Miracle-dz/UniFAR-FTUs huggingface dataset:
Neglected seed dispersers: endozoochory by Javan lutungs (Trachypithecus auratus) in Indonesia

Leaf monkeys are known to be leaf eaters, and thus, their potential role as seed dispersers has been neglected. However, they do also feed on fruits. To examine the role of leaf monkeys as endozoochorous seed dispersers, we studied the Javan lutung (Trachypithecus auratus) in Indonesia. We compared multiple aspects of seed dispersal processes (amount and diversity of seeds ingested, dispersal distance, and germination rate) of lutungs with that of the sympatric long‐tailed macaque (Macaca fascicularis). Over the study period, 54 percent of the lutung feces contained intact seeds, which was equivalent to the macaque feces contained seeds (62%). Seeds of at least six plant species were detected in the lutung feces, which was less than those found in the macaque feces (>19 plant species). The main species of seeds defecated by both lutungs and macaques was Ficus spp. (seed size: 0.7 mm). Seed shadow, estimated from travel distance (range: 1–299 m) and gut passage rate (24–96 h), had a unimodal‐distribution with a peak at 51–100 m, and was shorter than that reported in published accounts of macaques and other similar and smaller sized frugivores. Finally, germination rates of Ficus spp. seeds ingested by both lutungs and macaques were lower than that of the control seeds. These results imply that the dispersal effectiveness of lutungs would be lower than that of the sympatric primate frugivores. However, at a population level, lutungs could play a significant role as seed dispersers for the small‐seeded species, and therefore, more research into their frugivorous habits is warranted.
The Roles of Mitochondrial Folate Metabolism in Supporting Mitochondrial DNA Synthesis, Oxidative Phosphorylation, and Cellular Function

ABSTRACT Folate-mediated one-carbon metabolism (FOCM) is compartmentalized within human cells to the cytosol, nucleus, and mitochondria. The recent identifications of mitochondria-specific, folate-dependent thymidylate [deoxythymidine monophosphate (dTMP)] synthesis together with discoveries indicating the critical role of mitochondrial FOCM in cancer progression have renewed interest in understanding this metabolic pathway. The goal of this narrative review is to summarize recent advances in the field of one-carbon metabolism, with an emphasis on the biological importance of mitochondrial FOCM in maintaining mitochondrial DNA integrity and mitochondrial function, as well as the reprogramming of mitochondrial FOCM in cancer. Elucidation of the roles and regulation of mitochondrial FOCM will contribute to a better understanding of the mechanisms underlying folate-associated pathologies.
Analysis of the Interaction of the Adenovirus L1 52/55-Kilodalton and IVa2 Proteins with the Packaging Sequence In Vivo and In Vitro

We previously showed that the adenovirus IVa2 and L1 52/55-kDa proteins interact in infected cells and the IVa2 protein is part of two virus-speciﬁc complexes (x and y) formed in vitro with repeated elements of the packaging sequence called the A1-A2 repeats. Here we demonstrate that both the IVa2 and L1 52/55-kDa proteins bind in vivo to the packaging sequence and that each protein-DNA interaction is independent of the other. There is a strong and direct interaction of the IVa2 protein with DNA in vitro. This interaction is observed when probes containing the A1-A2 or A4-A5 repeats are used, but it is not found by using an A5-A6 probe. Furthermore, we show that complex x is likely a heterodimer of IVa2 and an unknown viral protein, while complex y is a monomer or multimer of IVa2. No in vitro interaction of puriﬁed L1 52/55-kDa protein with the packaging sequence was found, suggesting that the L1 52/55-kDa protein–DNA interaction may be mediated by an intermediate protein. Results support roles for both the L1 52/55-kDa and IVa2 proteins in DNA encapsidation.
Crystallization of ApoA1 and ApoE4 nanolipoprotein particles and initial XFEL-based structural studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via HDL and LDL maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics and develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar in characteristics to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
Fusarium in winter wheat: mycotoxin accumulation in straw and a survey of roots

