Miracle-dz/UniFAR-FTUs huggingface dataset:
An Applications-focused Review of Comparative Genomics Tools: Capabilities, Limitations and Future Challenges

A team at the Lawrence Livermore National Laboratory (LLNL) was given the task of using computational tools to speed up the development of DNA diagnostics for pathogen detection. This work will be described in another paper in this issue (see pages 133-149). To achieve this goal it was necessary to understand the merits and limitations of the various available comparative genomics tools. A review of some recent tools for multisequence/genome alignment and substring comparison is presented, within the general framework of applicability to a large-scale application. We note that genome alignments are important for many things, only one of which is pathogen detection. Understanding gene function, gene regulation, gene networks, phylogenetic studies and other aspects of evolution all depend on accurate nucleic acid and protein sequence alignment. Selecting appropriate tools can make a large difference in the quality of results obtained and the effort required.
Methane and ammonia in the near-infrared spectra of late-T dwarfs

Analysis of T dwarfs using model atmospheres has been hampered by the absence of reliable line lists for methane and ammonia. Newly computed high temperature line lists for both of these important molecules are now available, so it is timely to investigate the appearance of the various absorption features in T dwarfs in order to better understand their atmospheres and validate the new line lists. We present high quality R~5000 Gemini/NIFS 1.0-2.4 microns spectra of the T8 standard 2MASS 0415-0935 and the T9 standard UGPS 0722-0540. We use these spectra to identify numerous methane and ammonia features not previously seen and we discuss the implications for our understanding of T dwarf atmospheres. Among our results, we find that ammonia is the dominant opacity source between ~1.233-1.266 microns in UGPS 0722-0540, and we tentatively identify several absorption features in this wavelength range in the T9's spectrum which may be due entirely to ammonia opacity. Our results also suggest that water rather than methane is the dominant opacity source in the red half of the J-band of the T8 dwarf. Water appears to be the main absorber in this wavelength region in the T9 dwarf until ~1.31 microns, when methane starts to dominate.
At the crossroads: Future directions in trust research

This forum paper is intended to stimulate a debate on a fundamental conceptual issue in trust research. It argues that the dominant stream of literature focuses too much on the micro level of trust building processes and hence promotes a reductionist understanding of the phenomenon. In future trust research, it is suggested to place considerably more emphasis on the ‘constitutive’ embeddedness of actors’ behaviour in the institutional environment. The latter is shown to be conducive to overcoming the limitations of current mainstream trust research and to developing new insights into the role and functioning of trust in modern business systems.
Intestinal Microbiota in Healthy U.S. Young Children and Adults—A High Throughput Microarray Analysis

It is generally believed that the infant's microbiota is established during the first 1–2 years of life. However, there is scarce data on its characterization and its comparison to the adult-like microbiota in consecutive years. Aim To characterize and compare the intestinal microbiota in healthy young children (1–4 years) and healthy adults from the North Carolina region in the U.S. using high-throughput bacterial phylogenetic microarray analysis. Methods Detailed characterization and comparison of the intestinal microbiota of healthy children aged 1–4 years old (n = 28) and healthy adults of 21–60 years (n = 23) was carried out using the Human Intestinal Tract Chip (HITChip) phylogenetic microarray targeting the V1 and V6 regions of 16S rRNA and quantitative PCR. Results The HITChip microarray data indicate that Actinobacteria, Bacilli, Clostridium cluster IV and Bacteroidetes are the predominant phylum-like groups that exhibit differences between young children and adults. The phylum-like group Clostridium cluster XIVa was equally predominant in young children and adults and is thus considered to be established at an early age. The genus-like level show significant 3.6 fold (higher or lower) differences in the abundance of 26 genera between young children and adults. Young U.S. children have a significantly 3.5-fold higher abundance of Bifidobacterium species than the adults from the same location. However, the microbiota of young children is less diverse than that of adults. Conclusions We show that the establishment of an adult-like intestinal microbiota occurs at a later age than previously reported. Characterizing the microbiota and its development in the early years of life may help identify ‘windows of opportunity’ for interventional strategies that may promote health and prevent or mitigate disease processes.
Unintended Consequences of Collegiate Living- Learning Community Programs at a Public University

