Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial and temporal expansions of Eastern equine encephalitis virus and phylogenetic groups isolated from mosquitoes and mammalian cases in New York State from 2013 to 2019

ABSTRACT Surveillance for the emerging infectious disease Eastern equine encephalitis, and its causative virus in mosquitoes, continued within New York State from 2013 to 2019. There were increases in geographic area and number of consecutive years, with cases in four mammalian species, and virus in 11 mosquito species. The first cases in a goat and in an emu were reported. The first detection of virus in Aedes cinereus was reported. Virus in phylogenetic group NY4 was isolated from a horse and from mosquitoes 6 kilometers and 13 days apart in 2013. Phylogenetic groups NY4 and NY5 were found 15 days apart in two towns 280 kilometers distant in 2013. Within four adjacent counties there was a pattern of overlap, where four had NY5, two adjacent counties had NY6, two adjacent counties had NY7, and one county had NY5, NY6, and NY7, reducible to a Euler diagram. Virus in phylogenetic group NY5, found within an 11-kilometer wide area in New York State, was related to FL4 found in Florida 1,398 kilometers distant. This was consistent with a phylogenetic group originating in Florida, then being moved to a specific location in New York State, by migratory birds in consecutive years 2013 and 2014.
Evaluation of Mayfly Species Originally Described as Baetis Leach (Ephemeroptera: Baetidae) from California

Abstract Eight species of mayflies described in Baetis Leach from California are evaluated for validity, generic classification, and distribution. Taxonomic status quo is maintained for the southwestern Baetis adonis Traver [ = B. sp. A Morihara and McCafferty, = B. caelestis Allen and Murvosh], B. devinctus Traver [synonym of Diphetor hageni (Eaton)], and B. leechi Day [synonym of Fallceon quilleri (Dodds)]. Baetis alius Day is shown to be common in the northwestern U.S.A. and somewhat variable but distinctive as larvae; B. moqui Wiersema, Nelson and Kuehnl is shown to be a junior synonym of B. alius, new synonym. Baetis diablus Day is correctly placed to genus but remains unknown as larvae and has been rarely taken only in California; it is possibly a variant of B. tricaudatus Dodds. Baetis palisadi Mayo is correctly placed to genus, and based on discovered larvae has diagnostic mandibles and labial palpi among rhodani group species; it is apparently endemic to California and of environmental concern. Baetis piscatoris Traver is correctly placed to genus, relatively common in California, and based on discovered larvae is the only known rhodani group species with elongate gills. Baetis sulfurosus Day belongs in Fallceon Waltz and McCafferty, as evidenced by discovered larvae; it is also a junior synonym of the western F. thermophilos (McDunnnough), new combination, new synonym, and is distinct from western congeners by size and color pattern of larvae, and hindwings and subgenital plate of adults.
Clinicopathological Significance of EBV-Infected Gastric Carcinomas: A Meta-Analysis

Background and objectives: The present study aims to elucidate the clinicopathologic significance of Epstein–Barr virus (EBV) infection in gastric carcinomas (GCs) through a meta-analysis. Materials and Methods: Sixty-one eligible studies were included in the present meta-analysis. The included patients, with and without EBV infection, were 2063 and 17,684, respectively. We investigated the clinicopathologic characteristics and various biomarkers, including programmed death-ligand 1 (PD-L1) expression and tumor-infiltrating lymphocytes (TILs). Results: The estimated EBV-infected rate of GCs was 0.113 (95% confidence interval (CI): 0.088–0.143). The EBV infection rates in GC cells were 0.138 (95% CI: 0.096–0.194), 0.103 (95% CI: 0.077–0.137), 0.080 (95% CI: 0.061–0.106), and 0.042 (95% CI: 0.016–0.106) in the population of Asia, America, Europe, and Africa, respectively. There was a significant difference between EBV-infected and noninfected GCs in the male: female ratio, but not other clinicopathological characteristics. EBV infection rates were higher in GC with lymphoid stroma (0.573, 95% CI: 0.428–0.706) than other histologic types of GCs. There were significant differences in high AT-rich interactive domain-containing protein 1A (ARID1A) and PD-L1 expressions, and high CD8+ TILs between EBV-infected and noninfected GCs. Conclusions: Our results showed that EBV infection of GCs was frequently found in male patients and GCs with lymphoid stroma. EBV infection was significantly correlated with ARID1A and PD-L1 expressions and CD8+ TILs in GCs.
Cycles of trans‐Arctic dispersal and vicariance, and diversification of the amphi‐boreal marine fauna

