Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetics ATF 6 Is Mutated in Early Onset Photoreceptor Degeneration With Macular Involvement

Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, Utah, United States Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, United States Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, United States Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States
Genetic variation in the mitochondrial 16S rRNA gene of the American dog tick, Dermacentor variabilis (Acari: Ixodidae).

Genetic variation in the mitochondrial (mt) 16S ribosomal RNA (rRNA) gene was examined for the American dog tick, Dermacentor variabilis (Say, 1821). Nine different haplotypes were detected among 369 adult D. variabilis collected from four localities in Canada. There were eight variable nucleotide positions in the 404 bp sequence alignment. Individuals of haplotype 1 occurred at frequency of >75% at all localities. Five haplotypes were detected at only one of the four localities. High haplotype diversity and low nucleotide diversity, combined with significantly negative Fs values for ticks at three localities, suggest a recent population expansion. Genetic differences were found between populations at different localities, but a Mantel regression analysis revealed no association between genetic differences and geographical distances. There was also no association between tick haplotype and the prevalence of the bacterium, Rickettsia montanensis Weiss and Moulder, 1984, in D. variabilis among localities or on opposite sides of Blackstrap Lake (Saskatchewan). The 16S rDNA haplotypes from Canadian populations of D. variabilis formed a clade with those from the eastern and central U.S.A. , to the exclusion of D. variabilis from geographically isolated populations in the western U.S.A. Although sample sizes for D. variabilis in the eastern U.S.A. are small, there may be genetic divergence between populations in Canada and those in the eastern U.S.A. , which may have implications for studies on the pathogenic agents transmitted by D. variabilis to its hosts.
Thermo and pH Dual‐Responsive Nanoparticles for Anti‐Cancer Drug Delivery

The emergence of stimuli-responsive drug carriers has opened the door to a new generation of anti-cancer drug delivery systems that are more intelligent and more effective than those conventional ones. [1–6] Certain malignancies can cause two stimuli around tumor site at the same time. One is a slight local temperature increase [7] and the other is a minor decrease in extracellular pH (6.8–7.2). [8] Thus, properly designed nanocarriers that are dual-responsive to both temperature and pH may be able to intelligently distinguish between normal and pathological tissues, achieving better targeting efficiency and treatment efficacy. Indeed, efforts for the preparation of dual-responsive drug carriers have been made for some time. Kim’s group did some pioneering work on the temperature and pH dual-responsive polymeric delivery system for targeted oral delivery of insulin. [9] Recently, dual-responsive systems are gradually being extended to anti-cancer drug delivery. For example, Soppimath et al. prepared pH-triggered thermo responsive nanoparticles made of terpo-lymer P( N -isopropylacrylamide- co - N , N -dimethylarylamide- co -10-undecenoic acid) (P(NIPAAm-co -DMAAm- co -UA)). [2] They found that weak acidic environment (pH6.6) could cause nanoparticle aggregation at body temperature and trigger the release of the loaded anti-cancer drug doxorubicin (DOX). Unfortunately, the drug loading capacity was quite low (2.7%), which limits their practical usefulness. Kang et al. fabricated DOX-loaded thermo and pH responsive nanoparticles based on copolymers of NIPAAm, DMAAm and a pH sensitive telomer sulfamethoxypyridazine. [3
Multi-target tracking of Zebrafish based on particle filter

Zebrafish is an excellent model organism, which has been widely used in the fields of biological experiments, drug screening, and swarm intelligence. In recent years, there are a large number of techniques for tracking of zebrafish involved in the study of behaviors, which makes it attack much attention of scientists from many fields. Multi-target tracking of zebrafish is still facing many challenges. The high mobility and uncertainty make it difficult to predict its motion; the similar appearances and texture features make it difficult to establish an appearance model; it is even hard to link the trajectories because of the frequent occlusion. In this paper, we use particle filter to approximate the uncertainty of the motion of zebrafish. Firstly, by analyzing the motion characteristics, we establish an efficient hybrid motion model to predict its positions; then we establish an appearance model based on the predicted positions to predict the postures of every targets, meanwhile weigh the particles by comparing the difference of predicted pose and observation pose; finally, we get the optimal position of single zebrafish through the weighted position, and use the joint particle filter to process trajectory linking of multiple zebrafish.
Comparative Study of Prions in Iatrogenic and Sporadic Creutzfeldt-Jakob Disease

