Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement

Crop productivity is severely limited by various biotic and abiotic stresses. Thus, it is highly needed to understand the underlying mechanisms of environmental stress response and tolerance in plants, which could be addressed by systems biology approach. To this end, high-throughput omics profiling and in silico modeling can be considered to explore the environmental effects on phenotypic states and metabolic behaviors of rice crops at the systems level. Especially, the advent of constraint-based metabolic reconstruction and analysis paves a way to characterize the plant cellular physiology under various stresses by combining the mathematical network models with multi-omics data. Rice metabolic networks have been reconstructed since 2013 and currently six such networks are available, where five are at genome-scale. Since their publication, these models have been utilized to systematically elucidate the rice abiotic stress responses and identify agronomic traits for crop improvement. In this review, we summarize the current status of the existing rice metabolic networks and models with their applications. Furthermore, we also highlight future directions of rice modeling studies, particularly stressing how these models can be used to contextualize the aﬄuent multi-omics data that are readily available in the public domain. Overall, we envisage a number of studies in the future, exploiting the available metabolic models to enhance the yield and quality of rice and other food crops.
A revised theory of cognitive consistency

Author(s): Fletcher, Jesse Bradford | Advisor(s): Burke, Peter J | Abstract: Decades of social psychological research have rested upon a simple assumption: people prefer incoming information to be consistent with their existing understandings of the social world. This simple premise, known as the cognitive consistency principle, is the foundation for many of the most prominent theories in sociological social psychology (e.g. affect control theory, justice theory, expectation states theory, identity theory, etc.). However, increasing evidence has accrued that suggests that this principle may be incorrect, or at least incomplete. This study reviews three well-established areas of research that challenge the cognitive consistency principle (over-reward/self-enhancement, amusement, varied experience theory), and reveals that all three areas point to an overarching truth: social actors often experience positive emotion or pleasure from small levels of cognitive inconsistency. In light of this, a modified cognitive consistency principle is formulated, and hypotheses are offered and tested using paired internet surveys and panel-clustered random-effects maximum-likelihood regression. Data supports a modified cognitive consistency principle which posits that actors can experience positive emotions and pleasure at low levels of cognitive inconsistency.
clinical Proton M r s pectroscopy in central nervous s ystem Disorders 1

A large body of published work shows that proton (hydro-gen 1 [ 1 H]) magnetic resonance (MR) spectroscopy has evolved from a research tool into a clinical neuroimaging modality. Herein, the authors present a summary of brain disorders in which MR spectroscopy has an impact on patient management, together with a critical consideration of common data acquisition and processing procedures. The article documents the impact of 1 H MR spectroscopy in the clinical evaluation of disorders of the central nervous system. The clinical usefulness of 1 H MR spectroscopy has been established for brain neoplasms, neonatal and pediatric disorders (hypoxia-ischemia, inherited metabolic diseases, and traumatic brain injury), demyelinating disorders, and infectious brain lesions. The growing list of disorders for which 1 H MR spectroscopy may contribute to patient management extends to neurodegenerative diseases, epilepsy, and stroke. To facilitate expanded clinical acceptance and standardization of MR spectroscopy methodology, guidelines are provided for data acquisition and analysis,
Exploiting temporal coherence in ray casted walkthroughs

We present a technique that aims at exploiting temporal coherence of ray casted walkthroughs. Our goal is to reuse ray/object inter sections computed in the last frame of the walkthrough for acceleration of ray casting in the current frame. In particular we aim at eliminating the ray traversal and computing only a single ray/object intersection per pixel. If our technique does not succeed in determining visibility, it falls back to the classical ray traversal. Visible point samples from the last frame are reprojected to the current frame. To identify whether these samples can be reused we apply splatting and epipolar geometry constraints. We discuss two additional techniques that handle correct appearance of small objects. We conducted a series of tests on walkthroughs of building interiors. Our method succeeded in determining visibility of more than 78% of pixels. For these pixels only a single ray/object intersection is executed. The frame rate is increased by up to 47%. Finally, we argue that the achieved speedup is relatively significant by comparing the performance of our algorithm to the "ideal" ray shooting algorithm.
Galectin-7 overexpression is associated with the apoptotic process in UVB-induced sunburn keratinocytes.