The amphi‐boreal faunal element comprises closely related species and conspecific populations with vicarious distributions in the North Atlantic and North Pacific basins. It originated from an initial trans‐Arctic dispersal in the Pliocene after the first opening of the Bering Strait, and subsequent inter‐oceanic vicariance through the Pleistocene when the passage through the Arctic was severed by glaciations and low sea levels. Opportunities for further trans‐Arctic dispersal have risen at times, however, and molecular data now expose more complex patterns of inter‐oceanic affinities and dispersal histories. For a general view on the trans‐Arctic dynamics and of the roles of potential dispersal–vicariance cycles in generating systematic diversity, we produced new phylogeographic data sets for amphi‐boreal taxa in 21 genera of invertebrates and vertebrates, and combined them with similar published data sets of mitochondrial coding gene variation, adding up to 89 inter‐oceanic comparisons involving molluscs, crustaceans, echinoderms, polychaetes, fishes and mammals. Only 39% of the cases correspond to a simple history of Pliocene divergence; in most taxonomical groups, the range of divergence estimates implies connections through the entire Pliocene–Pleistocene–Holocene time frame. Repeated inter‐oceanic exchange was inferred for 23 taxa, and the latest connection was usually post‐glacial. Such repeated invasions have usually led to secondary contacts and occasionally to widespread hybridization between the different invasion waves. Late‐ or post‐glacial exchange was inferred in 46% of the taxa, stressing the importance of the relatively recent invasions to the current diversity in the North Atlantic. Individual taxa also showed complex idiosyncratic patterns and histories, and several instances of cryptic speciation were recognized. In contrast to a simple inter‐oceanic vicariance scenario underlying amphi‐boreal speciation, the data expose complex patterns of reinvasion and reticulation that complicate the interpretation of taxon boundaries in the region.
Evaluating the Brief Parental Intake Form (BPIF) for psychosocial difficulties in childhood cancer survivors

Childhood cancer survivors (CCS) are at increased risk for psychosocial difficulties compared to their peers. Consequently, guidelines recommend routine assessment for psychosocial late effects as part of survivorship care. However, empirical evidence to guide selection and implementation of behavioral screening in survivorship clinics is limited. Based on literature review and experience with a variety of measures in our clinic, we currently assess psychosocial function of CCS under age 18 by asking parents to complete the Brief Parental Intake Form (BPIF), a brief checklist measure developed by our team, and the Pediatric Symptom Checklist 17 (PSC-17), an established checklist measure. This study aimed to evaluate how accurately the BPIF identifies CCS with psychosocial difficulties compared to the PSC-17, and if the BPIF is feasible as a stand-alone screener.
RegulatorofG-ProteinSignaling10PromotesDopaminergic NeuronSurvivalviaRegulationoftheMicroglial InflammatoryResponse

Epidemiological studies suggest that chronic use of nonsteroidal anti-inflammatory drugs lowers the incidence of Parkinson’s disease (PD) in humans and implicate neuroinflammatory processes in the death of dopamine (DA) neurons. Here, we demonstrate that regulator of G-protein signaling 10 (RGS10), a microglia-enriched GAP (GTPase accelerating protein) for G subunits, is an important regulator of microglia activation. Flow-cytometric and immunohistochemical analyses indicated that RGS10-deficient mice displayed increased microglial burden in the CNS, and exposure to chronic systemic inflammation induced nigral DA neuron loss measured by unbiasedstereology.PrimarymicrogliaisolatedfrombrainsofRGS10-deficientmicedisplayeddysregulatedinflammation-relatedgene expression profiles under basal and stimulated conditions in vitro compared with that of primary microglia isolated from wild-type littermates.Similarly,knockdownofRGS10intheBV2microgliacelllineresultedindysregulatedinflammation-relatedgeneexpression, overproduction of tumor necrosis factor (TNF), and enhanced neurotoxic effects of BV2 microglia on the MN9D dopaminergic cell line that could be blocked by addition of the TNF decoy receptor etanercept. Importantly, ablation of RGS10 in MN9D dopaminergic cells further enhanced their vulnerability to microglial-derived death-inducing inflammatory mediators, suggesting a role for RGS10 in modulating the sensitivity of dopaminergic neurons against inflammation-mediated cell death. Together, our findings indicate that RGS10 limits microglial-derived TNF secretion and regulates the functional outcome of inflammatory stimuli in the ventral midbrain. RGS10emergesasanoveldrugtargetforpreventionofnigrostriatalpathwaydegeneration,theneuropathologicalhallmarkofPD.
Cell stress induces association of heat shock proteins with the cytoskeleton

