Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic Dissection of Quantitative Trait Loci for Hemostasis and Thrombosis on Mouse Chromosomes 11 and 5 Using Congenic and Subcongenic Strains

Susceptibility to thrombosis varies in human populations as well as many inbred mouse strains. Only a small portion of this variation has been identified, suggesting that there are unknown modifier genes. The objective of this study was to narrow the quantitative trait locus (QTL) intervals previously identified for hemostasis and thrombosis on mouse distal chromosome 11 (Hmtb6) and on chromosome 5 (Hmtb4 and Hmtb5). In a tail bleeding/rebleeding assay, a reporter assay for hemostasis and thrombosis, subcongenic strain (6A-2) had longer clot stability time than did C57BL/6J (B6) mice but a similar time to the B6-Chr11A/J consomic mice, confirming the Hmtb6 phenotype. Six congenic and subcongenic strains were constructed for chromosome 5, and the congenic strain, 2A-1, containing the shortest A/J interval (16.6 cM, 26.6 Mbp) in the Hmtb4 region, had prolonged clot stability time compared to B6 mice. In the 3A-2 and CSS-5 mice bleeding time was shorter than for B6, mice confirming the Hmtb5 QTL. An increase in bleeding time was identified in another congenic strain (3A-1) with A/J interval (24.8 cM, 32.9 Mbp) in the proximal region of chromosome 5, confirming a QTL for bleeding previously mapped to that region and designated as Hmtb10. The subcongenic strain 4A-2 with the A/J fragment in the proximal region had a long occlusion time of the carotid artery after ferric chloride injury and reduced dilation after injury to the abdominal aorta compared to B6 mice, suggesting an additional locus in the proximal region, which was designated Hmtb11 (5 cM, 21.4 Mbp). CSS-17 mice crossed with congenic strains, 3A-1 and 3A-2, modified tail bleeding. Using congenic and subcongenic analysis, candidate genes previously identified and novel genes were identified as modifiers of hemostasis and thrombosis in each of the loci Hmtb6, Hmtb4, Hmtb10, and Hmtb11.
Robust Transceiver Optimization in Downlink Multiuser MIMO Systems with Channel Uncertainty

The problem of transceiver optimization in multiuser multiple-input multiple-output downlink wireless systems is considered. The base station is assumed to possess only estimated, erroneous values of channel coefficients. The exact channels lie in uncertainty regions, specified by the Frobenius norms of the error matrices. An iterative optimization of the transmit and receive filters is performed with the goal of minimizing the total transmit power, while satisfying the users' mean square error (MSE) targets for all channels from the uncertainty regions. Each iteration consists of two steps that can be equivalently rewritten as semidefinite programs with efficient numerical solutions. It is shown that the whole algorithm converges. The proposed framework can be applied for solving robust counterparts of several related MSE-optimization problems. The modifications of the proposed algorithms for accommodating box-like disturbances are analyzed, as well.
ESDF: Ensemble Selection using Diversity and Frequency

Recently ensemble selection for consensus clustering has emerged as a research problem in Machine Intelligence. Normally consensus clustering algorithms take into account the entire ensemble of clustering, where there is a tendency of generating a very large size ensemble before computing its consensus. One can avoid considering the entire ensemble and can judiciously select few partitions in the ensemble without compromising on the quality of the consensus. This may result in an efficient consensus computation technique and may save unnecessary computational overheads. The ensemble selection problem addresses this issue of consensus clustering. In this paper, we propose an efficient method of ensemble selection for a large ensemble. We prioritize the partitions in the ensemble based on diversity and frequency. Our method selects top K of the partitions in order of priority, where K is decided by the user. We observe that considering jointly the diversity and frequency helps in identifying few representative partitions whose consensus is qualitatively better than the consensus of the entire ensemble. Experimental analysis on a large number of datasets shows our method gives better results than earlier ensemble selection methods.
Studying the influence of hydrogel injections into the infarcted left ventricle using the element‐free Galerkin method

