Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of an upstream open reading frame in mediating arginine-specific translational control in Neurospora crassa

The Neurospora crassa arg-2 transcript contains an upstream open reading frame (uORF) specifying a 24-residue leader peptide and is subject to a novel form of negative translational regulation in response to arginine. The role of the arg-2 uORF in arginine-specific negative regulation was investigated by using translational fusions of wild-type and mutant arg-2 sequences to the Escherichia coli lacZ reporter gene specifying beta-galactosidase. The wild-type uORF conferred Arg-specific regulation on the reporter gene in N. crassa, but mutated or truncated uORFs did not, as determined by measurements of beta-galactosidase activity produced in N. crassa strains expressing arg-2-lacZ fusion genes. All effects on reporter gene expression were posttranscriptional, as determined by measurement of RNA levels. Both sequence-dependent and sequence-independent effects of uORFs were observed. Genes containing the wild-type uORF or a 21-codon mutated uORF showed reduced translation in comparison with that of a gene lacking a uORF. Both uORF-containing transcripts showed reduced association with polysomes relative to transcripts lacking a uORF, but only the transcript with the wild-type uORF showed a reduced average number of ribosomes associated with it in response to arginine addition. Direct translational fusions between uORF sequences and lacZ sequences indicated that the uORF is translated. Overlapping the uORF with the lacZ initiation codon indicated that ribosome reinitiation at a downstream start codon is not integral to uORF-mediated, Arg-specific translational regulation. These studies provide direct biochemical evidence for arg-2 uORF function in translational control.
High Level Resistance against Rhizomania Disease by Simultaneously Integrating Two Distinct Defense Mechanisms

With the aim of achieving durable resistance against rhizomania disease of sugar beet, the employment of different sources of resistance to Beet necrotic yellow vein virus was pursued. To this purpose, Nicotiana benthamiana transgenic plants that simultaneously produce dsRNA originating from a conserved region of the BNYVV replicase gene and the HrpZPsph protein in a secreted form (SP/HrpZPsph) were produced. The integration and expression of both transgenes as well as proper production of the harpin protein were verified in all primary transformants and selfed progeny (T1, T2). Transgenic resistance was assessed by BNYVV-challenge inoculation on T2 progeny by scoring disease symptoms and DAS-ELISA at 20 and 30 dpi. Transgenic lines possessing single transformation events for both transgenes as well as wild type plants were included in inoculation experiments. Transgenic plants were highly resistant to virus infection, whereas in some cases immunity was achieved. In all cases, the resistant phenotype of transgenic plants carrying both transgenes was superior in comparison with the ones carrying a single transgene. Collectively, our findings demonstrate, for a first time, that the combination of two entirely different resistance mechanisms provide high level resistance or even immunity against the virus. Such a novel approach is anticipated to prevent a rapid virus adaptation that could potentially lead to the emergence of isolates with resistance breaking properties.
Coping with the Forced Swim Stressor: Towards Understanding an Adaptive Mechanism

In the forced swim test (FST) rodents progressively show increased episodes of immobility if immersed in a beaker with water from where escape is not possible. In this test, a compound qualifies as a potential antidepressant if it prevents or delays the transition to this passive (energy conserving) behavioural style. In the past decade however the switch from active to passive “coping” was used increasingly to describe the phenotype of an animal that has been exposed to a stressful history and/or genetic modification. A PubMed analysis revealed that in a rapidly increasing number of papers (currently more than 2,000) stress-related immobility in the FST is labeled as a depression-like phenotype. In this contribution we will examine the different phases of information processing during coping with the forced swim stressor. For this purpose we focus on the action of corticosterone that is mediated by the closely related mineralocorticoid receptors (MR) and glucocorticoid receptors (GR) in the limbic brain. The evidence available suggests a model in which we propose that the limbic MR-mediated response selection operates in complementary fashion with dopaminergic accumbens/prefrontal executive functions to regulate the transition between active and passive coping styles. Upon rescue from the beaker the preferred, mostly passive, coping style is stored in the memory via a GR-dependent action in the hippocampal dentate gyrus. It is concluded that the rodent's behavioural response to a forced swim stressor does not reflect depression. Rather the forced swim experience provides a unique paradigm to investigate the mechanistic underpinning of stress coping and adaptation.
The parental "acceptance-rejection syndrome": universal correlates of perceived rejection.