Galectin-7 is a beta-galactoside binding protein specifically expressed in stratified epithelia and notably in epidermis, but barely detectable in epidermal tumors and absent from squamous carcinoma cell lines. Galectin-7 gene is an early transcriptional target of the tumor suppressor protein P53 [Polyak, K. , Xia, Y. , Zweier, J., Kinzler, K. & Vogelstein, B. (1997) Nature (London) 389, 300-305]. Because p53 transcriptional activity is increased by genotoxic stresses we have examined the possible effects of ultraviolet radiations (UVB) on galectin-7 expression in epidermal keratinocytes. The amounts of galectin-7 mRNA and protein are increased rapidly after UVB irradiation of epidermal keratinocytes. The increase of galectin-7 is parallel to P53 stabilization. UVB irradiation of skin reconstructed in vitro and of human skin ex vivo demonstrates that galectin-7 overexpression is associated with sunburn/apoptotic keratinocytes. Transfection of a galectin-7 expression vector results in a significant increase in terminal deoxynucleotidyltransferase-mediated UTP end labeling-positive keratinocytes. The present findings demonstrate a keratinocyte-specific protein involved in the UV-induced apoptosis, an essential process in the maintenance of epidermal homeostasis.
CO and Near-Infrared Observations of High-Redshift Submillimeter Galaxies

I discuss our ongoing Owens Valley Millimeter Array observations and Keck near-infrared wavelength observations of the high-redshift sub-mm population of galaxies. These observations are important for our understanding of the distant universe since the sub-mm population accounts for a large fraction of the extragalactic background at mm/sub-mm wavelengths and contributes significantly to the total amount of star-formation and AGN activity at high redshift. The CO data suggest that the sub-mm galaxies are analogous to the gas-rich ultraluminous systems found in the local universe. Initial near-infrared data show that many of the sub-mm galaxies are faint-red sources which are undetected at ultraviolet/optical wavelengths. These results highlight the importance that future sensitive mm-wavelength instruments, such as the LMT and ALMA, will have on our understanding of the early evolution and formation of galaxies.
Long-Term Results of Ossiculoplasty: Reasons for Surgical Failure

Objectives: To present the value of a dedicated ear audit clinic, the overall long-term results of ossiculoplasty, and the reasons for surgical failure. Study Design: Retrospective analysis was performed on ossiculoplasty cases in a county hospital. The information was extracted from a computer database. Individual patient case records were reviewed in all cases of surgical failure. Methods: All patients who had ossiculoplasty were routinely followed-up in a dedicated ear audit clinic on a yearly basis. Between 1988 and 1999, the author performed 242 ossiculoplasties and their outcomes were monitored in the ear audit clinic. The 5-year results are presented. Results: Even with the benefit of a dedicated audit clinic and a stable population, only 74.4% of ears had a known outcome at 5 years after ossiculoplasty. In the present series, 61.1% of partial and 37.6% of total ossicular reconstructions have an air-bone gap of 20 dB or better at 5 years. Of 83 identifiable late failures, 47 were caused by persistent or recurrent abnormalities within the middle ear and only 36 were thought to be caused by prosthesis-related or surgeon-related problems. Conclusion: The overall long-term results of ossiculoplasty have not dramatically improved in recent years, in spite of all the great advances in biomedical technologies. Unless there is a breakthrough in the understanding and management of the underlying otitis media, the long-term outcome of ossiculoplasty is unlikely to improve dramatically.
A Sub-100 mW Dual-Core HOG Accelerator VLSI for Parallel Feature Extraction Processing for HDTV Resolution Video

SUMMARY This paper describes a Histogram of Oriented Gradients (HOG) feature extraction accelerator that features a VLSI-oriented HOG algorithm with early classiﬁcation in Support Vector Machine (SVM) clas-siﬁcation, dual core architecture for parallel feature extraction and multiple object detection, and detection-window-size scalable architecture with reconﬁgurable MAC array for processing objects of several shapes. To achieve low-power consumption for mobile applications, early classiﬁcation reduces the amount of computations in SVM classiﬁcation e ﬃ ciently with no accuracy degradation. The dual core architecture enables parallel feature extraction in one frame for high-speed or low-power computing and detection of multiple objects simultaneously with low power consumption by HOG feature sharing. Objects of several shapes, a vertically long object, a horizontally long object, and a square object, can be detected because of cooperation between the two cores. The proposed methods provide processing capability for HDTV resolution video (1920 × 1080 pixels) at 30 frames per second (fps). The test chip, which has been fabricated using 65nm CMOS technology, occupies 4 . 2 × 2 . 1mm 2 containing 502 Kgates and 1.22Mbit on-chip SRAMs. The simulated data show 99.5mW power consumption at 42.9MHz and 1.1V.
Inconsistent Distances in Substitution Matrices can be Avoided by Properly Handling Hydrophobic Residues

