Miracle-dz/UniFAR-FTUs huggingface dataset:
An Alignment-free Regression Approach to Estimating Allele-Specific Expression in F 1 Animals

We wish to study allele-specific expression in diploid organisms, specifically in F1 animals with inbred parental strains. Current methods for analyzing allele-specific expression rely on read alignment, which leads to reference bias unless there is prior knowledge of all genomic variants in the parental strains. However, in the case where RNA-seq data is available for both parental strains, we do not need prior knowledge of parental genomic variants. Our approach first uses parental RNA-seq reads to create maternal and paternal versions of transcript sequences, then estimates allele-specific expression levels in the F1 animal for each transcript. Using the parental versions of all candidate transcripts as features, we use a modified lasso penalized linear regression model for estimating abundance levels of expressed transcripts in the F1 animal. We tested our methods on synthetic data from the mouse transcriptome and compared our results with those of Trinity, a state-of-the-art de novo RNA-seq assembler. Our methods achieved much higher sensitivity and specificity in both identifying expressed transcripts and transcripts exhibiting allele-specific expression. We were also able to separately predict relative expression levels from paternal and maternal strains with more accuracy.
Medication management concerns of ethnic minority family caregivers of people living with dementia

This qualitative study explored the medication management experiences of Australian ethnic minority family caregivers of people living with dementia. From the perspective of this group of caregivers, medication management was a source of stress resulting from the progressive loss of ability of care recipients to manage their own medications; the complexity of the medication regime and the caregiver’s lack of trust of the care recipient to safely and effectively manage medications. Caregivers used various strategies to manage medications and avoid conflict with care recipients including being watchful and involving other family members in medication management tasks. Family caregivers indicated that a lack of information and access to support to inform their medication management role added to their stress, which was exacerbated in some cases by limited English proficiency. Supportive factors noted by caregivers included a well-established relationship with a community pharmacist, involvement of a geriatrician, family support and caregiver support group participation.
Robot Aided Stereo Panorama

This article describes the generation of a stereo panorama from images acquired by the rotation of a single camera. The camera is mounted on a robotic arm which ensures stability and a steady rotational velocity. Strips are taken from the right and left side of the collected images. These strips are then mosaiced together to form two images. The strips from the right side form the image for the left eye and vice versa. An automatic disparity control algorithm is then applied to the obtained stereo pair to control disparity. The stereo panorama obtained can be viewed on virtual reality displays or using other methods like anaglyphs.
Paradox of student gender: a case study of economic education from China

In many Chinese universities and colleges, female students outperform male students in social science subjects. This paper presents a case study, which examines gender difference in economic education in a Chinese university. We look at a sample of students from the Chinese university and find that holding constant observed student characteristics, female students on average appear to earn higher scores than male students and the gender difference is primarily driven by low achieving students. We further find that the gender difference in exam scores is not because of female students' ability, family background and other unobservable student characteristics. Instead, it is simply a result of female students exerting more effort than male students. We finally explore a wide range of possible explanations for the gender difference in diligence, but find little support for any of the explanations.
Systematic approaches to identify E3 ligase substrates

Protein ubiquitylation is a widespread post-translational modification, regulating cellular signalling with many outcomes, such as protein degradation, endocytosis, cell cycle progression, DNA repair and transcription. E3 ligases are a critical component of the ubiquitin proteasome system (UPS), determining the substrate specificity of the cascade by the covalent attachment of ubiquitin to substrate proteins. Currently, there are over 600 putative E3 ligases, but many are poorly characterized, particularly with respect to individual protein substrates. Here, we highlight systematic approaches to identify and validate UPS targets and discuss how they are underpinning rapid advances in our understanding of the biochemistry and biology of the UPS. The integration of novel tools, model systems and methods for target identification is driving significant interest in drug development, targeting various aspects of UPS function and advancing the understanding of a diverse range of disease processes.
Primary school councils

School councils have been an integral part of primary school life for the last decade and, despite not being mandatory in England, they are now to be found in the vast majority of primary schools. This research article aims to examine the current position of school councils in terms of their organization, the issues they address and the views held by senior leaders regarding the setting of agendas, their management and composition. The fieldwork took place in 50 primary schools within one local authority in the North West of England. This involved quantitative analysis based on a questionnaire sent directly to the head teachers. The data confirmed the widespread use of councils, with 100 per cent of responding schools having one in place. Certain themes relating to school council membership emerged, such as a positive emphasis on councillors being role models and possessing strong organizational and communication skills. Little importance, however, was given by head teachers to high academic attainment or creativity. The indications given by school leaders is that there is a clear commitment to having in place effective mechanisms via which children can raise their views, ideas and concerns, whilst promoting equality. However, in practice the emphasis on effective communication skills appears to actually limit the diversity of children actively taking part in primary schools councils. Therefore, school leaders need to take steps to allow a wider intake into their councils, in order to generate a truly representative council.
Realizable Hamiltonians for Universal Adiabatic Quantum Computers

