Miracle-dz/UniFAR-FTUs huggingface dataset:
Genetic and Phenotypic Variation through the Migratory Season Provides Evidence for Multiple Populations of Wild Steelhead in the Dean River, British Columbia

Abstract We provide evidence for previously undetected population structure in a wild run of summer steelhead Oncorhynchus mykiss within a river that has considerable recreational importance (Dean River, British Columbia). Data were gathered from an existing catch-and-release fishery and examined for phenotypic and genetic variation through the migratory season. Specifically, we compared fish captured in different periods during the migration: early (July 2-30), middle (July 31-September 5), and late (September 6-30). Age (freshwater and saltwater), sex ratio, and body girth did not differ significantly among these groups for females or males. Body length increased through the migratory season for both sexes, perhaps because late-migrating fish had more time to feed in the ocean. Based on genotypes at 10 microsatellite loci, early and late groups showed highly significant genetic differences (P < 0.001). Assignment tests were able to classify individuals back to early or late groups with 84% accuracy (122.
The glycolytic enzyme, phosphoglycerate mutase, has critical roles in stomatal movement, vegetative growth, and pollen production in Arabidopsis thaliana

Stomatal movements require massive changes in guard cell osmotic content, and both stomatal opening and stomatal closure have been shown to be energy-requiring processes. A possible role for glycolysis in contributing to the energetic, reducing requirements, or signalling processes regulating stomatal movements has not been investigated previously. Glycolysis, oxidization of glucose to pyruvate, is a central metabolic pathway and yields a net gain of 2 ATP and 2 NADH. 2,3-biphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a key enzymatic activity in glycolysis and catalyses the reversible interconversion of 3-phosphoglycerate to 2-phosphoglycerate. To investigate functions of iPGAMs and glycolysis in stomatal function and plant growth, Arabidopsis insertional mutants in At1g09780 and At3g08590, both of which have been annotated as iPGAMs on the basis of sequence homology, were identified and characterized. While single mutants were indistinguishable from the wild type in all plant phenotypes assayed, double mutants had no detectable iPGAM activity and showed defects in blue light-, abscisic acid-, and low CO2-regulated stomatal movements. Vegetative plant growth was severely impaired in the double mutants and pollen was not produced. The data demonstrate that iPGAMs and glycolytic activity are critical for guard cell function and fertility in Arabidopsis.
Occupational Exposure to Particulate Matter and Respiratory Symptoms in Portuguese Swine Barn Workers

Certain environmental conditions in animal and plant production have been associated with increased frequency in respiratory illnesses, including asthma, chronic bronchitis, and hypersensitivity pneumonitis, in farmers occupationally exposed in swine production. The aim of this study was to characterize particulate matter (PM) contamination in seven Portuguese swine farms and determine the existence of clinical symptoms associated with asthma and other allergy diseases, utilizing the European Community Respiratory Health Survey questionnaire. Environmental assessments were performed with portable direct-reading equipment, and PM contamination including five different sizes (PM0.5, PM1.0, PM2.5, PM5.0, PM10) was determined. The distribution of particle size showed the same trend in all swine farms, with high concentrations of particles with PM5 and PM10. Results from the questionnaire indicated a trend such that subjects with diagnosis of asthma were exposed to higher concentrations of PM with larger size (PM2.5, PM5, and PM10) while subjects with sneezing, runny nose, or stuffy nose without a cold or flu were exposed to higher concentrations of PM with smaller size (PM0.5 and PM1). Data indicate that inhalation of PM in swine farm workers is associated with increased frequency of respiratory illnesses.
Heavy quark potentials in quenched QCD at high temperature

Heavy quark potentials are investigated at high temperatures. The temperature range covered by the analysis extends from $T$ values just below the deconfinement temperature up to about ${4T}_{c}$ in the deconfined phase. We simulated the pure gauge sector of QCD on lattices with temporal extents of 4, 6, and 8, with spatial volumes of ${32}^{3}. $ On the smallest lattice a tree level improved action was employed, while in the other two cases the standard Wilson action was used. Below ${T}_{c}$ we find a temperature-dependent logarithmic term contributing to the confinement potential, and observe a string tension which decreases with rising temperature but retains a finite value at the deconfinement transition. Above ${T}_{c}$ the potential is Debye screened; however, simple perturbative predictions do not apply.
Portable compiler optimisation across embedded programs and microarchitectures using machine learning