Differentiating iatrogenic Creutzfeldt-Jakob disease (iCJD) from sporadic CJD (sCJD) would be useful for the identification and prevention of human-to-human prion transmission. Currently, the diagnosis of iCJD depends on identification of a recognized source of contamination to which patients have been exposed, in addition to fulfilling basic requirements for the establishment of diagnosis of CJD. Attempts to identify differences in clinical manifestations, neuropathological changes and pathological prion protein (PrPSc) between iCJD and sCJD have been unsuccessful. In the present study, using a variety of more sophisticated methods including sucrose step gradient sedimentation, conformational stability immunoassay, protein misfolding cyclic amplification (PMCA), fragment-mapping, and transmission study, we show no significant differences in gel profiles, oligomeric state, conformational stability and infectivity of PrPSc between iCJD and sCJD. However, using PMCA, we find that convertibility and amplification efficiency of PrPSc is greater in iCJD than in sCJD in a polymorphism-dependent manner. Moreover, two protease-resistant PrP C-terminal fragments (termed PrP-CTF12/13) were detected in all 9 cases of sCJD but not in 6 of 8 cases of iCJD tested in this study. The use of fragment mapping- and PMCA-based assays thus provides a means to distinguish most cases of iCJD from sCJD.
DDoS/EDoS attack in cloud: affecting everyone out there!

DDoS attacks have become fatal attacks in recent times. There are large number of incidents which have been reported recently and caused heavy downtime and economic losses. Evolution of utility computing models like cloud computing and its adoption across enterprises is visible due to many promising features. Effects of DDoS attacks in cloud are no more similar to what they were in traditional fixed or on premise infrastructure. In addition to effects on the service, economic or sustainability effects are significant in the form of Economic Denial of Sustainability (EDoS) attacks. We argue that in a multi-tenant public cloud, multiple stakeholders are involved other than the victim server. Some of these important stakeholders are co-hosted virtual servers, physical server(s), network and, cloud service providers. We have shown through system analysis, experiments and simulations that these stakeholders are indeed affected though they are not the actual targets. Effects to other stakeholders include performance interference, web service performance, resource race, indirect EDoS, downtime and, business losses. Cloud scale simulations have revealed that overall energy consumption and no. of VM migrations are adversely affected due to DDoS/EDoS attacks. Losses to these stakeholders should be properly accounted and there is a need to devise methods to isolate these components well.
Epigenetic profile of the euchromatic region of human Y chromosome

The genome of a multi-cellular organism acquires various functional capabilities in different cell types by means of distinct chromatin modifications and packaging states. Acquired during early development, the cell type-specific epigenotype is maintained by cellular memory mechanisms that involve epigenetic modifications. Here we present the epigenetic status of the euchromatic region of the human Y chromosome that has mostly been ignored in earlier whole genome epigenetic mapping studies. Using ChIP-on-chip approach, we mapped H3K9ac, H3K9me3, H3K27me3 modifications and CTCF binding sites while DNA methylation analysis of selected CpG islands was done using bisulfite sequencing. The global pattern of histone modifications observed on the Y chromosome reflects the functional state and evolutionary history of the sequences that constitute it. The combination of histone and DNA modifications, along with CTCF association in some cases, reveals the transcriptional potential of all protein coding genes including the sex-determining gene SRY and the oncogene TSPY. We also observe preferential association of histone marks with different tandem repeats, suggesting their importance in genome organization and gene regulation. Our results present the first large scale epigenetic analysis of the human Y chromosome and link a number of cis-elements to epigenetic regulatory mechanisms, enabling an understanding of such mechanisms in Y chromosome linked disorders.
Learning Representations of Student Knowledge and Educational Content

Students in online courses generate large amounts of data that can be used to personalize the learning process and improve quality of education. The goal of this work is to develop a statistical model of students and educational content that can be used for a variety of tasks, such as adaptive lesson sequencing and learning analytics. We formulate this problem as a regularized maximum-likelihood embedding of students, lessons, and assessments from historical student-module interactions. Akin to collaborative filtering for recommender systems, the algorithm does not require students or modules to be described by features, but it learns a representation using access traces. An empirical evaluation on large-scale data from Knewton, an adaptive learning technology company, shows that this approach predicts assessment results more accurately than baseline models and is able to discriminate between lesson sequences that lead to mastery and failure.
Improving Priority Enforcement via Non-Work-Conserving Scheduling