Myocardial infarction is an increasing health problem worldwide. Because of an under‐supply of blood, the cardiomyocytes in the affected region permanently lose their ability to contract. This in turn gradually weakens the overall heart function. A new therapeutic approach based on the injection of a gel into the infarcted area aims to support the healing and to inhibit adverse remodelling that can lead to heart failure. A computational model is the basis for obtaining a better understanding of the heart mechanics, in particular, how myocardial infarction and gel injections affect its pumping performance. A strain invariant‐based stored energy function is proposed to account for the passive mechanical behaviour of the model, which also makes provision for active contraction. To incorporate injections an additive homogenization approach is introduced. The numerical framework is developed using an in‐house code based on the element‐free Galerkin method. The main focus of this contribution is to investigate the influence of gel injections on the mechanics of the left ventricle during the diastolic filling and systolic isovolumetric (isochoric) contraction phases. It is found that gel injections are able to reduce the elevated fibre stresses caused by an infarct. Copyright © 2013 John Wiley & Sons, Ltd.
Extraction of Biological Apatite from Cow Bone at Different Calcination Temperatures: A Comparative Study

The purpose of this study is to extract natural hydroxyapatite (HAP) from cow bone. The hydrothermal method followed by calcination treatment at different temperatures is used in this current research. Cow bone has the potential for producing hydroxyapatite, a chief component present in bone and teeth of vertebrates. HAP is an excellent material used in bone restoration and tissue regeneration. Characterizations of the cow bone natural HAP powder were done by X-ray diffraction (XRD) and Thermogravimetric analysis (TGA). TGA data revealed that biological apatite is thermally stable at 1100°C. XRD data showed that the extracted HAP is, highly crystalline and hexagonal crystal structure having a crystallite size in the range of 10-83 nm. The extracted HAP material is found to be thermally stable up to 1300°C.
Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome

Investigating the expression of genes in cancer-associated immune cells (immunome) is imperative for prognosis prediction. However, evaluating the expression of immune-associated genes within cancer biopsy is subject to significant inconsistencies related to the sampling methodology. Here, we present immFocus, a method for extracting immune signals from total RNA sequencing of tumor biopsies, intended for immunity depiction and prognosis evaluation. It is based on reducing the variation which biopsy preparation adds to the apparent expression levels of immune genes. We employed immFocus to normalize gene expression with an immune index using data obtained from renal clear cell carcinoma biopsies. Genes that became less variable due to normalization were found to be preferentially immune-related. Moreover, immune-related genes tended to become more prognostic due to the normalization. These results demonstrate, for the first time, that whole transcriptome sequencing can be used for interrogation of a cancer immunome and for advancing immune-based prognosis.
Caenorhabditis elegans DAF-2 as a Model for Human Insulin Receptoropathies

Human exome sequencing has dramatically increased the rate of identification of disease-associated polymorphisms. However, examining the functional consequences of those variants has created an analytic bottleneck. Insulin-like signaling in Caenorhabditis elegans has long provided a model to assess consequences of human insulin signaling mutations, but this has not been evaluated in the context of current genetic tools. We have exploited strains derived from the Million Mutation Project (MMP) and gene editing to explore further the evolutionary relationships and conservation between the human and C. elegans insulin receptors. Of 40 MMP alleles analyzed in the C. elegans insulin-like receptor gene DAF-2, 35 exhibited insulin-like signaling indistinguishable from wild-type animals, indicating tolerated mutations. Five MMP alleles proved to be novel dauer-enhancing mutations, including one new allele in the previously uncharacterized C-terminus of DAF-2. CRISPR-Cas9 genome editing was used to confirm the phenotypic consequence of six of these DAF-2 mutations and to replicate an allelic series of known human disease mutations in a highly conserved tyrosine kinase active site residue, demonstrating the utility of C. elegans for directly modeling human disease. Our results illustrate the challenges associated with prediction of the phenotypic consequences of amino acid substitutions, the value of assaying mutant isoform function in vivo, and how recently developed tools and resources afford the opportunity to expand our understanding even of highly conserved regulatory modules such as insulin signaling. This approach may prove generally useful for modeling phenotypic consequences of candidate human pathogenic mutations in conserved signaling and developmental pathways.
Tracing the Most Parsimonious Indel History