Building an optimising compiler is a difficult and time consuming task which must be repeated for each generation of a microprocessor. As the underlying microarchitecture changes from one generation to the next, the compiler must be retuned to optimise specifically for that new system. It may take several releases of the compiler to effectively exploit a processor's performance potential, by which time a new generation has appeared and the process starts again. We address this challenge by developing a portable optimising compiler. Our approach employs machine learning to automatically learn the best optimisations to apply for any new program on a new microarchitectural configuration. It achieves this by learning a model off-line which maps a microarchitecture description plus the hardware counters from a single run of the program to the best compiler optimisation passes. Our compiler gains 67% of the maximum speedup obtainable by an iterative compiler search using 1000 evaluations. We obtain, on average, a 1.16x speedup over the highest default optimisation level across an entire microarchitecture configuration space, achieving a 4.3x speedup in the best case. We demonstrate the robustness of this technique by applying it to an extended microarchitectural space where we achieve comparable performance.
Effects of Acupuncture at GV20 and ST36 on the Expression of Matrix Metalloproteinase 2, Aquaporin 4, and Aquaporin 9 in Rats Subjected to Cerebral Ischemia/Reperfusion Injury

Background/Purpose Ischemic stroke is characterized by high morbidity and mortality worldwide. Matrix metalloproteinase 2 (MMP2), aquaporin (AQP) 4, and AQP9 are linked to permeabilization of the blood-brain barrier (BBB) in cerebral ischemia/reperfusion injury (CIRI). BBB disruption, tissue inflammation, and MMP/AQP upregulation jointly provoke brain edema/swelling after CIRI, while acupuncture and electroacupuncture can alleviate CIRI symptoms. This study evaluated the hypothesis that acupuncture and electroacupuncture can similarly exert neuroprotective actions in a rat model of middle cerebral artery occlusion (MCAO) by modulating MMP2/AQP4/APQ9 expression and inflammatory cell infiltration. Methods Eighty 8-week-old Sprague-Dawley rats were randomly divided into sham group S, MCAO model group M, acupuncture group A, electroacupuncture group EA, and edaravone group ED. The MCAO model was established by placement of a suture to block the middle carotid artery, and reperfusion was triggered by suture removal in all groups except group S. Acupuncture and electroacupuncture were administered at acupoints GV20 (governing vessel-20) and ST36 (stomach-36). Rats in groups A, EA, and ED received acupuncture, electroacupuncture, or edaravone, respectively, immediately after MCAO. Neurological function (assessed using the Modified Neurological Severity Score), infarct volume, MMP2/AQP4/AQP9 mRNA and protein expression, and inflammatory cell infiltration were all evaluated at 24 h post-reperfusion. Results Acupuncture and electroacupuncture significantly decreased infarct size and improved neurological function. Furthermore, target mRNA and protein levels and inflammatory cell infiltration were significantly reduced in groups A, EA, and ED vs. group M. However, MMP2/AQP levels and inflammatory cell infiltration were generally higher in groups A and EA than in group ED except MMP2 mRNA levels. Conclusions Acupuncture and electroacupuncture at GV20 and ST36 both exercised neuroprotective actions in a rat model of MCAO, with no clear differences between groups A and EA. Therefore, acupuncture and electroacupuncture might find utility as adjunctive and complementary treatments to supplement conventional therapy for ischemic stroke.
A Qos Based Mac Protocol for Wireless Multimedia Sensor Network