This article reviews theory, methods, and evidence supporting the concept of a relational diagnosis here called the parental acceptance–rejection syndrome. This syndrome is composed of 2 complementary sets of factors. First, 4 classes of behaviors appear universally to convey the symbolic message that “my parent (or other attachment figure) . loves me (or does not love me—i.e., rejects me). ” These classes of behavior include perceived warmth– affection (or its opposite, coldness–lack of affection), hostility–aggression, indifference–neglect, and undifferentiated rejection. Second, the psychological adjustment of children and adults (defined by a constellation of 7 specific personality dispositions) tends universally to vary directly with the extent to which individuals perceive themselves to be accepted or rejected in their relationship with the people most important to them.
Survey of the Mosquitoes (Diptera: Culicidae) of Mayotte

A transversal survey of immature mosquitoes was conducted on Mayotte Island (France) in the Comoros Archipelago, western Indian Ocean, with the aim to inventory the Culicidae and to document inter-species relationships in different habitats. In total 420 habitats were sampled for larvae and/or pupae mosquitoes, resulting in more than 6,000 specimens. Forty species belonging to 15 genera were collected, with eight taxa integrated for the first time to the Mayotte mosquito list. The most frequently recorded species were Stegomyia aegypti, St. albopicta, Anopheles gambiae and Eretmapodites subsimplicipes, the first three species being known vectors of viruses and parasites transmitted to humans. Mean species richness in habitats ranged from 1.00 to 3.29, with notable differences between habitats. For example, water-filled axils of banana leaves, tree-holes and crab-holes had low species richness, while cut bamboo, water pools, abandoned tires and marsh and swamp water had notably higher species richness. Twenty-seven mosquito species belonging to 12 genera were routinely collected (in ≥20% of at least one type of larval habitat) suggesting that multiple species play a role in the biocenosis of these aquatic habitats. Multispecies association was observed in 52% of the habitats. The co-occurrence of up to six species belonging to five genera was recorded in a single habitat. The mosquitoes of Mayotte show notable biogeographical affinities to those of Madagascar, as compared to the African continent. These two potential source areas are nearly equidistant from Mayotte, which in turn indicates biased dispersal from east to west. Our findings suggest that with relatively short-term intensive sampling in different habitats, it is possible to approach exhaustive species inventories based on collection of larvae. Mayotte, with its modest elevation range and land surface, has a notable species richness of mosquitoes with 45 well-documented species belonging to 15 genera.
Daytime Summer Microclimate Influence of Large Woody Debris on Dewatered Sediments in Lake Mills, WA Following Dam Removal

In 2014, dam removal from the Elwha River, Washington state, exposed large areas of previously submerged sediment. The Olympic National Park placed 100 large logs on 2 ha of exposed sediment to promote plant establishment. I quantified patterns of three microclimate variables near logs: wind speed at 10-cm height (u10), sediment temperature (TS), and evaporation rate (E); and their relationships to broader environmental factors. The northern-most log, exposed to northerly winds, was measured along 3-m perpendicular transects 14 times during August and September 2015. I determined nonlinear and multilevel regressions to investigate patterns and create models of microclimate as functions of environmental factors and distance from the log. Maximum u10 decreased to the lee. Decreases near the log occurred for u10 to the north and south, and for TS and E to the shaded north. Windward and leeward u10 models include local wind speed and distance from log. Northern TS is related to solar radiation, air temperature and distance from log. Southern TS is related to air temperature. Northern E is related to solar radiation, vapor pressure deficit and distance from log. Southern E is related to solar radiation and vapor pressure deficit. Models of southern u10 and northern TS and E were validated with data from 8 wind-protected logs, but lack of validation of the other microclimate models indicate the northern-most log has unique microclimate. Species-specific physiological information is required to predict plant reactions to near-log microclimate. All models require more data to broaden their scope.
A comparison of the induction of myeloid and lymphoid leukemias in x-radiated RF mice.

