Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential Partially Overlapping Gene Arrangement in the Tricistronic S1 Genome Segments of Avian Reovirus and Nelson Bay Reovirus: Implications for Translation Initiation

ABSTRACT Previous studies of the avian reovirus strain S1133 (ARV-S1133) S1 genome segment revealed that the open reading frame (ORF) encoding the ςC viral cell attachment protein initiates over 600 nucleotides distal from the 5′ end of the S1 mRNA and is preceded by two predicted small nonoverlapping ORFs. To more clearly define the translational properties of this unusual polycistronic RNA, we pursued a comparative analysis of the S1 genome segment of the related Nelson Bay reovirus (NBV). Sequence analysis indicated that the 3′-proximal ORF present on the NBV S1 genome segment also encodes a ςC homolog, as evidenced by the presence of an extended N-terminal heptad repeat characteristic of the coiled-coil region common to the cell attachment proteins of reoviruses. Most importantly, the NBV S1 genome segment contains two conserved ORFs upstream of the ςC coding region that are extended relative to the predicted ORFs of ARV-S1133 and are arranged in a sequential, partially overlapping fashion. Sequence analysis of the S1 genome segments of two additional strains of ARV indicated a similar overlapping tricistronic gene arrangement as predicted for the NBV S1 genome segment. Expression analysis of the ARV S1 genome segment indicated that all three ORFs are functional in vitro and in virus-infected cells. In addition to the previously described p10 and ςC gene products, the S1 genome segment encodes from the central ORF a 17-kDa basic protein (p17) of no known function. Optimizing the translation start site of the ARV p10 ORF lead to an approximately 15-fold increase in p10 expression with little or no effect on translation of the downstream ςC ORF. These results suggest that translation initiation complexes can bypass over 600 nucleotides and two functional overlapping upstream ORFs in order to access the distal ςC start site.
Evolution of Massive Black Hole Binaries

We present the results of large-scale N-body simulations of the stellar-dynamical evolution of massive black hole binaries at the center of spherical galaxies. We focus on the dependence of the hardening rate on the relaxation timescale of the parent galaxy. A simple theoretical argument predicts that a binary black hole creates a "loss cone" around it. Once the stars in the loss cone are depleted, the hardening rate is determined by the rate at which field stars diffuse into the loss cone. Therefore, the hardening timescale becomes proportional to the relaxation timescale. Recent N-body simulations, however, have failed to confirm this theory, and various explanations have been proposed. By performing simulations with sufficiently large N (up to 106) for sufficiently long time, we found that the hardening rate does indeed depend on N. Our result is consistent with the simple theoretical prediction that the hardening timescale is proportional to the relaxation timescale. This dependence implies that massive black hole binaries are unlikely to merge within a Hubble time through interaction with field stars and gravitational wave radiation alone.
Higher Education, Women, and Sociocultural Change: A Closer Look at the Statistics

This article reports an analysis of the relationship between women’s increased participation in higher education and other recent social changes over the last four decades. To date, women’s increased involvement in higher education has been studied as either a force for or a consequence of other sociocultural changes. Drawing on data from key international data sets and with a focus on a range of Organisation for Economic Co-Operation and Development (OECD) countries, this article details an exploratory factor analysis of women’s higher education participation and a range of other variables identified as indicators of or mediators for social change. This analysis reveals the existence of four underlying factors showing the structural interrelationship between the variables.
NOVEL ALGORITHMS FOR IN VITRO GENE SYNTHESIS

Methods for reliable synthesis of long genes offer great promise for novel protein synthesis via expression of synthetic genes. Current technologies use computational methods for design of short oligos, which can then be reliably synthesized and assembled into the desired target gene. A precursor to this process is optimization of the gene sequence for improved protein expression. In this thesis, we provide the first results on the computational complexity of oligo design for gene synthesis. For collision-oblivious oligo design – when mishybridizations between oligos are ignored – we give an efficient dynamic programming algorithm. We show that an abstraction of the collision-aware oligo design problem is NP-hard. We extend our collision-oblivious algorithm to achieve collision-aware oligo design, when the target gene can be partitioned into independently-assembled segments. We propose additional algorithms for gene optimization and demonstrate their utility for collision-aware design. All methods are evaluated on a large biological gene set.
Effect of Different Forms of Adenylate Cyclase Toxin of Bordetella pertussis on Protection Afforded by an Acellular Pertussis Vaccine in a Murine Model