Management of Fusarium graminearum-associated mycotoxins in wheat grain has been extensively evaluated, but little is known about management of mycotoxins in straw tissue. Two studies were conducted from 2011 to 2014 to determine the efficacy of fungicides and the use of integrated disease management strategies for the control of Fusarium head blight (FHB) and the subsequent accumulation of the Fusarium mycotoxins deoxynivalenol (DON), 3-acetyldeoxynivalenol (3ADON), and 15-acetyl-deoxynivalenol (15ADON) in the straw. The first study tested the effect of fungicides at four locations with mycotoxin accumulations ranging from 0.19 to 154.5 parts per million (ppm), 0 to 10.1 ppm, and 0 to 29.8 ppm for DON, 3ADON, and 15ADON, respectively, across all locations and years. In this study, it was determined that demethylation inhibitor (DMI) fungicides did not offer significant (P ≤ 0.05) control of mycotoxin accumulation in the straw over no-fungicide control treatment, but significant (P ≤ 0.05) reductions in mycotoxin accumulation were seen when compared treatments with the application of quinone outside inhibitor (QoI) fungicides. In the second study, the level of mycotoxin accumulation in straw was compared in a susceptible cultivar to that of a moderately resistant cultivar, with and without fungicide applications at four locations. The accumulation of mycotoxins ranged from 0 to 47.1 ppm, 0 to 3.3 ppm, and 0 to 15.7 ppm for DON, 3ADON, and 15ADON, respectively, across all locations and years. Results from this study indicated that the use of a moderately resistant cultivar offered significant (P ≤ 0.05) control of mycotoxin
Carnian (Upper Triassic) Lavas and Tuffites from the Mersin Mélange: Evidence for Intraoceanic Arc Rifting in the Northern Neotethys

In Anatolia, the northern branch of Neotethys is represented by Izmir-Ankara-Erzincan (IAE) Ocean, whose fragments and associated continental entities are preserved in the IAE Suture. However, the traces of this northerly located ocean are not solely bound to the IAE Suture, but can also be found further to the south. The Mersin Mélange, situated in southern Turkey, is such a place that preserves the southerly transported remnants of the northern Neotethys. The Mersin Mélange essentially displays block-in-matrix features, with blocks/slices of different age and lithological characteristics embedded in a clastic matrix. Within the mélange, the Degirmenocagi region consists of a volcano-sedimentary sequence of middle Carnian age, which is characterized by lavas and tuffites interbedded with pelagic sedimentary lithologies. The lavas are chemically of basaltic/basaltic-andesitic composition, whereas the tuffites are of rhyolitic composition. Both lavas and tuffites display negative Nb anomalies, suggesting the involvement of subduction-related components. The high Zr/Nb and low Nb/Yb ratios (compared with normal mid-ocean ridge basalt [N-MORB]) imply a variably depleted mantle source, which has experienced previous melt extraction. The ratio-based melting systematics reflects melt generation largely dominated by spinel-facies melts. The overall geological and geochemical characteristics of the Degirmenocagi sequence suggest an oceanic backarc setting during the Carnian, which may have developed by the rifting of the Sorgun Arc. Although this new finding shows that the Triassic intraoceanic subduction is not uncommon in the Neotethys, it also strengthens a pre-Liassic opening of the northern domain (i.e., the IAE Ocean) and may further explain the longevity of the Middle–Late Triassic intraoceanic subduction in the northern Neotethys.
Functional diversity enhances detection of ecosystem stability and resolution of predator-prey interactions within a multitrophic community

Kissick, Ashley L. Ph.D., Purdue University, December 2016. Functional Diversity Enhances Detection of Ecosystem Stability and Resolution of Predator-Prey Interactions Within a Multitrophic Community. Major Professor: Jeffrey D. Holland. Habitat fragmentation and loss are principal factors that contribute to the decline of biodiversity which in turn has a negative impact on ecosystem function. There has been growing interest in understanding diversity’s role in the mechanisms behind ecosystem resilience with much attention focusing on how functional diversity, or the range of species’ ecological roles in a community, impacts ecosystem function. Under the functional insurance hypothesis, stability in ecosystems is maintained by species that perform similar functions but have asynchronous responses to disturbance. There are three proposed stability mechanisms that operate through species’ asynchronous responses: cross-scale resilience, response diversity, and density compensation. My objective in this study was to examine change in functional diversity resulting from habitat fragmentation and detect ecological stability mechanisms in a multitrophic community consisting of longhorned beetles and their beetle predators. I also considered predator-prey interactions between beetles and their insectivore avian predators at the community level.
MAPLE Deposition of Binary and Ternary Organic Bulk Heterojunctions Based on Zinc Phthalocyanine