The current body of living-learning community (LLC) research primarily documents programmatic impact relative to intended outcomes such as social integration and improved academic performance. Conversely, few published studies address potential unintended consequences of LLCs. Just as intended outcomes often result from purposive action, unintended consequences may also occur when intentional programming produces unforeseen results. Evidence suggests LLCs—particularly those serving first-time freshmen—may contribute to unanticipated outcomes because of the complex social process occurring within peer groups of post-adolescent students (Jaffee, 2007). Despite evidence that LLCs may produce unforeseen outcomes, the impact of unintended consequences on LLCs remains relatively undocumented in the research literature. This qualitative comparative case study uncovered and documented unintended consequences related to participation in two well-established LLC programs at a large public university. Study participants included students, staff, faculty, and administrators who participated in multiple data collection procedures. The findings of this study revealed that unintended consequences occurred when relationships between program stakeholders eroded over time. In the absence of programming to sustain group cohesion, LLC cohorts became susceptible to an array of destructive social practices including social marginalization, insularity, risky behavior, rebellion, and conflict. Findings further illustrated the importance of faculty members and administrative personnel associated with LLCs in establishing and maintaining a sense of community among program stakeholders. Implications for practitioners and recommendations for future research are included.
The Influence of Campaign Contributions in State Legislatures: The Effects of Institutions and Politics

Campaign contributions are widely viewed as a corrupting influence but most scholarly research concludes that they have marginal impact on legislative behavior. Lynda W. Powell shows that contributions have considerable influence in some state legislatures but very little in others.Using a national survey of legislators, shedevelops an innovative measure of influence and delineates the factors that explain this great variation across the 99 U.S. state legislative chambers. Powell identifies the personal, institutional, and political factors that determine how muchtime alegislatordevotes to personal fundraising and fundraising for the caucus. She shows that the extent of donors' legislative influence varies in ways corresponding to the same variations in the factors that determine fundraising time. She also confirmsa link between fundraising and lobbying with evidence supporting the theory that contributors gain access to legislators based on donations, Powell's findingshave important implications for the debate over the role of money in the legislative process. "
Evaluation of Efficacy, Safety, and Cognitive Profile of Amisulpride Per Se and Its Comparison with Olanzapine in Newly Diagnosed Schizophrenic Patients in an 8-Week, Double-Blind, Single-Centre, Prospective Clinical Trial

Background. Impaired cognitive functions in schizophrenia are the major deciding factors in response to treatment. Conventional antipsychotics have minimal impact on cognitive dysfunctions and are associated with adverse effects. Atypical antipsychotics have shown promise in treatment of cognitive and negative symptoms of schizophrenia. Efforts are underway to find out the best drug amongst atypical antipsychotics. Objective. To compare efficacy, safety, and cognitive profile of amisulpride and olanzapine in the treatment of acute psychotic exacerbations of schizophrenia. Method. A prospective, randomized, double-blind, single-center, 8-week clinical trial we used. Subjects and Treatments. Seventy four patients were treated for two months with either amisulpride (400–800 mg/d) or olanzapine (10–20 mg/d). Statistics. Mann Whitney U test we used for independent samples with P < 0.05 taken as significant. Results. Brief psychiatric rating scale (BPRS) was used as a primary measure of efficacy. Other measures of efficacy and safety were also evaluated. Both amisulpride and olanzapine groups showed equivalent improvement in psychotic symptoms on BPRS scale. Less than five percent of patients suffered adverse effects only to withdraw from the study. Olanzapine group showed statistically significant (P < 0.05) weight gain compared with amisulpride group. Amisulpride group showed significant improvement (P < 0.05) in various cognitive parameters as compared to olanzapine group.
CS 424 Network Security : Bayesian Network Intrusion Detection ( BNIDS )