Summary 1.The susceptibility of mice of the RF strain to radiation-induced myeloid leukemia and lymphomas was studied under a variety of experimental conditions. 2.Although the rate of induction of both diseases varied in relation to the dose of radiation, the relation between disease incidence and dose was not the same for both neoplasms; neither was it linear over the dosage range 0–500 r. 3.On fractionation of a given dose of radiation, the rate of induction of leukemia varied depending on the total dose, dose per exposure, interval between exposures, and hematologic type of leukemia produced. 4.Shielding of the pelvis and lower extremities during irradiation of the remainder of the body greatly inhibited the induction of myeloid leukemia as well as of lymphomas. 5.Susceptibility to lymphoma induction, which is higher in females than in males, was decreased by ovariectomy but was not affected by orchidectomy. Susceptibility to the induction of myeloid leukemia, which is higher in males than in females, was not significantly affected by gonadectomy in either sex. The sex differences in the susceptibility to induction of lymphomas and myeloid leukemia persisted even after removal of the gonads. 6.Removal of the spleen before irradiation greatly lowered susceptibility to the induction of myeloid leukemia but did not influence the induction of lymphomas. 7.Newborn mice were resistant to the induction of myeloid leukemia despite susceptibility to lymphoma formation, whereas the reverse was true of mice irradiated at 6 months of age. 8.Removal of the thymus before irradiation, which eliminated the induction of thymic lymphomas, permitted the induction of lymphomas in extrathymic lymphoid tissues but did not influence the formation of myeloid leukemia.
A genetic variant in pseudogene E2F3P1 contributes to prognosis of hepatocellular carcinoma

ABSTRACT Certain pseudogenes may regulate their protein-coding cousins by competing for miRNAs and play an active biological role in cancer. However, few studies have focused on the association of genetic variations in pseudogenes with cancer prognosis. We selected six potentially functional single nucleotide polymorphisms (SNPs) in cancer-related pseudogenes, and performed a case-only study to assess the association between those SNPs and the prognosis of hepatocellular carcinoma (HCC) in 331 HBV-positive HCC patients without surgical treatment. Log-rank test and Cox proportional hazard models were used for survival analysis. We found that the A allele of rs9909601 in E2F3P1 was significantly associated with a better prognosis compared with the G allele [adjusted hazard ratio (HR) = 0.69, 95% confidence interval (CI) = 0.56–0.86, P = 0.001]. Additionally, this protective effect was more predominant for patients without chemotherapy and transcatheter hepatic arterial chemoembolization (TACE) treatment. Interestingly, we also detected a statistically significant multiplicative interaction between genotypes of rs9909601 and chemotherapy or TACE status on HCC survival (P for multiplicative interaction < 0.001). These findings indicate that rs9909601 in the pseudogene E2F3P1 may be a genetic marker for HCC prognosis in Chinese.
Feeding patterns, trophic structure and damming rivers effect: studies applied in freshwater environments in the Brazilian semi-arid region

The knowledge of the fish trophic structure has been outstanding for providing relevant information on the functioning of the ecosystem in which they are inserted, mainly in dammed environments of semiarid regions that suffer constant changes in the level of water, resulting in alterations, especially in the feeding of the fish due to the variation of the food resources throughout the year, causing changes in the diet of the local ichthyofauna. Within this context, the objective was to describe the trophic categories of fish species in freshwater environments of the Rio Grande do Norte state. Seven trophic guilds were recorded: Detritivore/iliophagous, Insectivorous, Carcinophagous, Piscivorous, Herbivorous and Omnivorous. Through the results, it is observed that the fish species inserted in different environments of the state present the same food pattern, demonstrating flexibility on the diet, prevailing a generalist
Saudi dental students’ opinions on the qualities and attributes of an effective dental teacher