Organic bulk heterojunctions (BHJ) based on zinc phthalocyanine (ZnPc), fullerene compounds (C60 fullerene and [6,6]-phenyl C71 butyric acid methyl ester (PC70BM)), and 5,6,11,12-tetraphenylnaphthacene (rubrene) were fabricated through the matrix-assisted pulsed-laser evaporation (MAPLE) technique. Thus, ZnPc:C60 and ZnPc:PC70BM binary BHJ and ZnPc:rubrene:PC70BM ternary BHJ were deposited as thin films on various substrates. The preservation of the chemical structure of the organic compounds during the MAPLE deposition was confirmed by infrared spectroscopy. The structural, optical, and morphological properties of the deposited layers were investigated by X-ray diffraction (XRD), UV-Vis spectroscopy, photoluminescence (PL), field emission scanning electron microscopy (FESEM), and atomic force microscopy (AFM), respectively. Further, the electrical properties of the developed structures based on ZnPc:C60, ZnPc:PC70BM, and ZnPc:rubrene:PC70BM were evaluated. The J-V characteristics of the organic structures, recorded under illumination, show that an increase in the open-circuit voltage (VOC) is achieved in the case of the ternary blend in comparison with that obtained for the binary blends. The results evidenced that MAPLE-deposited thin films containing binary and ternary organic bulk heterojunctions can find applications in the field of photovoltaic devices.
Optimization Of Motion Compensation Based On GPU And CPU For VVC Decoding

To achieve higher compression efficiency, the new developing video coding standard Versatile Video Coding(VVC) introduced a large amount of new coding technologies, which increases the computational complexity of the decoder significantly. Among these technologies, the inter prediction methods, including affine motion compensation and decoder side motion vector refinement(DMVR), make inter prediction become the most time consuming module and bring new challenges for real-time decoding. In this paper, we proposed an efficient GPU-based motion compensation scheme to speedup the decoding. Through re-partition of coding unit(CU) according to the data dependency and different thread organization methods for different situation, the computational resources of GPU are utilized efficiently. Experiments on NVIDIA GeForce RTX 2080Ti GPU showed the motion compensation can be done in 5ms for Ultra HD 4K, which means the decoding speed is accelerated by 16 times compared to the VVC reference software on CPU.
Attentional capture by threatening stimulus: effect of SOA

In the present study, we investigated whether exposure duration of threatening stimuli modulate the effect on automatic capture of visual attention. We used dot probe task to assess the extent to which emotional valence would influence deployment of attention with short and long exposure durations (300ms and 1000ms). The results of this study showed that reaction times (RTs) to a small dot (i.e., probe) that followed threatening stimuli were longer than those to the same probe that followed positive stimuli. Moreover, this difference between positive and negative emotion was significant for 1000ms exposure duration. It is suggested that inhibitory effect by aversive emotion was likely to increase as exposure duration became longer. (本研究では、情動刺激の提示時間が、その刺激の情動価が視覚的注意へ及ぼす影響を 変化させるのかを検討した。 本研究では、情動価が注意へ及ぼす影響を評価するためにプ ローブ課題を使用した。 さらに、その影響の大きさと提示時間との関連を検討するために 2種類の提示時間を採用した。 その結果、ネガティブ刺激が提示された場合には、引き続 き出現するターゲットへの反応時間が、ポジティブ刺激と比較して長くなることが示され た。 また、この傾向はSOAが1000msの条件で顕著であった。 以上の結果は、恐怖関連刺 激による抑制効果は提示時間と関連することを示唆する。 )
Barriers to Early Detection of Breast Cancer Among Women Living in Poverty