ABSTRACT Four recombinant forms of the cell-invasive adenylate cyclase toxin (CyaA) of Bordetella pertussis were compared for the ability to enhance protection against B. pertussis in mice when coadministered with an acellular pertussis vaccine (ACV). The four forms were as follows: fully functional CyaA, a CyaA form lacking adenylate cyclase enzymatic activity (CyaA*), and the nonacylated forms of these toxins, i.e., proCyaA and proCyaA*, respectively. None of these forms alone conferred significant (P > 0.05) protection against B. pertussis in a murine intranasal challenge model. Mice immunized with ACV alone showed significant (P < 0.05) reductions in bacterial numbers in the lungs after intranasal challenge compared with those for control mice. When administered with ACV, both CyaA and CyaA* further reduced bacterial numbers in the lungs of mice after intranasal challenge compared with those for ACV-immunized mice, but the enhanced protection was only significant (P < 0.05) with CyaA*. Coadministration of CyaA* with ACV caused a significant (P < 0.05) increase in immunoglobulin G2a antibody levels against pertactin compared with those in mice immunized with ACV alone. Spleen cells from mice immunized with ACV plus CyaA* secreted larger amounts of interleukin-5 (IL-5), IL-6, gamma interferon (IFN-γ), and granulocyte-macrophage colony-stimulating factor (GM-CSF) than did cells from mice immunized with ACV plus CyaA or ACV alone after stimulation in vitro with a mixture of B. pertussis antigens. Spleen cells from mice immunized with ACV plus CyaA* also secreted larger amounts of IFN-γ and GM-CSF than did cells from mice immunized with CyaA* alone after stimulation in vitro with CyaA*. Macrophages from mice immunized with ACV plus CyaA* produced significantly (P < 0.05) higher levels of nitric oxide than did macrophages from mice immunized with CyaA* alone, ACV alone, or ACV plus CyaA after stimulation in vitro with a mixture of B. pertussis antigens or heat-killed B. pertussis cells. These data suggest that the enhancement of protection provided by CyaA* was due to an augmentation of both Th1 and Th2 immune responses to B. pertussis antigens.
Dissolution Rate Enhancement of Clarithromycin Using Ternary Ground Mixtures: Nanocrystal Formation

Clarithromycin (CLA), a broad-spectrum macrolide, is a poorly soluble drug with dissolution rate limited absorption. The aim of this investigation was to prepare CLA nanoparticles from a ternary ground mixture in the presence of sodium lauryl sulfate (SLS) and polyvinyl pyrrolidone (PVP) as co-grinding water-soluble compounds, in order to improve the drug dissolution rate. Different weight ratios of CLA: SLS: PVP were ground in a dry process by planetary ball mill using different grinding ball size. Following the dissolution rate study, physical properties of the best dissolved co-ground formulation was studied. The accelerated stability studies were also conducted on the co-ground formulation. The results revealed that the dissolution rate of ternary ground mixtures was much higher than that of the intact drug (p < 0.001). Decreasing the grinding ball size and weight with the same rotation speed resulted in particles with decreased dissolution. On the other hand, increasing the PVP concentration in the formulations reduced the drug dissolution. Dissolution efficiencies (DE10 and DE30) for the best dissolved formulation, which consisted of the equal ratio of each co-ground component, were 8.7 and 5 folds higher than the untreated CLA, respectively. This formulation formed nanocrystals with enhanced solubility after dispersing in water. X-ray diffraction, differential scanning calorimetry and infrared spectrophotometry confirmed no chemical interaction and phase transition during the process. Accelerated stability studies confirmed that the co-ground mixture almost remained unchanged in terms of dissolution rate, drug assay and particle size after exposing in stability conditions for three months.
Applications of Majorization Theory in Space-Time Cooperative Communications