Although law enforcement sometimes employ informants or video/audio surveillance, often it uses simple observations to catch criminals. For example, if a guard works at a number of different banks, each of which has been robbed during or shortly after his employment, then clearly investigators should be astute enough to suspect the guard of some involvement in the crime. Although helpful, investigators should not have to track and document each action of each bank employee. Such a course would swamp the investigators with an excessive amount of detail. Investigators need to focus their efforts and not get lost in the noise.
PA6 Stromal Cell Co-Culture Enhances SH-SY5Y and VSC4.1 Neuroblastoma Differentiation to Mature Phenotypes

Neuroblastoma cell lines such as SH-SY5Y have been used for modelling neurodegenerative diseases and for studying basic mechanisms in neuroscience. Since neuroblastoma cells proliferate and generally do not express markers of mature or functional neurons, we exploited a co-culture system with the stromal cell line PA6 to better induce differentiation to a more physiologically relevant status. We found that co-culture of the neuroblastoma cell lines in the presence of neural inducers such retinoic acid was able to generate a high proportion of quiescent neurons with very long neurites expressing differentiation markers. The co-culture system additionally cuts short the time taken to produce a more mature phenotype. We also show the application of this system to study proteins implicated in motor neuron disease.
RPL: IPv6 Routing Protocol for LOW Power and Lossy Networks

Today, Low Power and Lossy Networks (LLNs) represent one of the most interesting research areas. They include Wireless Personal Area Networks (WPANs), low-power Power Line Communication (PLC) networks and Wireless Sensor Networks (WSNs). Such networks are often optimized to save energy, support tra c patterns di↵erent from the standard unicast communication, run routing protocols over link layers with restricted frame-sizes and many others [14]. This paper presents the IPv6 Routing Protocol for Low power and Lossy Networks (RPL) [19], which has been designed to overcome routing issues in LLNs. It implements measures to reduce energy consumption such as dynamic sending rate of control messages and addressing topology inconsistencies only when data packets have to be sent. The protocol makes use of IPv6 and supports not only tra c in the upward direction, but also tra c flowing from a gateway node to all other network participants. This paper focuses on the employment of RPL in WSNs and gives a brief overview of the protocol’s performance in two di↵erent testbeds.
Nonlinear Decline-Rate Dependence and Intrinsic Variation of Type Ia Supernova Luminosities

Published B and V fluxes from nearby Type Ia supernovae (SNe) are fitted to light-curve templates with four to six adjustable parameters. Separately, B magnitudes from the same sample are fitted to a linear dependence on B - V color within a postmaximum time window prescribed by the CMAGIC method. These fits yield two independent SN magnitude estimates Bmax and BBV. Their difference varies systematically with decline-rate Δm15 in a form that is compatible with a bilinear but not a linear dependence; a nonlinear form likely describes the decline-rate dependence of Bmax itself. A Hubble fit to the average of Bmax and BBV requires a systematic correction for observed B - V color that can be described by a linear coefficient ℛ = 2.59 ± 0.24, well below the coefficient RB ≈ 4.1 commonly used to characterize the effects of Milky Way dust. At 99.9% confidence the data reject a simple model in which no color correction is required for SNe that are clustered at the blue end of their observed color distribution. After systematic corrections are performed, Bmax and BBV exhibit mutual rms intrinsic variation equal to 0.074 ± 0.019 mag, of which at least an equal share likely belongs to BBV. SN magnitudes measured using maximum luminosity or CMAGIC methods show comparable rms deviations of order ≈0.14 mag from the Hubble line. The same fit also establishes a 95% confidence upper limit of 486 km s-1 on the rms peculiar velocity of nearby SNe relative to the Hubble flow.
Self-advocacy and self-determination skills in middle school and high school students: A Transition needs assessment for the East Rochester Union Free School District

