the GPi of PD patients was compared to that in dystonia I found that in dystonia, oscillatory LFP activity is less likely to reflect the neuronal firing. These findings indicate that beta oscillatory activity in the basal ganglia might reflect the degree of dopamine deficiency in
Effects of Temperature Change on Heat Shock Protein 70 Expression in Rat Testes

Purpose: It has been reported that exposure of the testes to elevated temperatures results in decreased spermatogenesis. The aim of this study was to investigate the effects of temperature change on the expression of heat shock protein 70 (HSP 70) during spermatogenesis in rat testes. Materials and Methods: Twenty-seven Sprague-Dawley rats (200-230g) were randomly divided into control, hot bath and hot bath followed by cold bath, groups. The hot bath consisted of immersion in a 41-43 water bath for 10 minutes, and the cold bath consisted of immersion in a 18-20 water bath for 3 minutes. Each bathing was performed twice a day, three times a week, for a total of four weeks. Hematoxylin & Eosin staining was performed to evaluate the degree of spermatogenesis, and Western blot & immunohistochemistry were performed to investigate the expression of HSP 70 in the rat testes. Results: From the histological tests, the spermatogenesis was severely impaired in hot bath group, but preserved in hot bath followed by cold bath group. The expression of HSP 70 in the hot bath group increased 1.5 times compared to that in the control group (p=0.075). However, the hot followed by cold bath group showed similar findings to those in the controls (p=0.934). Immunohistochemical analysis for the expression of HSP 70 demonstrated significant elevations in the hot bath group, and HSP 70 immunoreactivity was found in the Leydig cells and fibroblasts in all three groups, but the levels of expression of the HSP 70 in the control, and the hot followed by cold bath, groups were similar. Conclusions: The results of this study demonstrate an elevation in the expression of the HSP 70 only occurred in the hot bath group, which suggests the induction of a coping mechanism for exposure to high temperature. As the levels of expression of the HSP 70 in the control, and hot followed by cold bath, groups were comparable, is suggestive of the levels of HSP 70 being consistent with those seen with normal spermatogenesis.
Development of kairomone-based lures and traps targeting Spilonota ocellana (Lepidoptera: Tortricidae) in apple orchards treated with sex pheromones

Abstract Spilonota ocellana (Denis and Schiffermüller) (Lepidoptera: Tortricidae) can be a serious pest of organic apples (Malus domestica Borkhausen (Rosaceae)) in British Columbia, Canada. Recent discovery that S. ocellana moths are attracted by a lure combining acetic acid (AA) and benzyl nitrile (BN), identified as a caterpillar-induced apple leaf volatile, provides an opportunity to develop bisexual mass-trapping or monitoring systems. Sticky white delta traps baited with benzyl nitrile (10 mg/red rubber septum) and an acetic-acid co-lure (3 mL AA/3-mm open 8-mL vial) caught significantly more moths than either component alone. Acetic-acid co-lures were weakly attractive but benzyl-nitrile-loaded septa were not attractive. Moth catches with AA+BN lures were unaffected by the size and type of rubber septum used to release benzyl nitrile, but catches increased with increasing loads of benzyl nitrile. Male and total moth catches were maximised using membrane release devices loaded with a mixture of benzyl nitrile and a second caterpillar-induced volatile, 2-phenylethanol (PET), in combination with an acetic-acid co-lure (AA+BN-PET). Female catches with AA+BN-PET and AA+BN lures were equivalent. Placing AA+BN lures in traps baited with female sex pheromone lures reduced male catches, but female catches were unchanged. When sticky liners were replaced weekly, white delta traps baited with AA+BN lures caught more moths than similarly baited white Multipher®-I bucket traps, or transparent UnitrapsTM. Multipher-I traps with a propylene glycol killing agent (250 mL) caught more moths than those with Vapona insecticide strips. In apple orchards treated with mating disruption sex pheromones, traps baited with AA+BN caught slightly more total moths than traps baited with sex pheromone. Weekly, total male+female moth catches with either AA+BN or sex pheromone lures showed similar seasonal patterns in both untreated and pheromone-disrupted orchards, respectively. Long-lasting release devices and an organic killing agent are needed to develop certified organic mass-trapping technologies for management of S. ocellana with the AA+BN kairomone.
Antioxidants and radical scavenging role of Leek (Allium kurrat) against aflatoxin-contaminated peanut

Abstract The rats treated with leek (Allium kurrat) extract before and after their hepatotoxicity induction by aflatoxins (AFs) B1 and B2 showed a significant decrease in the levels of the oxidation radicals and a significant increase in the level of these hepatic enzymes compared to their corresponding values of the AF-treatment. These levels approached to those corresponding values of the negative control. The histological investigation confirmed strongly the highly protective effect of the leek extract in the hepatocytes. These findings suggest that the leek extract is effective in improving both the function and structure of the hepatocytes through a potent antioxidant effect.