In recent years, the goal of providing high speed wireless data services has generated a huge amount of interest among the research community. Recent information theoretic results have demonstrated that the ability of a system to support a high link quality and higher data rates in the presence of Rayleigh fading improves significantly with the use of multiple transmit and receive antennas (Telatar 1999; Foschini & Gans 1998; Tarokh, Seshadri, & Calderbank 1998), so called MIMO (multiple input multiple output) systems. However, due to the size and power requirements the number of antennas at the mobile units is limited. Furthermore, shadowing and the impact of scatterers distribution limits the available degrees of freedom. With this restriction in addition to a disturbed link between mobile and destination, reliable communication can not be guaranteed by using a conventional point-to-point connection. AbstrAct
Congestion and Tax Competition in a Parallel Network

The purpose of this paper is to study tax competition on a parallel road network when different governments have tolling authority on the different links of the network. Reflecting many current situations in Europe, each link is used by both local and transit traffic; moreover, transit has a choice of route. Each government maximises the surplus of local users plus total tax revenues in controlling local and transit transport. Three types of tolling systems are considered: (i) toll discrimination between local traffic and transit, (ii) uniform tolls on local and transit transport, (iii) local tolls only. The results suggest that the welfare effects of introducing transit tolls are large, but that differentiation of tolls between local and transit transport as compared to uniform tolls does not yield large welfare differences. It is also found that the welfare effects of coordination between countries are relatively small in comparison with the welfare gains of tolling transit. The numerical model further illustrates the effects of different transit shares and explicitly considers the role of asymmetries between countries. Higher transit shares strongly raise the Nash equilibrium transit toll and slightly decrease local tolls. With asymmetric demands, the welfare gains of introducing differentiated tolling rise strongly for the country with lower local demand.
5. Biologically Important Areas for Cetaceans Within U.S. Waters – Hawai‘i Region

Of the 18 species of odontocetes known to be present in Hawaiian waters, small resident populations of 11 species—dwarf sperm whales, Blainville’s beaked whales, Cuvier’s beaked whales, pygmy killer whales, short-finned pilot whales, melonheaded whales, false killer whales, pantropical spotted dolphins, spinner dolphins, rough-toothed dolphins, and common bottlenose dolphins—have been identified, based on two or more lines of evidence, including results from small-boat sightings and survey effort, photo-identification, genetic analyses, and satellite tagging. In this review, we merge existing published and unpublished information along with expert judgment for the Hawai‘i region of the U.S. Exclusive Economic Zone and territorial waters in order to identify and support the delineation of 20 Biologically Important Areas (BIAs) for these small and resident populations, and one reproductive area for humpback whales. The geographic extent of the BIAs in Hawaiian waters ranged from approximately 700 to 23,500 km. BIA designation enhances existing information already available to scientists, managers, policymakers, and the public. They are intended to provide synthesized information in a transparent format that can be readily used toward analyses and planning under U.S. statutes that require the characterization and minimization of impacts of anthropogenic activities on marine mammals. Odontocete BIAs in Hawai‘i are biased toward the main Hawaiian Islands and populations off the island of Hawai‘i, reflecting a much greater level of research effort and thus certainty regarding the existence and range of small resident populations off that island. Emerging evidence of similar small resident populations off other island areas in Hawaiian waters suggest that further BIA designations may be necessary as more detailed information becomes available.
Evaluation of the Class Pass Intervention: An Application to Improve Classroom Behavior in Children With Disabilities

The Class Pass Intervention (CPI) is designed to be implemented within School-Wide Positive Behavioral Interventions and Supports (SWPBIS) to decrease disruptive behavior and teach replacement behavior for students needing Tier 2 intervention. The CPI has two components: (a) providing negative reinforcement for requesting a break by using a class pass, and (b) providing positive reinforcement for continued engagement in activities without breaks by exchanging unused passes. The purpose of the present study was to extend the literature on the CPI by further evaluating the impact of the first component of the CPI on mild to moderate disruptive behavior, hypothesized to be maintained by social negative reinforcement, and academic engagement of three elementary school students with disabilities. A multiple baseline across participants design was used to demonstrate the impact of the CPI on student behavior during a problematic academic time period. The results indicated that the use of CPI was functionally related to a decrease in disruptive behavior and increase in academic engagement for all participating students whose problem behavior was hypothesized to be maintained by social reinforcement. Results were maintained for one participant while fading the magnitude of the intervention. Students and teachers rated CPI as effective and acceptable.
Cognitive behavioral therapy for depression in Japanese Parkinson’s disease patients: a pilot study