The association of heat shock proteins (HSPs) with the cytoskeleton is important, since the actinbased cytoskeleton is a sensitive monitor of extra cellular stimuli and is critical in healing. Regarding HSPs, they operate with a number of homeostatic mechanisms to maintain the cellular functions during and after stress. Current investigation assesses the interaction of the heat shock proteins with the cytoskeleton proteins. For this purpose, HEp-2 cells were stressed by UVA or by caloric irradiation. The expression of HSP and cytoskeleton proteins was monitored by immunofluorescence and Western blot with monoclonal antibodies directed against HSP60, HSP70, HSP90, actin, tubulin and cytokeratin and polyclonal anti-HSP27. As expected, UVA irradiation and heat induced a ubiquitous expression of HSP, detected as sparse granules in the nucleus, the cytoplasm and the perinuclear area; HSP90 was chiefly expressed along the cytoskeleton, and was associated with actin and cytokeratin. Finally, the stress triggers HSP response, which is involved in cytoskeleton modification.
Impact of processing method on donated human breast milk microRNA content

Pasteurization of donated human milk preserves it for storage and makes it safe for feeding, but at the expense of its composition, nutritional values and functions. Here, we aimed to investigate the impact of Holder Pasteurization (HoP) and High Pressure Processing (HPP) methods on miRNA in human milk and to evaluate impact of these changes on miRNA functions. Milk samples obtained from women in 50th day of lactation (n = 3) were subjected either to HoP, HPP or remained unpasteurized as a control. Subsequently, miRNA was isolated from whole material and exosomal fraction and sequenced with Illumina NextSeq 500. Sequencing data were processed, read counts were mapped to miRNA and analyzed both quantitatively with DESeq2 and functionally with DIANA mirPath v.3. While HPP caused statistically insignificant decrease in number of miRNA reads compared to unprocessed material, HoP led to 82-fold decrease in whole material (p = 0.0288) and 302-fold decrease in exosomes (p = 0.0021) not leaving enough reads for further analysis. Changes in composition of miRNA fraction before and after HPP indicated uneven stability of individual miRNAs under high pressure conditions, with miR-30d-5p identified as relatively stable and miR-29 family as sensitive to HPP. Interestingly, about 2/3 of unprocessed milk miRNA content consists of only 10 distinct miRNAs with miR-148a-3p at the top. Functional analysis of most abundant human milk miRNAs showed their involvement in signaling pathways, cell communication, proliferation and metabolism that are obviously important in rapidly growing infants. Functions of miRNAs which suffered the greatest depletion during HPP were similar to roles of the majority of unprocessed human milk’s miRNA, which indicates that those functions may be weakened although not completely lost. Our findings indicate that HPP is less detrimental to human milk miRNAs than HoP and should be considered in further research on recommended processing procedures for human milk banks.
Dissecting distinct proteolytic activities of FMDV Lpro implicates cleavage and degradation of RLR signaling proteins, not its deISGylase/DUB activity, in type I interferon suppression