Wireless Multimedia Sensor Networks (WMSNs) have emerged and shifted the focus from the typical scalar wireless sensor networks to networks with multimedia devices that are capable to retrieve video, audio, images, as well as scalar sensor data. WMSNs are able to deliver multimedia content due to the availability of inexpensive CMOS cameras and microphones coupled with the significant progress in distributed signal processing and multimedia source coding techniques. MAC in WMSNs is essential to coordinate the channel access among competing devices. Therefore, a proposal of MAC layer protocol for WMSNs should satisfy the following feature like Maximize network throughput, Enhance transmission reliability, and Minimize control overhead, be energy-efficient, Guarantee a certain level of QoS In this project, using NS2 simulation tool, we have proposed a new QoS-based sensory MAC protocol, which not only adapts to application oriented QoS, but also attempts to conserve energy without violating QoS-constraints.
Non-Preemptive Min-Sum Scheduling with Resource Augmentation

We give the first O(l)-speed O(l) approximation polynomial-time algorithms for several nonpreemptive min-sum scheduling problems where jobs arrive over time and must be processed on one machine. More precisely, we give the first O(l)-speed O(l)-approximations for the non-preemptive scheduling problems; l|r<sub>j</sub>| Sigmaw<sub>j</sub>F<sub>j</sub> (weighted flow time), l |r<sub>j</sub>| SigmaT<sub>j</sub> (total tardiness), the broadcast version of 1 |r<sub>j</sub>| Sigmaw<sub>j</sub>F<sub>j</sub> , an O(I)-speed, 1-approximation for l |r<sub>j</sub>| Sigma U macr<sub>j</sub> (throughput maximization), and an O(l)-machine, O(l)-speed O(1)-approximation for l |r<sub>j</sub>| Sigmaw<sub>j</sub>T<sub>j</sub> (weighted tardiness). Our main contribution is an integer programming formulation whose relaxation is sufficiently close to the integer optimum, and which can be transformed to a schedule on a faster machine.
Mitogen-activated protein kinases in the porcine retinal arteries and neuroretina following retinal ischemia-reperfusion

Purpose The aim of the present study was to examine changes in the expression of intracellular signal-transduction pathways, specifically mitogen-activated protein kinases, following retinal ischemia-reperfusion. Methods Retinal ischemia was induced by elevating the intraocular pressure in porcine eyes, followed by 5, 12, or 20 h of reperfusion. The results were compared to those of the sham- operated fellow eye. The retinal arteries and neuroretina were isolated separately and examined. Tissue morphology and DNA fragmentation were studied using histology. Extracellular signal-regulated kinase 1 and 2 (ERK1/2), p38, c-junNH2-terminal kinases (JNK), and c-jun protein and mRNA expression were examined using immunofluorescence staining, western blot, and real-time PCR techniques. Results Pyknotic cell nuclei, terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells, and glial fibrillary acidic protein mRNA expression were increased in ischemia, suggesting injury. Phosphorylated ERK1/2 protein levels were increased in the neuroretina following ischemia, while mRNA levels were unaltered. p38 protein and mRNA levels were not affected by ischemia. Immunofluorescence staining for phosphorylated p38 was especially intense in the retinal blood vessels, while only weak in the neuroretina. Phosphorylated JNK protein and mRNA were slightly decreased in ischemia. Phosphorylated c-jun protein and mRNA levels were higher in the neuroretina after ischemia-reperfusion. Conclusions Retinal ischemia-reperfusion alters expression of mitogen-activated protein kinases, particularly ERK1/2, in the neuroretina and retinal arteries. The development of pharmacological treatment targeting these intracellular transduction pathways may prevent injury to the eye following retinal circulatory failure.
Recent advances in the development of breast cancer vaccines