Sequence alignment (the grouping of homologous bases into one column) is fundamental to almost any task in comparative genomics. This translates to positing gaps in the genomic sequences to account for events of insertions and deletions (indels). The interrelationship between sequence alignment and phylogenetic reconstruction has drawn substantial attention recently with works showing the significance of differences in alignments. One of the plausible approaches in this direction is to grade the suitability of a tree to an associated alignment and vice verse. We here present a combinatorial (as opposed to statistical) approach based on the indel history. We show--both by simulations and by using real biological data from the Encyclopedia of DNA Elements (ENCODE)--that this criterion is sound. The novelty of our approach is the distinguishing between insertions and deletions, and augmenting the analysis with a dimension of "depth," extending it from the sequence space to the phylogenetic space. Using this approach, we perform a comprehensive study of indel characteristic behavior among mammals in both coding and non-coding regions. Our results show significant differences in indel patterns between coding and non-coding regions. We also show other characteristic patterns of indel evolution in the depth of the underlying phylogeny.
Mesoporous Magnetic Gold “Nanoclusters” as Theranostic Carrier for Chemo-Photothermal Co-therapy of Breast Cancer

Photothermal therapy (PTT) is proved to be an efficient manner for superficial tumor therapy in preclinical studying. The tumor suppression of chemotherapy can be enhanced by combining with PTT. In this study, we reported a mesoporous magnetic gold “nanoclusters” (MMGNCs) structure as theranostic carrier for chemo-photothermal co-therapy. MMGNCs were successfully prepared and they exhibited efficient photo-thermal effect for PTT. The mesoporous structure provided MMGNCs with high drug loading capacity. By in vitro cytotoxicity testing, we revealed that the combination of PTT and chemotherapy could cause more damage than chemotherapy or PTT did alone. By topically targeting mediated by the extra-magnetic field (MF), MMGNCs can be targeted to the tumor site efficiently. In vivo chemo-photothermal co-therapy of 4T1 breast cancer, under the combinational treatments of chemo-photothermal co-therapy and extra-MF targeting, the tumor growth has been efficiently inhibited, and the pulmonary and mediastinal metastasis have also been prevented. The survival of the cancer bearing mice was prolonged. The bio-imaging applications of this system and the mechanism of the metastasis prevention are ongoing.
POSTECH at NTCIR-5 Patent Retrieval: Smoothing Experiments in a Language Modeling Approach to Patent Retrieval

This report describes the experimental results of our participation at the Document Retrieval Subtask of NTCIR-5 Patent Retrieval Task. Unlike newspaper articles which belong to the main document type handled in previous information retrieval experiments, patent documents have many different characteristics in terms of length, technicality, structureness, etc. Among these, we focus on the length of patent documents. Since patent documents are long and cover a diverse spectrum of topicality, document models estimated from them by the language modeling approach are expected to show different characteristics from those estimated from short document samples such as newspaper articles. Based on such contemplation, this report investigates the effect of smoothing in the language modeling approach on retrieving patent documents.
SIGMa: simple greedy matching for aligning large knowledge bases

The Internet has enabled the creation of a growing number of large-scale knowledge bases in a variety of domains containing complementary information. Tools for automatically aligning these knowledge bases would make it possible to unify many sources of structured knowledge and answer complex queries. However, the efficient alignment of large-scale knowledge bases still poses a considerable challenge. Here, we present Simple Greedy Matching (SiGMa), a simple algorithm for aligning knowledge bases with millions of entities and facts. SiGMa is an iterative propagation algorithm that leverages both the structural information from the relationship graph and flexible similarity measures between entity properties in a greedy local search, which makes it scalable. Despite its greedy nature, our experiments indicate that SiGMa can efficiently match some of the world's largest knowledge bases with high accuracy. We provide additional experiments on benchmark datasets which demonstrate that SiGMa can outperform state-of-the-art approaches both in accuracy and efficiency.
Drosophila Transposon Insertions as Unknowns for Structured Inquiry Recombination Mapping Exercises in an Undergraduate Genetics Course