Objective: Early detection and screening are the most effective means to reduce breast cancer mortality in all populations. In this study, the inhibiting factors in the applications of qualitative research methods used for early diagnosis of breast cancer among poor women were identified. Material and methods: Through focus group interviews, 40 women ranging between 20-60 years of age, meeting the absolute poverty criteria, without regular breast self-examination, clinical breast examination and mammography were recruited for the study. A conventional content analysis method was used in the data analysis. Interviews were recorded using a voice recorder, and the average duration of the interviews was 53 minutes. Results: Factors inhibiting women's behaviors regarding early detection of breast cancer were identified as, respectively; individual attitudes and beliefs, provision of healthcare services and, cultural factors. Conclusion: According to the data achieved, we concluded that, initiatives should be planned in order to reduce the inhibiting factors in the breast cancer screening behaviors of women living in poverty. In addition, health policies concerning provision of health care services should be revised.
Detection and quantification of viral RNA in human tumors using open source pipeline: viGEN

Introduction An estimated 17% of cancers worldwide are associated with infectious causes. The extent and biological significance of viral presence/infection in actual tumor samples is generally unknown but could be measured using human transcriptome (RNA-seq) data from tumor samples. We present an open source bioinformatics pipeline viGEN that combines existing well-known and novel RNA-seq tools for not only detection and quantification of viral RNA, but also variants in the viral transcripts. Methods The pipeline includes 4 major modules: The first module allows to align and filter out human RNA sequences; second module maps and count (remaining un-aligned) reads against reference genomes of all known and sequenced human viruses; the third module quantifies read counts at the individual viral genes level thus allowing for downstream differential expression analysis of viral genes between experimental and controls groups. The fourth module calls variants in these viruses. To the best of our knowledge, there are no publicly available pipelines or packages that would provide this type of complete analysis in one open source package.
Influence of Roundup Ready Soybean Production Systems and Glyphosate Application on Pest and Beneficial Insects in Narrow-Row Soybean

Roundup Ready® soybeans, Glycine max (L.) Merrill, in narrow-row planting systems were investigated in 1998 in Mississippi to evaluate the effects of the transgenic crop and glyphosate herbicide on pest and beneficial insects. Insects found in sufficient numbers for meaningful analysis included adult bean leaf beetle, Cerotoma trifurcata (Forster); adult three-cornered alfalfa hopper, Spissistilus festinus (Say); adult big-eyed bug, Geocoris punctipes (Say), and; larvae of green cloverworm, Plathypena scabra (F.), and velvetbean caterpillar, Anticarsia gemmatalis (Hubner). Populations of C. trifurcata, S. festinus, P. scabra and A. gemmatalis were not reduced in genetically altered Roundup Ready soybean, or by recommended (by label) or delayed applications of glyphosate. Numbers of G. punctipes also were not reduced in Roundup Ready soybean, but were reduced by recommended applications of glyphosate during weeks three and four following the second recommended herbicide application. Geocoris punctipes dens.
Characterization of Rps 8 and Rps 3 Resistance Genes to Phytophthora sojae through Genetic Fine Mapping and Physical Mapping of Soybean Chromosome 13