Objective To evaluate Saudi dental students’ opinions on the qualities and attributes of an effective dental teacher. Methods This cross-sectional study was conducted between March and May 2014 at the College of Dentistry, King Saud University. Self-administered questionnaires were distributed to all students enrolled in the 2013/2014 academic year. The questionnaire contained 43 items regarding students’ opinions on the qualities and attributes of a good dental teacher. The attributes were grouped into two main categories: performance and personality. Mean and standard deviations were calculated for each item and then for the whole category. Performance and personality were compared between male and female students and between junior and senior students using Mann–Whitney U test. Results Four hundred and seventy-seven questionnaires were completed, representing a response rate of 79%. Performance attributes were significantly more important than personality attributes to Saudi dental students (P<0.001). Perceptions of performance and personality attributes did not differ between male and female students; however, junior students put more emphasis on personality attributes than senior students. Conclusion Saudi dental students consider performance attributes more important than personality attributes for their successful learning. Teachers’ educational skills are valued more than the attributes, which do not connect directly to students’ learning process.
Utilization and Predictability in Scheduling the IBM SP2 with Backfilling

Scheduling jobs on the IBM SP2 system is usually done by giving each job a partition of the machine for its exclusive use. Allocating such partitions in the order that the jobs arrive (FCFS scheduling) is fair and predictable, but su ers from severe fragmentation, leading to low utilization. This motivated Argonne National Lab, where the rst large SP1 was installed, to develop the EASY scheduler. This scheduler, which has since been adopted by many other SP2 sites, uses aggressive backfilling: small jobs are moved ahead to fill in holes in the schedule, provided they do not delay the first job in the queue. We show that a more conservative approach, in which small jobs move ahead only if they do not delay any job in the queue, produces essentially the same benefits in terms of utilization. Our conservative scheme has the added advantage that queueing times can be predicted in advance, whereas in EASY the queueing time is
Security in Wireless Sensor Networks

Recently, wireless sensor networks (WSN) have gained great popularity, mainly because they provide a low cost alternative to solving a great variety of real-world problems (Akyildiz, Su, & Sankarasubramaniam, 2003). Their low cost enableds the deployment of large amounts of sensor nodes (in the order of thousands, and in the future perhaps millions), which most of the time operate under harsh environments. WSN present extreme AbstrAct
Ultrasonographic assessment of the equine palmar tendons

Aim: The present study was conducted to evaluate the equine palmar tendon by ultrasonography (USG) in standing the position. Materials and Methods: USG of palmar tendons was performed in 40 adult horses using linear transducer having frequency of 10-18 MHz (e-soate, My Lab FIVE) and L52 linear array transducer (Titan, SonoSite) with frequencies ranging from 8 to 10 MHz. Palmar tendon was divided into 7 levels from distal to accessory carpal bone up to ergot in transverse scanning and 3 levels in longitudinal scanning. Results: The USG evaluation was very useful for diagnosis of affections of the conditions such as chronic bowed tendon, suspensory ligament desmitis, carpal sheath tenosynovitis and digital sheath effusions. The mean cross-sectional area (cm2) of affected tendons was significantly increased in affected than normal tendons. The echogenicity was also found reduced in affected tendons and ligaments along with disorganization of fiber alignment depending on the severity of lesion and injury. Conclusion: USG proved ideal diagnostic tool for diagnosis and post-treatment healing assessment of tendon injuries in horses.
Novel forms of neuronal migration in the rat cerebellum