It has been established that local lattice spin Hamiltonians can be used for universal adiabatic quantum computation. However, the two-local model Hamiltonians used in these proofs are general and hence do not limit the types of interactions required between spins. To address this concern, the present paper provides two simple model Hamiltonians that are of practical interest to experimentalists working toward the realization of a universal adiabatic quantum computer. The model Hamiltonians presented are the simplest known quantum-Merlin-Arthur-complete (QMA-complete) two-local Hamiltonians. The two-local Ising model with one-local transverse field which has been realized using an array of technologies, is perhaps the simplest quantum spin model but is unlikely to be universal for adiabatic quantum computation. We demonstrate that this model can be rendered universal and QMA-complete by adding a tunable two-local transverse ${\ensuremath{\sigma}}^{x}{\ensuremath{\sigma}}^{x}$ coupling. We also show the universality and QMA-completeness of spin models with only one-local ${\ensuremath{\sigma}}^{z}$ and ${\ensuremath{\sigma}}^{x}$ fields and two-local ${\ensuremath{\sigma}}^{z}{\ensuremath{\sigma}}^{x}$ interactions.
A phase 1/2 study of a multiclade HIV-1 DNA plasmid prime and recombinant adenovirus serotype 5 boost vaccine in HIV-Uninfected East Africans (RV 172).

BACKGROUND Human immunodeficiency virus (HIV) vaccine development remains a global priority. We describe the safety and immunogenicity of a multiclade DNA vaccine prime with a replication-defective recombinant adenovirus serotype 5 (rAd5) boost. METHODS The vaccine is a 6-plasmid mixture encoding HIV envelope (env) subtypes A, B, and C and subtype B gag, pol, and nef, and an rAd5 expressing identical genes, with the exception of nef. Three hundred and twenty-four participants were randomized to receive placebo (n=138), a single dose of rAd5 at 10(10) (n = 24) or 10(11) particle units (n = 24), or DNA at 0, 1, and 2 months, followed by rAd5 at either 10(10) (n= 114) or 10(11) particle units (n = 24) boosting at 6 months. Participants were followed up for 24 weeks after the final vaccination. RESULTS The vaccine was safe and well tolerated. HIV-specific T cell responses were detected in 63% of vaccinees. Titers of preexisting Ad5 neutralizing antibody did not affect the frequency and magnitude of T cell responses in prime-boost recipients but did affect the response rates in participants that received rAd5 alone (P = .037). CONCLUSION The DNA/rAd5 vaccination regimen was safe and induced HIV type 1 multi-clade T cell responses, which were not significantly affected by titers of preexisting rAd5 neutralizing antibody. Trial Registration. ClinicalTrials.gov identifier: NCT00123968 .
Object-oriented metrics

The paper introduces class complexity, cohesion ratio, and weighted method send out as improved/new metrics for object-oriented software. The work of Chidamber and Kemerer (1991, 1994) is used as a comparison platform. Illustrations are provided by solving a simple graphical problem using two design approaches. They are also used to validate the model proposed. Desirability of a composite complexity model is discussed and one possible approach is given.
Querying for relations from the semi-structured Web

We present a class of web queries whose result is a multi-column relation instead of a collection of unstructured documents as in standard web search. The user species the query either via a few example records, or a text description of columns of the relation. Starting from this seed, we show how to compile the result from several, possibly overlapping, tables and lists on the web. Many challenges arise in the process. First, we need to be able to extract structured records from HTML pages with little user supervision. We present algorithms for jointly aligning arbitrary record sets on the web with the query table. We adapt state of the art extraction models like Conditional Random Fields to exploit inter and intra source regularity in a unied framework. Second, we need to be able to consolidate the results from several sources in the face of missing columns, noisy extractions, and zero human supervision. We show how a suitably designed Bayesian networks allows us to compose a resolver from a library of type-specic similarity functions and table statistics. Finally, we discuss the problem of ranking the result rows by their estimated membership in the hidden target relation.
Effect of RH-2485 on development, metamorphosis and synthesis of major proteins in female silkworm Bombyx mori