Structured inquiry approaches, in which students receive a Drosophila strain of unknown genotype to analyze and map the constituent mutations, are a common feature of many genetics teaching laboratories. The required crosses frustrate many students because they are aware that they are participating in a fundamentally trivial exercise, as the map locations of the genes are already established and have been recalculated thousands of times by generations of students. We modified the traditional structured inquiry approach to include a novel research experience for the students in our undergraduate genetics laboratories. Students conducted crosses with Drosophila strains carrying P[lacW] transposon insertions in genes without documented recombination map positions, representing a large number of unique, but equivalent genetic unknowns. Using the eye color phenotypes associated with the inserts as visible markers, it is straightforward to calculate recombination map positions for the interrupted loci. Collectively, our students mapped 95 genetic loci on chromosomes 2 and 3. In most cases, the calculated 95% confidence interval for meiotic map location overlapped with the predicted map position based on cytology. The research experience evoked positive student responses and helped students better understand the nature of scientific research for little additional cost or instructor effort.
Sodium Fluoride Promotes Apoptosis by Generation of Reactive Oxygen Species in Human Lymphocytes

Fluoride generated the attention of toxicologists due to its deleterious effects at high concentrations in human populations suffering from fluorosis and with in vivo experimental models. Interest in its undesirable effects has resurfaced due to the awareness that this element interacts with cellular systems even at low doses. This study focused on examining the adverse effects of inorganic fluoride (NaF) on human lymphocyte cells in vitro. Mitochondrial function, oxidative stress, cell cycle progression, and mode of cell death were combined with genotoxic endpoints. Data demonstrated that NaF at lower concentrations, although not significantly cytotoxic and genotoxic, induced oxidative stress leading to apoptotic cell death. The results also suggested that at low concentrations (<1 μg/ml), NaF may affect cell cycle progression. Taken together, our findings confirm earlier reports on mechanisms involved in NaF-induced apoptosis.
Project ReConnect: Fostering Resilience within Disconnected Youths.

This qualitative research study identifies protective factors that foster resilience in disconnected youths (ages 16-18) who are participants in Project ReConnect, an alternative education program in New York City. Observations, participant observations, interviews, and focus groups were utilized to collect data from ten participants. Findings suggest a small class size, caring environment, and building unity among at-risk youths contribute to enhanced resilience in these youths. Examples of resilience, as well as implications for education will be discussed.
Assessing Facial Image Accordance to ISO/ICAO Requirements

Face has been adopted as default biometric validation method and the International Standard Organization (ISO) proposed a standard which states constraints for facial image. This paper presents methods for evaluating face image conformance to the following ISO/ICAO requirements: pixelation, hair across eyes, veil over face and mouth opened. Each requirement is individually evaluated. The algorithm for analyzing pixelation achieved an equal error rate (EER) equals to 1.7%, result very close to state-of-the-art (0.0% EER). The "Hair Across Eyes" analysis method achieved an EER equals to 11.9% which surpass the best state-of-art result (12.4%). The algorithm for evaluating "Veil Over Face" requirement achieved EER equals to 1.2% which also surpass the best state-of-art result (2.5%). The "Mouth Opened" requirement achieved an EER equals to 4.20%, a result compatible with state-of-art rates for this requirement (3.3%).
Regulation of nerve growth factor receptor gene expression by nerve growth factor in the developing peripheral nervous system