Objectives This study evaluated the feasibility of cognitive behavioral therapy (CBT) for Japanese Parkinson’s disease (PD) patients with depression. To increase cultural acceptability, we developed the CBT program using manga, a type of Japanese comic novel. Methods Participants included 19 non-demented PD patients who had depressive symptoms (GRID-Hamilton Rating Scale for Depression score ≥8). A CBT program comprising six sessions was individually administered. We evaluated the feasibility and safety of the CBT program in terms of the dropout rate and occurrence of adverse events. The primary outcome was depressive symptom reduction in the GRID-Hamilton Rating Scale for Depression upon completion of CBT. Secondary outcomes included changes in the self-report measures of depression (Beck Depression Inventory-II, Hospital Anxiety and Depression Scale-Depression), anxiety (Hospital Anxiety and Depression Scale-Anxiety, State and Trait Anxiety Inventory, Overall Anxiety Severity and Impairment Scale), functional impairment, and quality of life (Medical Outcomes Study 36-Item Short-Form Health Survey). Results Of the 19 participants (mean age =63.8 years, standard deviation [SD] =9.9 years; mean Hohen–Yahr score =1.7, SD =0.8), one patient (5%) withdrew. No severe adverse event was observed. The patients reported significant improvements in depression (Hedges’ g =−1.02, 95% confidence interval =−1.62 to −0.39). The effects were maintained over a 3-month follow-up period. Most of the secondary outcome measurements showed a small-to-moderate but nonsignificant effect size from baseline to post-intervention. Conclusion This study provides preliminary evidence that CBT is feasible among Japanese PD patients with depression. Similar approaches may be effective for people with PD from other cultural backgrounds. The results warrant replication in a randomized controlled trial.
Segment-Based Land Cover Mapping of a Suburban Area - Comparison of High-Resolution Remotely Sensed Datasets Using Classification Trees and Test Field Points

In order to better understand and exploit the rich information content of new remotely sensed datasets, there is a need for comparative land cover classification studies. In this study, the automatic classification of a suburban area was investigated by using (1) digital aerial image data; (2) digital aerial image data and laser scanner data; (3) a high-resolution optical QuickBird satellite image; (4) high-resolution airborne synthetic aperture radar (SAR) data; and (5) SAR data and laser scanner data. A segment-based approach was applied. The classification rules for distinguishing buildings, trees, vegetated ground, and non-vegetated ground were created automatically by using permanent test field points in a training area and the classification tree method. The accuracy of the results was evaluated by using test field points in validation areas. The highest overall accuracies were obtained when laser scanner data were used to separate high and low objects: 97% in Test 2, and 82% in Test 5. The overall accuracies in the other tests were 74% (Test 1), 67% (Test 3), and 68% (Test 4). An important contributing factor for the lower accuracy in Tests 3 and 4 was the lower spatial resolution of the datasets. The classification tree method and test field points provided a feasible and automated means of comparing the classifications. The approach is well suited for rapid analyses of new datasets to predict their quality and potential for land cover classification.
Brain and Plasma Molecular Characterization of the Pathogenic TBI-AD Interrelationship in Mouse Models