Infrared video microscopy of neonatal rat cerebellum (P0‐P14) was used to directly visualize migrating granule neurons in relation to other cerebellar cells in a brain slice for up to 24 hr. Initially (P0‐P5), granule neurons move along radial migration pathways of other neuronal fibers. These pathways are probably established by the bipolar granule neurons that attach to the external basement membrane via one process and extend another process toward the Purkinje cell layer. At P5‐P8, a substantial number of granule neurons move horizontally and extend long parallel fibers. Both radially and horizontally migrating granule neurons move by nuclear translocation inside their preformed processes with a speed that varies between 6 and 120 μ/hr. In P10‐P12 animals, the horizontally oriented granule neurons start to migrate radially. They move into the internal granule cell layer either along the radial pathways of other neuronal fibers or in contact with the matured glial processes. The radial neuronal migration pathways disappear by P14 whereas the glial cell processes are maintained and reach the basal lamina. These results describe novel radial and horizontal modes of neuronal migration that proceed independently of the physical glial guidance. © 1995 Wiley‐Liss, Inc.
The Heterogeneous Allelic Repertoire of Human Toll-Like Receptor (TLR) Genes

Toll-Like Receptors (TLR) are critical elements of the innate arm of the vertebrate immune system. They constitute a multigenic family of receptors which collectively bind a diverse array of – exogeneous as well as endogeneous – ligands. An exponential burst of knowledge has defined their biological role in fight against infections and generation/modulation of auto-immune disorders. Hence, they could at least be conceptually recognized – despite being structurally unrelated – as innate counterparts to Major Histocompatibility Complex (MHC) molecules – equally recognizing antigenic ligands (albeit structurally more homogeneous i.e., peptides), again derived from self and/or non-self sources – preeminent this time in adaptive immunity. Our great disparities in face of infections and/or susceptibility to auto-immune diseases have provoked an intense search for genetic explanations, in part satisfied by the extraordinary MHC allelic repertoire. An equally in-depth and systematic analysis of TLR diversity is lacking despite numerous independent reports of a growing number of SNPs within these loci. The work described here aims at providing a preliminary picture of the allelic repertoire – and not purely SNPs – of all 10 human TLR coding sequences (with exception of TLR3) within a single cohort of up to 100 individuals. It appears from our work that TLR are unequally polymorphic: TLR2 (DNA alleles: 7/protein alleles: 3), 4 (4/3), 7 (6/3), 8 (9/2) and 9 (8/3) being comparatively least diverse whereas TLR1 (11/10), 5 (14/12), 6 (10/8) and 10 (15/10) show a substantial number of alleles. In addition to allelic assignment of a large number of SNPs, 10 new polymorphic positions were hereby identified. Hence this work depicts a first overview of the diversity of almost all human TLR genes, a prelude for large-scale population genetics as well as genetic association studies.
Victim replication: maximizing capacity while hiding wire delay in tiled chip multiprocessors

In this paper, we consider tiled chip multiprocessors (CMP) where each tile contains a slice of the total on-chip L2 cache storage and tiles are connected by an on-chip network. The L2 slices can be managed using two basic schemes: 1) each slice is treated as a private L2 cache for the tile; 2) all slices are treated as a single large L2 cache shared by all tiles. Private L2 caches provide the lowest hit latency but reduce the total effective cache capacity, as each tile creates local copies of any line it touches. A shared L2 cache increases the effective cache capacity for shared data, but incurs long hit latencies when L2 data is on a remote tile. We present a new cache management policy, victim replication, which combines the advantages of private and shared schemes. Victim replication is a variant of the shared scheme which attempts to keep copies of local primary cache victims within the local L2 cache slice. Hits to these replicated copies reduce the effective latency of the shared L2 cache, while retaining the benefits of a higher effective capacity for shared data. We evaluate the various schemes using full-system simulation of both single-threaded and multi-threaded benchmarks running on an 8-processor tiled CMP. We show that victim replication reduces the average memory access latency of the shared L2 cache by an average of 16% for multi-threaded benchmarks and 24% for single-threaded benchmarks, providing better overall performance than either private or shared schemes.