The type I interferon response is an important innate antiviral pathway. Recognition of viral RNA by RIG-I-like receptors (RLRs) activates a signaling cascade that leads to type I interferon (IFN-α/β) gene transcription. Multiple proteins in this signaling pathway (e.g. RIG-I, MDA5, MAVS, TBK1, IRF3) are regulated by (de)ubiquitination events. Most viruses have evolved mechanisms to counter this antiviral response. The leader protease (Lpro) of foot-and-mouth-disease virus (FMDV) has been recognized to reduce IFN-α/β gene transcription; however, the exact mechanism is unknown. The proteolytic activity of Lpro is vital for releasing itself from the viral polyprotein and for cleaving and degrading specific host cell proteins, such as eIF4G and NF-κB. In addition, Lpro has been demonstrated to have deubiquitination/deISGylation activity. Lpro’s deubiquitination/deISGylation activity and the cleavage/degradation of signaling proteins have both been postulated to be important for reduced IFN-α/β gene transcription. Here, we demonstrate that TBK1, the kinase that phosphorylates and activates the transcription factor IRF3, is cleaved by Lpro in FMDV-infected cells as well as in cells infected with a recombinant EMCV expressing Lpro. In vitro cleavage experiments revealed that Lpro cleaves TBK1 at residues 692–694. We also observed cleavage of MAVS in HeLa cells infected with EMCV-Lpro, but only observed decreasing levels of MAVS in FMDV-infected porcine LFPK αVβ6 cells. We set out to dissect Lpro’s ability to cleave RLR signaling proteins from its deubiquitination/deISGylation activity to determine their relative contributions to the reduction of IFN-α/β gene transcription. The introduction of specific mutations, of which several were based on the recently published structure of Lpro in complex with ISG15, allowed us to identify specific amino acid substitutions that separate the different proteolytic activities of Lpro. Characterization of the effects of these mutations revealed that Lpro’s ability to cleave RLR signaling proteins but not its deubiquitination/deISGylation activity correlates with the reduced IFN-β gene transcription.
Cytoplasmic Linker Proteins: Keeping in Shape by Regulating the Cytoskeleton

textabstractMicrotubules are an essential component of the eukaryotic cytoskeleton. Proper functioning of the microtubular network depends highly on its dynamic properties, with frequent transitions from phases of prolonged growth to rapid shrinkage (catastrophe) and vice versa (rescue). Several proteins have been shown to bind to microtubules, some of them, the so-called plus-end-tracking proteins (+TIPs), binding specifically to the growing ends of microtubules. This thesis describes the functional analysis of two +TIPs, the Cytoplasmic Linker Proteins CLIP-115 and CLIP-170. These proteins are structurally highly similar resulting in a high level of redundancy. Although single CLIP-115 or CLIP-170 knockout mice both have characteristic features, no large abnormalities were found in fibroblasts derived from them. To learn more about the CLIPs and their redundant functions, CLIP double knockout (DKO) mice were generated. The dynamic properties of the microtubules in ce! lls derived from these mice were profoundly altered with a five-fold decrease in rescue-frequency. In addition, the microtubule network was changed notably, with large microtubule-free areas in which proteins aggregates were found. These aggregates contained the microtubule motor-protein cytoplasmic dynein and several components of the dynactin complex. Furthermore DKO fibroblasts spread abnormally, resulting in a two-fold increase of the surface area in attached cells compared to wild type cells. The mice deficient for both CLIP-115 and CLIP-170 have an abnormal posture and show hind limb clasping. Although they perform poorly on certain behavioral and strength-related tasks, they show a surprising age-related improvement of motor coordination. At older ages, certain tasks start to deteriorate again. Using magnetic resonance imaging (MRI) and histological analysis a progressive form of hydrocephalus is detected. In younger mice, an accumulation of cerebellar neurons is see! n in other parts of the brain, indicating a defect in neuronal migrati on. Taken together, the results described in this thesis confirm that CLIP-115 and CLIP-170 act as rescue factors, but that they also have important functions in regulating cell spreading and neuronal migration.
Study strategies and “study drugs”: investigating the relationship between college students’ study behaviors and prescription stimulant misuse