The manipulation of the immune system through the administration of a vaccine to direct an effective and long-lasting immune response against breast cancer (BC) cells is an attractive strategy. Vaccines would have several theoretical advantages over standard therapies, including low toxicities, high specificity, and long-lasting efficacy due to the establishment of immunological memory. However, BC vaccines have failed to demonstrate meaningful results in clinical trials so far. This reflects the intrinsic difficulty in breaking the complex immune-escaping mechanisms developed by cancer cells. New vaccines should be able to elicit complex immunologic response involving multiple immune effectors such as cytotoxic and antibody-secreting B cells, innate immunity effectors, and memory cells. Moreover, especially in patients with large tumor burdens and metastatic disease, combining vaccines with other strategies, such as systemic BC therapies, passive immunotherapy, or immunomodulatory agents, could increase the effectiveness of each approach. Here, we review recent advances in BC vaccines, focusing on suitable targets and innovative strategies. We report results of most recent trials investigating active immunotherapy in BC and provide possible future perspectives in this field of research.
An Efficient Dynamic Multi-Angular Feature Points Matcher for Catadioptric Views

A new efficient matching algorithm dedicated to catadioptric sensors is proposed in this paper. The presented approach is designed to overcome the varying resolution of the mirror. The aim of this work is to provide a matcher that gives reliable results similar to the ones obtained by classical operators on planar projection images. The matching is based on a dynamical size windows extraction, computed from the viewing angular aperture of the neighborhood around the points of interest. An angular scaling of this angular aperture provides a certain number of different neighborhood resolution around the same considered point. A combinatory cost method is introduced in order to determine the best match between the different angular neighborhood patches of two interest points. Results are presented on sparse matched corner points, that can be used to estimate the epipolar geometry of the scene in order to provide a dense 3D map of the observed environment.
Clustering on Social Web Tomás Kuzár

Social web increases its potential rapidly. Growing number of involved users leads to significant increase in amount of user-generated content. End users have great opportunity to express themselves by publishing statuses, blogs or photos and in the meantime they consume the content generated by others. In our work we focus on process of social web data consumption gathering, processing and visualization. In our research we focus on processing of unstructured textual content of Social Web in order to achieve more efficient access to relevant information. We have designed and evaluated methods for building precise content clusters by mining social web data. Our findings indicate the need to encounter external knowledge and the internal relationships between objects on social web to increase the accuracy of extracted knowledge. In user study we demonstrate how the accurate content clusters augment the access to relevant information on the social web.
Parallel Evolution of Auditory Genes for Echolocation in Bats and Toothed Whales

The ability of bats and toothed whales to echolocate is a remarkable case of convergent evolution. Previous genetic studies have documented parallel evolution of nucleotide sequences in Prestin and KCNQ4, both of which are associated with voltage motility during the cochlear amplification of signals. Echolocation involves complex mechanisms. The most important factors include cochlear amplification, nerve transmission, and signal re-coding. Herein, we screen three genes that play different roles in this auditory system. Cadherin 23 (Cdh23) and its ligand, protocadherin 15 (Pcdh15), are essential for bundling motility in the sensory hair. Otoferlin (Otof) responds to nerve signal transmission in the auditory inner hair cell. Signals of parallel evolution occur in all three genes in the three groups of echolocators—two groups of bats (Yangochiroptera and Rhinolophoidea) plus the dolphin. Significant signals of positive selection also occur in Cdh23 in the Rhinolophoidea and dolphin, and Pcdh15 in Yangochiroptera. In addition, adult echolocating bats have higher levels of Otof expression in the auditory cortex than do their embryos and non-echolocation bats. Cdh23 and Pcdh15 encode the upper and lower parts of tip-links, and both genes show signals of convergent evolution and positive selection in echolocators, implying that they may co-evolve to optimize cochlear amplification. Convergent evolution and expression patterns of Otof suggest the potential role of nerve and brain in echolocation. Our synthesis of gene sequence and gene expression analyses reveals that positive selection, parallel evolution, and perhaps co-evolution and gene expression affect multiple hearing genes that play different roles in audition, including voltage and bundle motility in cochlear amplification, nerve transmission, and brain function.
Population genetic study of 10 short tandem repeat loci from 600 domestic dogs in Korea