5 Literature Review/ 6 Introduction / 6 Is it Self-Advocacy or Self-Determination? / 7 Locus of Control / 9 Learned Helplessness / 1 0 Overprotection / 1 1 Students Benefit from Direct Instruction / 13 Individuals with Disabilities Education Act / 15 Student Involvement / 16 Transition / 1 7 Project Overview/ 19 East Rochester Union Free School District Transition Needs Assessment Project /19 District Demographics / 20 Community Demographics / 21 Participants / 21 Measures / 23 Procedure / 25 East Rochester Union Free School District Transition Needs Assessment/ 26 Special Education Survey Part One/ 26 Self-Awareness / 26 Knowledge of Special Education System and Rights Under the Law / 28 Attitudes and Skills Related to Goal Attainment / 28 Self-Advocacy 3 Special Education Survey Part Two /29 Discussion /30 Developmental Trends / 30 Does Knowledge as Assessed on Part One Predict Outcome on Locus of Control Measure? / 31 Implications of Project Results /31 Self-Advocacy/Self-Determination Program Implementation /32 Project Limitations / 33
Genetic Associations of Type 2 Diabetes with Islet Amyloid Polypeptide Processing and Degrading Pathways in Asian Populations

Type 2 diabetes (T2D) is a complex disease characterized by beta cell dysfunctions. Islet amyloid polypeptide (IAPP) is highly conserved and co-secreted with insulin with over 40% of autopsy cases of T2D showing islet amyloid formation due to IAPP aggregation. Dysregulation in IAPP processing, stabilization and degradation can cause excessive oligomerization with beta cell toxicity. Previous studies examining genetic associations of pathways implicated in IAPP metabolism have yielded conflicting results due to small sample size, insufficient interrogation of gene structure and gene-gene interactions. In this multi-staged study, we screened 89 tag single nucleotide polymorphisms (SNPs) in 6 candidate genes implicated in IAPP metabolism and tested for independent and joint associations with T2D and beta cell dysfunctions. Positive signals in the stage-1 were confirmed by de novo and in silico analysis in a multi-centre unrelated case-control cohort. We examined the association of significant SNPs with quantitative traits in a subset of controls and performed bioinformatics and relevant functional analyses. Amongst the tag SNPs, rs1583645 in carboxypeptidase E (CPE) and rs6583813 in insulin degrading enzyme (IDE) were associated with 1.09 to 1.28 fold increased risk of T2D (P Meta = 9.4×10−3 and 0.02 respectively) in a meta-analysis of East Asians. Using genetic risk scores (GRS) with each risk variant scoring 1, subjects with GRS≥3 (8.2% of the cohort) had 56% higher risk of T2D than those with GRS = 0 (P = 0.01). In a subcohort of control subjects, plasma IAPP increased and beta cell function index declined with GRS (P = 0.008 and 0.03 respectively). Bioinformatics and functional analyses of CPE rs1583645 predicted regulatory elements for chromatin modification and transcription factors, suggesting differential DNA-protein interactions and gene expression. Taken together, these results support the importance of dysregulation of IAPP metabolism in T2D in East Asians.
LOW MILKY-WAY-LIKE MOLECULAR GAS EXCITATION OF MASSIVE DISK GALAXIES AT z ∼ 1.5

We present evidence for Milky-Way-like, low-excitation molecular gas reservoirs in near-IR-selected massive galaxies at z ∼ 1.5, based on IRAM Plateau de Bure Interferometer CO[3–2] and NRAO Very Large Array CO[1–0] line observations for two galaxies that had been previously detected in CO[2–1] emission. The CO[3–2] flux of BzK − 21000 at z = 1.522 is comparable within the errors to its CO[2–1] flux, implying that the CO[3–2] transition is significantly subthermally excited. The combined CO[1–0] observations of the two sources result in a detection at the 3σ level that is consistent with a higher CO[1–0] luminosity than that of CO[2–1]. Contrary to what is observed in submillimeter galaxies and quasi-stellar objects, in which the CO transitions are thermally excited up to J ⩾ 3, these galaxies have low-excitation molecular gas, similar to that in the Milky Way and local spirals. This is the first time that such conditions have been observed at high redshift. A Large Velocity Gradient analysis suggests that molecular clouds with density and kinetic temperature comparable to local spirals can reproduce our observations. The similarity in the CO excitation properties suggests that a high, Milky-Way-like, CO to H2 conversion factor could be appropriate for these systems. If such low-excitation properties are representative of ordinary galaxies at high redshift, centimeter telescopes such as the Expanded Very Large Array and the longest wavelength Atacama Large Millimeter Array bands will be the best tools for studying the molecular gas content in these systems through the observations of CO emission lines.
Stable and efficient miscible liquid-liquid interactions