Current operating system schedulers are not fully aware of multi-core and multi-threaded architectures, and as a result, schedule threads in a way that may cause contention for critical resources such as the last level in the cache memory hierarchy or the memory access bandwidth. This contention has a significant impact on the system productivity and the quality of service that each individual thread gets from the platform, which can widely vary depending on the behavior of its simultaneous co-runners.In this paper we describe the design and implementation of a non-work-conserving framework to schedule threads that tries to improve priority enforcement, based on on-line statistics collected through hardware performance counters. We have implemented our scheme in Linux running on both multicore and SMT processors. For synthetic workloads based on the latest SPEC CPU2006 benchmarks, our framework speeds up high-priority threads by up to 50%, while keeping or even slightly improving the overall system throughput.
Phenomenological description of strain rate and temperature-dependent yield stress of PMMA

SYNOPSIS A constitutive equation to describe the yield behavior of poly(methy1 methacrylate) (PMMA) is useful not only from the technological point of view, but also for the comprehension of the nonlinear mechanisms acting in the material. In both compression and tension, the yield stress is usually represented as a function of the strain rate at different temperatures. In PMMA and other glassy polymers these curves are related by scaling, that is, they can be matched to form a master curve. Particularly in PMMA the temperature and strain rate dependence of the master curve has been characterized by two different models. The first involves two thermally activated rate processes, one acting only at high strain rates. The second model interprets the yield process as a cooperative movement of several independent structural units, all with the same activation energy. In this article it is demonstrated that only the second phenomenological model is correct because it provides a good fit to the master curve of PMMA both in compression and tension, and verifies the properties of a set of curves related by scaling. Moreover, it is pointed out that the first model leads to severe inconsistencies because it does not consider the nonlinear behavior of PMMA. Finally, the physical parameters obtained (internal stress, activation volume, and enthalpy) are compared with those given in the literature. 0 1995 John Wiley & Sons, Inc.
Flexible codebook design for limited feedback downlink systems via smooth optimization on the Grassmannian manifold

Grassmannian quantization codebooks play a central role in a number of limited feedback schemes for single and multi-user MIMO communication systems. In practice, it is often desirable that these codebooks possess additional properties that facilitate their implementation, beyond the provision of good quantization performance. Although some good codebooks exist, their design tends to be a rather intricate task. The goal of this paper is to suggest a flexible approach to the design of Grassmannian codebooks based on smooth optimization algorithms for the Grassmannian manifold and the use of smooth penalty functions to obtain additional desirable properties. As one example, rank-2 codebooks with a nested structure and elements from a discrete alphabet are designed. In some numerical comparisons, codebooks designed using the proposed approach have better Fubini-Study distance properties than some existing codebooks, and provide tangible performance gains when applied to a simple MIMO downlink scenario with zero-forcing beamforming, PU2RC, and block diagonalization signalling. Furthermore, the proposed approach yields codebooks that attain desirable additional properties without incurring a substantial degradation in performance.
Multi-pivot translation by system combination

This paper describes a technique to exploit multiple pivot languages when using machine translation (MT) on language pairs with scarce bilingual resources, or where no translation system for a language pair is available. The principal idea is to generate intermediate translations in several pivot languages, translate them separately into the target language, and generate a consensus translation out of these using MT system combination techniques. Our technique can also be applied when a translation system for a language pair is available, but is limited in its translation accuracy because of scarce resources. Using statistical MT systems for the 11 different languages of Europarl, we show experimentally that a direct translation system can be replaced by this pivot approach without a loss in translation quality if about six pivot languages are available. Furthermore, we can already improve an existing MT system by adding two pivot systems to it. The maximum improvement was found to be 1.4% abs. in BLEU in our experiments for 8 or more pivot languages.
Guarded execution and branch prediction in dynamic ILP processors

Evaluates the effects of guarded (or conditional, or predicated) execution on the performance of an instruction level parallel processor employing dynamic branch prediction. First, the authors assess the utility of guarded execution, both qualitatively and quantitatively, using a variety of application programs. The assessment shows that guarded execution significantly increases the opportunities, for both compiler and dynamic hardware, to extract and exploit parallelism. However, existing methods of specifying guarded execution have several drawbacks that limit its use. Second, the authors study the interaction of guarded execution and dynamic branch prediction and show that the use of guarded execution significantly increases the number of instructions between mispredicted branches. Third, they propose a new method of specifying guarded execution. The proposed method uses special GUARD instructions, which can be used to incorporate guarded execution into existing instruction sets. GUARD instructions realize the full power of guarded execution, without the drawbacks of existing methods of specifying guarded execution. <<ETX>>
Mechanisms That Determine the Internal Environment of the Developing Brain: A Transcriptomic, Functional and Ultrastructural Approach