Dogs have long shared close relationships with many humans. Due to the large number of dogs in human populations, they are often involved in crimes. Occasionally, canine biological evidence such as saliva, bloodstains and hairs can be found at crime scenes. Accordingly, canine DNA can be used as forensic evidence. The use of short tandem repeat (STR) loci from biological evidence is valuable for forensic investigations. In Korea, canine STR profiling-related crimes are being successfully analyzed, leading to diverse crimes such as animal cruelty, dog-attacks, murder, robbery, and missing and abandoned dogs being solved. However, the probability of random DNA profile matches cannot be analyzed because of a lack of canine STR data. Therefore, in this study, 10 STR loci were analyzed in 600 dogs in Korea (344 dogs belonging to 30 different purebreds and 256 crossbred dogs) to estimate canine forensic genetic parameters. Among purebred dogs, a separate statistical analysis was conducted for five major subgroups, 97 Maltese, 47 Poodles, 31 Shih Tzus, 32 Yorkshire Terriers, and 25 Pomeranians. Allele frequencies, expected (Hexp) and observed heterozygosity (Hobs), fixation index (F), probability of identity (P(ID)), probability of sibling identity (P(ID)sib) and probability of exclusion (PE) were then calculated. The Hexp values ranged from 0.901 (PEZ12) to 0.634 (FHC2079), while the P(ID)sib values were between 0.481 (FHC2079) and 0.304 (PEZ12) and the P(ID)sib was about 3.35 × 10−5 for the combination of all 10 loci. The results presented herein will strengthen the value of canine DNA to solving dog-related crimes.
Kernel Cuts: MRF meets Kernel & Spectral Clustering

We propose a new segmentation model combining common regularization energies, e.g. Markov Random Field (MRF) potentials, and standard pairwise clustering criteria like Normalized Cut (NC), average association (AA), etc. These clustering and regularization models are widely used in machine learning and computer vision, but they were not combined before due to significant differences in the corresponding optimization, e.g. spectral relaxation and combinatorial max-flow techniques. On the one hand, we show that many common applications using MRF segmentation energies can benefit from a high-order NC term, e.g. enforcing balanced clustering of arbitrary high-dimensional image features combining color, texture, location, depth, motion, etc. On the other hand, standard clustering applications can benefit from an inclusion of common pairwise or higher-order MRF constraints, e.g. edge alignment, bin-consistency, label cost, etc. To address joint energies like NC+MRF, we propose efficient Kernel Cut algorithms based on bound optimization. While focusing on graph cut and move-making techniques, our new unary (linear) kernel and spectral bound formulations for common pairwise clustering criteria allow to integrate them with any regularization functionals with existing discrete or continuous solvers.
Molecular and clinical evaluation of a patient hemizygous for TIGR/MYOC.

OBJECTIVE To determine if a patient with an interstitial deletion of chromosome 1 is hemizygous for the TIGR/MYOC gene and if that patient has glaucoma. METHODS A patient with an interstitial deletion of chromosome 1 was clinically examined for evidence of glaucoma. DNA samples from the patient and her family were used for molecular studies to determine the boundaries of the chromosome 1 deletion using polymorphic markers located on chromosome 1q21 to 1q24. Additional markers located in the vicinity of the TIGR/MYOC gene, including 2 derived from the ends of the gene, were used to determine if it was included in the deletion. RESULTS The patient and her family showed no evidence of glaucoma. Molecular analysis demonstrated that a complex deletion of the maternal copy of chromosome 1 included the entire TIGR/MYOC gene. CONCLUSIONS We have determined that the patient has only 1 functional copy of TIGR/MYOC. The lack of clinical evidence of glaucoma suggests that haploinsufficiency of the TIGR/MYOC protein is not the cause of early-onset glaucoma associated with mutations in TIGR/MYOC. CLINICAL RELEVANCE Missense and nonsense mutations in the TIGR/MYOC gene have been associated with juvenile- and adult-onset primary open-angle glaucoma. Although many different mutations have been correlated with the disease, the underlying genetic mechanism (haploinsufficiency, gain of function, or a dominant negative effect) remains unknown. Information regarding the genetic mechanism responsible for TIGR/MYOC-associated glaucoma is necessary for further studies designed to develop transgenic animal models and gene-related therapy.