In our surrounding environment, we may often see many various miscible liquid-liquid mixture phenomena, like pouring honey or ink into water, Coca Cola into strong wine etc., while few papers have devoted to the simulation of the phenomena. In this paper, we use a two-fluid lattice Boltzmann method (TFLBM) to simulate the underlying dynamics of miscible mixtures. By the method, a subgrid model is applied to improve its numerical stability so that the free surface of the mixture, accompanying with higher Reynolds number, can be simulated. We also apply control forces to the mixture with interesting animation created. By optimizing the memory structure and taking the advantage of dual-core or multi-core systems, we achieve real time computation for a domain in 643 cells full of fluid mixtures.
Comparison of 4D Phase-Contrast MRI Flow Measurements to Computational Fluid Dynamics Simulations of Cerebrospinal Fluid Motion in the Cervical Spine

Cerebrospinal fluid (CSF) dynamics in the cervical spinal subarachnoid space (SSS) have been thought to be important to help diagnose and assess craniospinal disorders such as Chiari I malformation (CM). In this study we obtained time-resolved three directional velocity encoded phase-contrast MRI (4D PC MRI) in three healthy volunteers and four CM patients and compared the 4D PC MRI measurements to subject-specific 3D computational fluid dynamics (CFD) simulations. The CFD simulations considered the geometry to be rigid-walled and did not include small anatomical structures such as nerve roots, denticulate ligaments and arachnoid trabeculae. Results were compared at nine axial planes along the cervical SSS in terms of peak CSF velocities in both the cranial and caudal direction and visual interpretation of thru-plane velocity profiles. 4D PC MRI peak CSF velocities were consistently greater than the CFD peak velocities and these differences were more pronounced in CM patients than in healthy subjects. In the upper cervical SSS of CM patients the 4D PC MRI quantified stronger fluid jets than the CFD. Visual interpretation of the 4D PC MRI thru-plane velocity profiles showed greater pulsatile movement of CSF in the anterior SSS in comparison to the posterior and reduction in local CSF velocities near nerve roots. CFD velocity profiles were relatively uniform around the spinal cord for all subjects. This study represents the first comparison of 4D PC MRI measurements to CFD of CSF flow in the cervical SSS. The results highlight the utility of 4D PC MRI for evaluation of complex CSF dynamics and the need for improvement of CFD methodology. Future studies are needed to investigate whether integration of fine anatomical structures and gross motion of the brain and/or spinal cord into the computational model will lead to a better agreement between the two techniques.
Not That Heart-Stopping After All: Visuo-Cardiac Synchrony Does Not Boost Self-Face Attribution

Recent experimental evidence and theoretical models suggest that an integration of exteroceptive and interoceptive signals underlies several key aspects of the bodily self. While it has been shown that self-attribution of both the hand and the full-body are altered by conflicting extero-exteroceptive (e.g. visuo-tactile) and extero-interoceptive (e.g. visuo-cardiac) information, no study has thus far investigated whether self-attribution of the face might be altered by visuo-cardiac stimulation similarly to visuo-tactile stimulation. In three independent groups of participants we presented ambiguous (i.e. morphed with a stranger's face) self-faces flashing synchronously or asynchronously with the participants’ heartbeat. We then measured the subjective percentages of self-face attribution of morphed stimuli. To control for a potential effect of visuo-cardiac synchrony on familiarity, a task assessing the attribution of a familiar face was introduced. Moreover, different durations of visuo-cardiac flashing and different degrees of asynchronicity were used. Based on previous studies showing that synchronous visuo-cardiac stimulation generally increases self-attribution of the full-body and the hand, and that synchronous visuo-tactile stimulation increases self-face attribution, we predicted higher self-face attribution during the synchronous visuo-cardiac flashing of the morphed stimuli. In contrast to this hypothesis, the results showed no difference between synchronous and asynchronous stimulation on self-face attribution in any of the three studies. We thus conclude that visuo-cardiac synchrony does not boost self-attribution of the face as it does that of hand and full-body.