Toxicological data on silkworm Bombyx mori are quite comparable to those of other lepidopteran pest insects, therefore, it is considered as a suitable model for exploring effects of any new synthetic formulations. In this study, female V instar larvae of silk moth B. mori were chosen to evaluate the lethal and sublethal toxicity effects of RH-2485 (methoxyfenozide), a non-steroidal ecdysteroid agonist and to substantiate the ecdysteroid mimicking action of RH-2485 on ovary development, vitellogenin incorporation and egg production in isolated pupal abdomen (IPA). Probit analysis was carried out to find the median lethal dose (LD50) from 96 h cumulative mortality percent. Protein profile of haemolymph, fat body, ovary and eggs were separated in SDS-PAGE. Western blot analysis was carried out to confirm vitellogenin in the ovary. Sublethal effects on feeding, cocoon spinning, pupation, adult emergence and egg production were studied at doses of 1/5th, 1/10th and 1/20th of LD50. Significant changes were observed in all these parameters at all three sublethal doses. The morphological effects were related to underlying biochemical changes by finding the changes in haemolymph, fat body, ovary and egg protein profile. Marked changes were observed in storage proteins (80 kDa) and 30 kDa proteins in the haemolymph at all three sublethal doses. The larvae that escaped the sublethal effects at a dose of 1/20 of LD50 and emerged as adults with malformed wings produced significantly lower number of eggs. The isolated pupal abdomen (IPA) treated with RH-2485 did not metamorphose into adult but the oocyte development and vitellogenesis were normal but the egg precursor processing was incomplete leading to failure in choriogenesis.
On the Achievable Rate-Regions for State-Dependent Gaussian Interference Channel

In this paper, we study a general additive state-dependent Gaussian interference channel (ASD-GIC) where we consider two-user interference channel with two independent states known non-causally at both transmitters, but unknown to either of the receivers. An special case, where the additive states over the two links are the same is studied in [1], [2], in which it is shown that the gap between the achievable symmetric rate and the upper bound is less than 1/4 bit for the strong interference case. Here, we also consider the case where each channel state has unbounded variance [3], which is referred to as the strong interferences. We first obtain an outer bound on the capacity region. By utilizing lattice-based coding schemes, we obtain four achievable rate regions. Depend on noise variance and channel power constraint, achievable rate regions can coincide with the channel capacity region. For the symmetric model, the achievable sum-rate reaches to within 0.661 bit of the channel capacity for signal to noise ratio (SNR) greater than one.
Understanding the Role of the ‘Self’ in the Social Priming of Mimicry

People have a tendency to unconsciously mimic other's actions. This mimicry has been regarded as a prosocial response which increases social affiliation. Previous research on social priming of mimicry demonstrated an assimilative relationship between mimicry and prosociality of the primed construct: prosocial primes elicit stronger mimicry whereas antisocial primes decrease mimicry. The present research extends these findings by showing that assimilative and contrasting prime-to-behavior effect can both happen on mimicry. Specifically, experiment 1 showed a robust contrast priming effect where priming antisocial behaviors induces stronger mimicry than priming prosocial behaviors. In experiment 2, we manipulated the self-relatedness of the pro/antisocial primes and further revealed that prosocial primes increase mimicry only when the social primes are self-related whereas antisocial primes increase mimicry only when the social primes are self-unrelated. In experiment 3, we used a novel cartoon movie paradigm to prime pro/antisocial behaviors and manipulated the perspective-taking when participants were watching these movies. Again, we found that prosocial primes increase mimicry only when participants took a first-person point of view whereas antisocial primes increase mimicry only when participants took a third-person point of view, which replicated the findings in experiment 2. We suggest that these three studies can be best explained by the active-self theory, which claims that the direction of prime-to-behavior effects depends on how primes are processed in relation to the ‘self’.
Predicting Search Intent Based on Pre-Search Context

While many studies have been conducted on query understanding, there is limited understanding on why users start searches and how to predict search intent. In this paper, we propose to study this important but less explored problem. Our key intuition is that searches are triggered by different pre-search contexts, but the triggering relations are often hidden. For example, a user may search "bitcoin" because of a news article or an email the user just read, but the system does not know which of the pre-search contexts (the news article or the email) is the triggering source. Following this intuition, we conduct an in-depth analysis of pre-search context on a large-scale user log, which not only verifies the hidden triggering relations in the real world but also identifies a set of important characteristics of pre-search context and their triggered queries. Since the hidden triggering relations make it challenging to directly use pre-search context for intent prediction, we develop a mixture generative model to learn without any supervision how queries are triggered by different types of pre-search context. Further, we discuss how to apply our model to improve query prediction and query auto-completion. Our experiments on a large-scale of real-world data show that our model could accurately predict user search intent with pre-search context and improve upon the state-of-the-art methods significantly.
Weblog-style video annotation and syndication

In this paper, we present a method to extend the mechanisms employed for Weblogs in order to make video contents accessible to Weblog communities. We also present a mechanism that generates Weblog entries from the browsing history of the video contents. These entries help Weblog users to reach the related video contents. By extracting knowledge on the video contents from communication among members of Weblog communities and syndicating the knowledge in the form of RDF, we can use the mechanism for annotation-based applications, such as a semantic video retrieval and summarization system.
Prediction of glaucomatous visual field loss by extrapolation of linear trends.