Abstract : Traumatic Brain Injury (TBI), in particular mild TBI (mTBI) is a major cause of disability in military and in civilian populations, and for many years has been known to be an epigenetic risk factor for Alzheimers Disease (AD) and other neurodegenerative conditions such as Parkinsons disease, Amyotrophic Lateral Sclerosis or Chronic Traumatic Encephalopathy (CTE) (Randolph, 2001; Gaetz and Weinberg, 2000; Gaetz et al., 2000; Guskiewicz et al., 2003; Gavett et al., 2011; Van Den Heuvel et al., 2007a; Gavett et al., 2010; Frstl et al., 2010; McKee et al.,2009; Costanza et al., 2011; Stern et al., 2011). The existence of a TBI-AD relationship is well recognized (Guo et al., 2000; Jellinger et al., 2001;Mauri et al., 2006; Mayeux et al., 1993; Mayeux et al., 1995; Schofield et al., 1997; Tang et al., 1996; Van Den Heuvel et al., 2007b; Blyth and Bazarian, 2010; Czonkowska and Kurkowska-Jastrzbska, 2011; Hinkebein et al., 2003; Sivanandam and Thakur, 2012; Verghese et al., 2011),and the overlaps and distinctions between pathological features of AD and TBI, including (more recently) CTE, have long been the subject of reporting and discussion (Tokuda et al., 1991; Graham et al., 1995; Irving et al., 1996; Geddes et al., 1996; Geddes et al., 1999; Jellinger et al.,2001; Schmidt et al., 2001; Smith et al., 2003; Uryu et al., 2007; Dekosky et al., 2007; McKee et al., 2009; Magnoni and Brody, 2010; Johnson etal., 2011; Magnoni et al., 2011; Shively et al., 2012; Johnson et al., 2013; McKee et al., 2013; Omalu et al., 2011). However, the precise nature of how TBI leads to or precipitates AD pathogenesis is not understood. The goal of this proposal is to use molecular level approaches in relevant animal models to identify overlapping profiles between TBI and AD and determine early critical cellular responses to TBI that can be targeted for therapeutic intervention.
Link-Based VoIP Aggregation in Mesh Networks

Voice over IP (VoIP) over wireless mesh network (WMNs) has become a topic of great interest in both enterprise and research arena. The IEEE 802.11 standard is the most popular wireless LAN standard for extending the access point (AP) based network. However, it does not provide guaranteed quality for real-time applications such as VoIP. Besides, with the large number of injected flows in WMNs, only a handful of these packets can be supported due to protocol overhead, packet collision and Interferences. In this paper, a link-based aggregation is proposed and its performance improvement is compared with those of fixed aggregation and performance under standard access network. Simulation results show that the proposed aggregation scheme increases the number of supported flow while also reducing end-to-end delay, jitter, and packet loss of VoIP in WMNs.
Factors associated with marketable milk production recovery after treatment of naturally occurring acute coliform mastitis

Milk production loss after recovery from acute coliform mastitis causes major economic losses for dairy industries. Declines in milk production and composition are caused by multiple factors, including cow factors, microorganisms and treatments, but the influence of each factor has not been determined. To investigate risk factors for milk loss after treatment for acute coliform mastitis, multiple logistic regression analyses were conducted in 53 clinical cases. Systemic administration of fluoroquinolone was significantly associated with recovery of marketable milk production. The time to slaughter was significantly shorter in cows with complete loss of quarter milk production than in cows that produced marketable milk. In this study, we identified factors associated with increased risk of milk production loss.
Just a Pebble Game

The two-player pebble game of Dymond-Tompa is identified as a barrier for existing techniques to save space or to speed up parallel algorithms for evaluation problems. Many combinatorial lower bounds to study I versus NI and NC versus P under different restricted settings scale in the same way as the pebbling algorithm of Dymond-Tompa. These lower bounds include, (1) the monotone separation of m-I from m-NI by studying the size of monotone switching networks in Potechin '10; (2) a new semantic separation of NC from P and of NCi from NCi+1 by studying circuit depth, based on the techniques developed for the semantic separation of NC1 from NC2 by the universal composition relation in Edmonds-Impagliazzo-Rudich-Sgall '01 and in Hastad- Wigderson '97; and (3) the monotone separation of m-NC from m-P and of m-NCi from m-NCi+1 by studying (a) the depth of monotone circuits in Raz-McKenzie '99; and (b) the size of monotone switching networks in Chan- Potechin '12. This supports the attempt to separate NC from P by focusing on depth complexity, and suggests the study of combinatorial invariants shaped by pebbling for proving lower bounds. An application to proof complexity gives tight bounds for the size and the depth of some refinements of resolution refutations.