ii Dedication . iv Acknowledgments. v Vita . vii List of Figures . xi List of Tables . xiii Chapter 1: Literature Review . 1 Soybean biology and cultivation . 1 Phytophthora rot of soybean . 2 Soybean resistance to Phytophthora sojae . 4 Characteristics of plant resistance genes. 7 Chromosome 13 and genetic sources of Rps8 and Rps3. 11 Soybean reference genome . 14 Soybean genetic markers and linkage mapping . 16 Bacterial Artificial Chromosome library and physical mapping . 16 Ongoing research in resistance to Phytophthora sojae . 17 List of References . 19 Chapter 2: Linkage Mapping of Rps3a, Rps3c, and Rps8 . 29 Introduction . 29 Materials and Methods . 34 Germplasm . 34 Identification and maintenance of isolates . 35 Phenotypic assays for resistance to Phytophthora sojae . 35 DNA isolation from soybean tissue . 36 PCR-based marker screening . 37 Allelism studies . 38 Linkage mapping . 39 Mapping Rps3c locus . 40 Results . 41 Phytophthora sojae mapping isolates . 41 ix Allelism studies with isolate OH25 . 41 Genetic map of L83-570 (Rps3aRps3a) x PI 399073 (RpsNRpsNRps8Rps8) F3:4 population . 42 Genetic maps of L92-7857 (Rps3cRps3c) x PI 399073 (RpsNRpsNRps8Rps8) F3:4 population . 43 Consistent association of Rps8 resistance to chromosome 13 . 44 Resistance from L92-7857 is associated to chromosome 18 . 45 Discussion . 45 List of References . 72 Chapter 3: Physical Mapping and the Identification of Resistance Gene Candidate Sequences in Chromosome 13 . 77 Introduction . 77 Materials and Methods . 83 Updated graphical genotyping of Williams (rps) PI 399073 (RpsNRpsNRps8Rps8) backcross lines . 83 Construction of BAC libraries . 84 Primer walking of soybean chromosome 13 . 85 BAC plasmid sequencing . 86 BAC insert sequence analysis . 87 Results . 87 Graphical genotyping analysis with OH25 . 87 Identification of chromosome 13-specific BAC clones from PI 399073 (RpsNRpsN Rps8Rps8) libraries . 88 Identification of chromosome 13-specific BAC clones from L83-570 (Rps3aRps3a) library . 89 Discussion . 89 List of References. 97 Bibliography . 100 Appendix A: Phenotypic Analysis of PI 172901 PI 399073 F3:4 Population . 112 Appendix B: Chromosome 13 SSR and PAMSA Markers . 114 Appendix C: Protocols . 127 Isolation of Phytophthora sojae from Infected Soybean Seedlings. 128 Rolled Towel Hypocotyl Inoculation of Soybean with Phytophthora sojae . 130 Isolation of Soybean Genomic DNA via Modified CTAB Method . 133 PCR-Based Screening of Bacteria Artificial Chromosome Libraries . 137 Screening PI 399073 BAC Libraries . 143 Screening L83-570 BAC Library. 145
Selenium concentration of Finnish foods: Effects of reducing the amount of selenate in fertilizers

The original two supplementation levels of selenium in multinutrient fertilizers (Se 16 and 6 mg kg1 fertilizer as sodium selenate; started in 1985) were reduced to one (6 mg kg 1 fertilizer) in 1991. The 16 mg supplementation level was intended for use in cereal production. Due to the lowering of the level of Se application, the Se content of spring cereals (spring wheat, oats and barley) has decreased more than that of any other food in the monitoring programme. The present level, 0.1 mg kg ' for cereal grains, is about 40% of the concentrations common in 1990. The Se concentrations have decreased less in other foods than in cereals. The present Se concentrations in milk products, meat and liver are about 70, 60 and 50%, respectively, of the concentrations in 1990. The average daily human Se intake was 0.08 mg day 1 at an energy level of 10 MJ in 1994. Animal protein is the main source of Se. About 40% of the intake comes from meat, 24% from dairy products and eggs, and 11% from fish.
Alpha-taxonomy in the cricetid rodent Neomicroxus, a first assessment

Neomicroxus , a recently named genus, comprises small-bodied cricetid rodents patchily distributed in high-Andean ranges from Ecuador to Venezuela. Currently, two species of Neomicroxus are recognized, N. bogotensis , endemic to the Cordillera Oriental in Colombia and Cordillera de Merida and Paramo de Tama in Venezuela, and N. latebricola that occurs northern Andes of Ecuador. The genus is among the most poorly understood Neotropical rodents and to date no formal assessment about its alpha taxonomy was conducted. Based on DNA evidence of the first portion of the mitochondrial cytochrome b gene (cytb) and the first exon of the interphotoreceptor retinoid binding protein (IRBP), as well as craniodental measurements, we explored the divergence degree, genetic structure and phyletic relationships of the two species currently allocated under Neomicroxus . Our analyses support the monophyly of the genus as well as its uncertain tribal affiliation. Neomicroxus was retrieved as structured in two main branches, in agreement with the traditional recognition of two species. The populations referred to N. bogotensis exhibit deep divergence values (> 6 %) pointing to the existence of undescribed species under its concept. In contrast, populations of N. latebricola show a shallow genetic structure although implying recognizable geographical breaks. A moderate degree of genetic and morphological differentiation supports a new subspecies for the western populations of N. latebricola . Our contribution is the first attempt to better understanding the alpha taxonomy of Neomicroxus , highlighting the importance of the geographic complexity as a barrier to the genetic flow in N. bogotensis and the significance of the subspecies concept to formalize the geographic variation recovered in N. latebricola