OBJECTIVE To investigate how well short-term progression rates can predict long-term visual field outcomes in patients with glaucoma. METHODS We calculated visual field rates of progression using linear regression analysis of the Visual Field Index (VFI) for 100 consecutive patients with glaucoma having 10 or more Swedish Interactive Thresholding Algorithm standard field tests. Final VFI was predicted on the basis of linear extrapolation of the slope defined by the initial 5 field test results. Final VFI also was estimated using linear regression of all qualifying examination results for each patient. Primary outcome measures were the absolute difference and the correlation between predicted and estimated final VFI values. RESULTS Patient follow-up averaged 8.2 years and 11 field examinations. Median VFI progression rate was -1.1% per year both for the initial 5 test results and also for the complete series. Seventy percent of patients had a predicted final VFI within +/-10% of the estimated final VFI, and the 2 VFI calculations had a correlation coefficient of 0.84. CONCLUSION Linear extrapolation based on 5 initial visual field test results was a reliable predictor of future field loss in most patients. Patients in whom linear regression analysis suggests dangerously rapid rates of visual field progression may be candidates for significant alterations in therapy.
‘Implicit justifications’ and self-serving group allocations†

In comparison to allocating resources to oneself, when allocating resources to one's group, people are able to ‘get away with’ taking more than a fair and equal share because there exists an implicit justification that fellow group members will benefit. Such an implicit justification enables people to hide their self-serving motivation. Results reveal that subjects allocating a sum of money between their group and a competing group took a significantly greater share of the resource than subjects allocating between themselves and a competing individual. Whether the allocation was made public or kept private had a significant impact on this relationship: the difference between group and self allocations was significantly greater when the allocation was made public than when kept private. However, subjects allocating only to themselves and in private were almost as self-serving as subjects allocating to their group (both in private and in public). The only case where subjects were overly constrained by equality was when they were allocating to only themselves and the allocation was made public. © 1997 John Wiley & Sons, Ltd.
Comparison of the Influence of Phospholipid-Coated Porous Ti-6Al-4V Material on the Osteosarcoma Cell Line Saos-2 and Primary Human Bone Derived Cells

Biomaterial surface functionalization remains of great interest in the promotion of cell osteogenic induction. Previous studies highlighted the positive effects of porous Ti-6Al-4V and phospholipid coating on osteoblast differentiation and bone remodeling. Therefore, the first objective of this study was to evaluate the potential synergistic effects of material porosity and phospholipid coating. Primary human osteoblasts and Saos-2 cells were cultured on different Ti-6Al-4V specimens (mirror-like polished or porous specimens) and were coated or not with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) for three weeks or five weeks. Selected gene expressions (e.g., classical bone markers: alkaline phosphatase, osteocalcin, osteoprotegerin (OPG), receptor activator of nuclear factor kappa-β ligand (RANKL) and runt-related transcription factor 2) were estimated in vitro. Furthermore, the expressions of osteocalcin and osteopontin were examined via fluorescent microscopy at five weeks (immunocytochemistry). Consequently, it was observed that phospholipid coating potentiates preferences for low and high porosities in Saos-2 and primary cells, respectively, at the gene and protein levels. Additionally, RANKL and OPG exhibited different gene expression patterns; primary cells showed dramatically increased RANKL expression, whereas OPG expression was decreased in the presence of POPE. A synergistic effect of increased porosity and phospholipid coating was observed in primary osteoblasts in bone remodeling. This study showed the advantage of primary cells over the standard bone cell model.
Inactivation of the Polycomb Group Protein Ring1B Unveils an Antiproliferative Role in Hematopoietic Cell Expansion and Cooperation with Tumorigenesis Associated with Ink4a Deletion

ABSTRACT Polycomb group (PcG) proteins act as positive regulators of cell proliferation. Ring1B is a PcG gene essential for embryonic development, but its contribution to cell turnover in regenerating tissues in not known. Here, we have generated a conditional mouse mutant line to study the Ring1B role in adult hematopoiesis. Mutant mice developed a hypocellular bone marrow that paradoxically contained an enlarged, hyperproliferating compartment of immature cells, with an intact differentiation potential. These alterations were associated with differential upregulation of cyclin D2, which occurred in all mutant bone marrow cells, and of p16Ink4a, observed only in the differentiated compartment. Concurrent inactivation of Ink4a rescued the defective proliferation of maturing cells but did not affect the hyperproliferative activity of progenitors and resulted in a shortening of the onset of lymphomas induced by Ink4a inactivation. These data show that Ring1B restricts the progenitors' proliferation and promotes the proliferation of their maturing progeny by selectively altering the expression pattern of cell cycle regulators along hematopoietic differentiation. The novel antiproliferative role of Ring1B's downregulation of a cell cycle activator may play an important role in the tight control of hematopoietic cell turnover.