Nerve growth factor (NGF) is a target-derived neurotrophic protein that promotes the survival and growth of developing sympathetic and sensory neurons. We have examined NGF receptor gene expression in these neurons after NGF administration. Northern blot and in situ hybridization analyses demonstrated that NGF given systemically to neonatal rats increased levels of NGF receptor mRNA in sympathetic neurons within the superior cervical ganglion. This increase was accompanied by a differential regulation of genes associated with neurotransmitter phenotype; tyrosine hydroxylase mRNA was increased, but neuropeptide Y mRNA was not. NGF receptor mRNA levels were also increased in L4-L5 dorsal root ganglia, although this mRNA was not expressed uniformly in sensory neurons of control or NGF-treated animals. Levels of T alpha 1 alpha-tubulin mRNA, a marker of neuronal growth, also increased. In contrast to developing neurons, systemic NGF did not increase NGF receptor mRNA in nonneuronal cells of the sciatic nerve. To determine if NGF regulated NGF receptor gene expression at the transcriptional level, we examined PC12 cells. NGF treatment for 6 h increased NGF receptor mRNA fourfold; this increase was inhibited by cycloheximide. Nuclear run-off transcription assays demonstrated that the increase in steady-state NGF receptor mRNA levels was mediated at the transcriptional level. In contrast, although NGF treatment increased steady-state tyrosine hydroxylase mRNA levels, this effect was not blocked by cycloheximide, and was not due to increased transcription. These data raise the possibility that transcriptional regulation of NGF receptor gene expression by target-derived NGF could be a molecular mechanism for potentiating NGF's effects on neurons during developmental periods of neuronal competition and cell death.
In vivo selection of RNAs that localize in the nucleus

Nuclear localization of an RNA is affected by cis‐acting elements (NLEs) that lead to nuclear import or retention or to blockage of export from the nucleus. To identify such elements, we selected and analyzed transcripts that localized in the nuclei of Xenopus laevis oocytes. The RNAs were isolated from a collection of m7G‐capped RNAs in which a combinatorial library (n = 20) of sequences had been inserted. One class of selected RNAs (Sm+) had a consensus Sm binding site (AAUUUUUGG) and bound Sm proteins in the cytoplasm; these RNAs resembled small nuclear RNAs like U1 and U5 RNAs in their bi‐directional nucleo–cytoplasmic transport and their 5′‐cap hypermethylation. Another class, Sm− RNAs, contained sequences that masked the m7G‐caps of the RNAs and promoted interaction with La protein. These RNAs were retained within nuclei after nuclear injection and were imported when injected into the cytoplasm. Their nuclear import and retention were independent of a 5′‐cap, required an imperfect double‐stranded stem near the 5′ end, and depended on interaction with La protein. Import of the Sm− RNAs, while using the import pathway of proteins, was distinct from that of U6 RNA.
Genomic-Based Optimum Contribution in Conservation and Genetic Improvement Programs with Antagonistic Fitness and Productivity Traits

Animal selection for genetic improvement of productivity may lead to an increase in inbreeding through the use of techniques that enhance the reproductive capability of selected animals. Therefore, breeding strategies aim to balance maintaining genetic variability and acceptable fitness levels with increasing productivity. The present study demonstrates the effectiveness of genomic-based optimum contribution strategies at addressing this objective when fitness and productivity are genetically antagonistic traits. Strategies are evaluated in directional selection (increasing productivity) or conservation (maintaining fitness) scenarios. In the former case, substantial rates of genetic gain can be achieved while greatly constraining the rate of increase in inbreeding. Under a conservation approach, inbreeding depression can be effectively halted while also achieving a modest rate of genetic gain for productivity. Furthermore, the use of optimum contribution strategies when combined with a simple non-random mating scheme (minimum kinship method) showed an additional delay in the increase of inbreeding in the short term. In conclusion, genomic-based optimum contribution methods can be effectively used to control inbreeding and inbreeding depression, and still allow genetic gain for productivity traits even when fitness and productivity are antagonistically correlated.
A meta-heuristic approach for cell formation problem

Cell Formation Problem (CFP) is used widely in Cellular Manufacturing. However, until now very few test cases out of 35 cases have been proved optimality [8]. The others are just feasible. In this paper, we apply 2 different meta-heuristic approaches which are Simulated Annealing and Tabu Search to find feasible solutions in a reasonable time. Then, we compare our results with that of the Genetic Algorithm [7] on the same 35 test data. In our experiments, the Tabu Search approach shows equal or better solutions than Genetic Algorithm and Simulated Annealing on all test data.