We provide comprehensive identification of embryonic (E15) and adult rat lateral ventricular choroid plexus transcriptome, with focus on junction-associated proteins, ionic influx transporters and channels. Additionally, these data are related to new structural and previously published permeability studies. Results reveal that most genes associated with intercellular junctions are expressed at similar levels at both ages. In total, 32 molecules known to be associated with brain barrier interfaces were identified. Nine claudins showed unaltered expression, while two claudins (6 and 8) were expressed at higher levels in the embryo. Expression levels for most cytoplasmic/regulatory adaptors (10 of 12) were similar at the two ages. A few junctional genes displayed lower expression in embryos, including 5 claudins, occludin and one junctional adhesion molecule. Three gap junction genes were enriched in the embryo. The functional effectiveness of these junctions was assessed using blood-delivered water-soluble tracers at both the light and electron microscopic level: embryo and adult junctions halted movement of both 286Da and 3kDa molecules into the cerebrospinal fluid (CSF). The molecular identities of many ion channel and transporter genes previously reported as important for CSF formation and secretion in the adult were demonstrated in the embryonic choroid plexus (and validated with immunohistochemistry of protein products), but with some major age-related differences in expression. In addition, a large number of previously unidentified ion channel and transporter genes were identified for the first time in plexus epithelium. These results, in addition to data obtained from electron microscopical and physiological permeability experiments in immature brains, indicate that exchange between blood and CSF is mainly transcellular, as well-formed tight junctions restrict movement of small water-soluble molecules from early in development. These data strongly indicate the brain develops within a well-protected internal environment and the exchange between the blood, brain and CSF is transcellular and not through incomplete barriers.
migration Transgenic overexpression of the CC chemokine CCL 21 disrupts T-cell

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Geochemical modelling and identification of leaching processes in MSWI bottom ash : implications for the short-term and long-term release of contaminants

Municipal Solid Waste Incinerator (MSWI) bottom ash is the major residue that remains after the incineration of Municipal Solid Waste. The slag-like material is produced world-wide in very large and everincreasing quantities. In the past the bottom ash was usually disposed, nowadays it is increasingly being used as a construction material. Incineration concentrates the mineral components of the original waste, including elements of environmental concern such as heavy metals, oxyanions, and salts. To ensure an environmentally safe utilisation or disposal of MSWI bottom ash it is, therefore, necessary to investigate its leaching properties. It is in particular necessary to identify the mechanisms that control leaching, because only then reliable predictions of the long-term leaching can be made. This thesis focuses on the geochemical processes that control the shortterm and long-term leaching of major and minor elements from MSWI bottom ash. The research is based on (I) carefully controlled laboratory leaching experiments on MSWI bottom ash at different stages of weathering, (II) geochemical modelling of aqueous (in)organic complexation, precipitation/dissolution, and sorption processes, (III) specific experiments to obtain parameters for the modelling of sorption reactions and organic complexation reactions, (IV) spectroscopic analyses of bottom ash samples, and (V) a field investigation of a 20-year old disposal of MSWI residues.
Observation of a new boson with a mass near 125 GeV The CMS Collaboration

Combined results are presented from searches for the standard model (SM) Higgs boson in proton-proton collisions at √ s = 7 and 8 TeV in five decay modes: γγ, bb, ττ, WW, and ZZ. The analysed data correspond to integrated luminosities of up to 5.1 fb−1 at 7 TeV and 5.3 fb−1 at 8 TeV. The data exclude the existence of a SM Higgs boson in the ranges 110–122.5 and 127–600 GeV at 95% confidence level. An excess of events above the expected SM background is observed with a local significance of 4. 9σ around 125 GeV, which we attribute to the production of a previously unobserved particle. The evidence is strongest in the two final states with the best mass resolution: the two-photon final state and the final state with two pairs of charged leptons (electrons or muons). The combined excess in these channels alone gives a local significance of 5. 0σ. An unconstrained fit to the excesses in these two final states yields a mass of 125.3 ± 0.4 (stat) ± 0.5 (syst) GeV. Within the statistical uncertainties, the results obtained in all search channels are consistent with the expectations for a SM Higgs boson. More data are needed to test whether the properties of this new state are indeed those of the SM Higgs boson or whether some differ, implying new physics beyond the standard model.