Abstract Objective The current study examined the regular use of study strategies between college students who misused prescription stimulants (N = 36) and college students who did not misuse prescription stimulants (N = 298) in an undergraduate sample. Participants: 334 college students at a large, Midwestern university. Methods: Using logistic regression, we examined whether students who misused prescription stimulants did so to compensate for poor study strategies and/or a lack of study strategies overall. We hypothesized that regularly spacing studying, using more study strategies, and using more effective study strategies would predict lower odds of prescription stimulant misuse among students. In contrast, we hypothesized that using more ineffective study strategies would predict higher odds of prescription stimulant misuse. Results: Results indicated that a greater number of total study strategies and effective study strategies, and higher importance of school predicted higher odds of prescription stimulant misuse. Conclusions: Thus, students may not be misusing prescription stimulants as a substitute for effective studying but, rather, to augment effective study habits.
Carbon Sequestration in Pastures, Silvo-Pastoral Systems and Forests in Four Regions of the Latin American Tropics

SUMMARY Tropical America (TA) holds 8% of the world's population, 11% of the world's continental area, 23% and 22%, respectively, of the world's forest and water resources, and 13% of the world's pasture and agro-pastoral land, this representing 77% of TA's agricultural land. Recent interest in carbon sequestration and preliminary research suggest that well-managed pasture systems in TA could provide a good combination of economic production, poverty reduction, recovery of degraded areas and delivery of environmental services, particularly, carbon sequestration. This paper presents 3-year research results generated by the “Carbon Sequestration Project, The Netherlands Cooperation CO-01002” on soil carbon stocks (SCS) for a range of pasture and silvo-pastoral systems prevalent in agro-ecosystems of TA compared to native forest and degraded land. In the tropical Andean hillsides, Colombia (1350-1900 m.a.s.L, 1800 mm rainfall/yr, 14-18°C mean annual temperature, medium to high slopes, medium fertility soils), SCS from Brachiaria decumbenspastures were statistically lower than those from native forest, but higher than those from natural regeneration of a degraded pasture (fallow land), degraded pasture and mixed-forage bank. In contrast, in the humid tropical forest of the Atlantic Coast, Costa Rica (200 ma.s.L, 28-35°C, 3500 mm/year, poor acid soils), pasture or silvo-pastoral systems with native or planted pasture species such as Ischaemum ciliare, Brachiaria brizantha + Arachis pintoiand Acacia mangium + Arachis pintoishowed statistically higher SCS than native forest. Similar rankings were found in the humid tropical forest of Amazonia, Colombia (800 ma.s.L, 30-42°C, 4200 mm/yr, flat, very poor acid soils) where improved Brachiariapastures (monoculture and legume-associated) showed statistically higher SCS than native forest. In the sub-humid tropical forest of the Pacific Coast, Costa Rica (200 ma.s.L, 6-monfh dry season, 2200 mm/year, poor acid soils) no statistical differences in SCS were found between land-use systems. In tropical ecosystems, improved pasture and silvo-pastoral systems show comparable or even higher SCS than those from native forests, depending on climatic and environmental conditions (altitude, temperature, precipitation, topography and soil), and represent attractive alternatives as C-improved systems.
Delimiting Geographic Distribution and Population History of Jumping Mice (Zapus trinotatus and Zapus princeps) in the Pacific Northwest

Abstract The Cascade Range has generally partitioned sister species and populations into western and eastern forms, although north-south phylogeographic breaks within the Cascades have also been documented. We examined the relationships between and within 2 species of jumping mice, Zapus trinotatus (Pacific Jumping Mouse) and Z. princeps (Western Jumping Mouse), in Washington, Oregon, and southern British Columbia. From 24 localities we sampled 135 specimens and generated sequence data for 782 base pairs of mitochondrial DNA (mtDNA) control region and cytochrome-b. The 2 species were geographically partitioned to the east and west in concordance with the Cascades. However, in both northern Washington and southern Oregon, we found individuals with mtDNA haplotypes assigned to both species in syntopy, at the same sampling localities. Within Z. trinotatus, clades were further subdivided north and south, with a genealogical break across the Columbia River. Zapus princeps clades were also divided north and south, but with deeper divergences than within Z. trinotatus. We conclude that while the Cascade Range has contributed to the historic and contemporary partitioning of these 2 species, it does not represent an absolute barrier, as evidenced by syntopic localities.