The adequacy of substitution matrices to model evolutionary relationships between amino acid sequences can be numerically evaluated by checking the mathematical property of triangle inequality for all triplets of residues. By converting substitution scores into distances, one can verify that a direct path between two amino acids is shorter than a path passing through a third amino acid in the amino acid space modeled by the matrix. If the triangle inequality is not verified, the intuition is that the evolutionary signal is not well modeled by the matrix, that the space is locally inconsistent and that the matrix construction was probably based on insufficient biological data. Previous analysis on several substitution matrices revealed that the number of triplets violating the triangle inequality increases with sequence divergence. Here, we compare matrices which are dedicated to the alignment of highly divergent proteins. The triangle inequality is tested on several classical substitution matrices as well as in a pair of “complementary” substitution matrices recording the evolutionary pressures inside and outside hydrophobic blocks in protein sequences. The analysis proves the crucial role of hydrophobic residues in substitution matrices dedicated to the alignment of distantly related proteins.
A Cognitive Framework for Reasoning with Scientific Models

Humans reason by analogy (Lakoff and Johnson, 1980; Gentner, 1983; 2003; Hofstadter, 2001, 2006; Pinker, 2007). Some have further argued that analogs can be scientific models (Hesse, 1966, Clement, 1989) although clearly not all analogies are models. Analogies based on mere physical similarity are not equivalent to scientific models but analogies based on shared relationships between the analog and target maybe equivalent to scientific models. A literature review of analogies and scientific models indicates that all scientific models in geology are relational analogs. Relational analogs are equivalent to models because both: 1) are based on recognizing relational characteristics of the analog (or model) and target, 2) map similarities and differences between the analog (or model) and target and 3) support inferences about the target based on relational similarities between the target and analog (or model). Therefore, the cognitive processes involved in analogical thinking provide a theoretical, research-based framework for instruction designed to improve students’ ability to learn how to use and generate scientific models.
A new capacity upper bound for “Relay-With-Delay” channel

In this paper we prove a new capacity upper bound for a class of relay channels known as Relay-With-Delay channels. The proposed bound is general and holds for any arbitrary amount of delay. We have shown that the previously introduced bounds can be considered as special cases of our proposed upper bound. The new introduced bound is, in some cases, tighter than the previously established bounds. It is also notable that the proposed bound coincides with the previously known capacity of “Relay-With-Delay” channels.
Degree project Space Time Coding For Wireless Communication

As the demand of high data rate is increasing, a lot of research is being conducted in the field of wireless communication. A well-known channel coding technique called Space-Time Coding has been implemented in the wireless Communication systems using multiple antennas to ensure the high speed communication as well as reliability by exploiting limited spectrum and maintaining the power. In this thesis, Space-Time Coding is discussed along with other related topics with special focus on Alamouti Space-Time Block Code. The Alamouti Codes show good performance in terms of bit error rate over Rayleigh fading channel. The performance of Altamonte " s code and MIMO capacity is evaluated by using MATLAB simulation.
Biomolecular Interaction Analysis of Gestrinone-anti-Gestrinone Using Arrays of High Aspect Ratio SU-8 Nanopillars

In this paper, label-free biosensing for antibody screening by periodic lattices of high-aspect ratio SU-8 nano-pillars (BICELLs) is presented. As a demonstration, the determination of anti-gestrinone antibodies from whole rabbit serum is carried out, and for the first time, the dissociation constant (KD = 6 nM) of antigen-antibody recognition process is calculated using this sensing system. After gestrinone antigen immobilization on the BICELLs, the immunorecognition was performed. The cells were interrogated vertically by using micron spot size Fourier transform visible and IR spectrometry (FT-VIS-IR), and the dip wavenumber shift was monitored. The biosensing assay exhibited good reproducibility and sensitivity (LOD = 0.75 ng/mL).
Error-prone chromosome-mediated spindle assembly favors chromosome segregation defects in human oocytes

Earliest stages of human development revealed Most of our knowledge about meiosis in mammalian oocytes stems from studies of mouse oocytes. However, chromosome segregation in mouse oocytes is much more reliable than in human oocytes. Working with the clinic that first pioneered IVF, Holubcové et al. studied freshly harvested human oocytes. They used high-resolution fluorescence microscopy to watch more than 100 human oocytes as they went through each step of meiosis. Science, this issue p. 1143 Studies using isolated human oocytes reveal details of human meiosis. Aneuploidy in human eggs is the leading cause of pregnancy loss and several genetic disorders such as Down syndrome. Most aneuploidy results from chromosome segregation errors during the meiotic divisions of an oocyte, the egg’s progenitor cell. The basis for particularly error-prone chromosome segregation in human oocytes is not known. We analyzed meiosis in more than 100 live human oocytes and identified an error-prone chromosome-mediated spindle assembly mechanism as a major contributor to chromosome segregation defects. Human oocytes assembled a meiotic spindle independently of either centrosomes or other microtubule organizing centers. Instead, spindle assembly was mediated by chromosomes and the small guanosine triphosphatase Ran in a process requiring ~16 hours. This unusually long spindle assembly period was marked by intrinsic spindle instability and abnormal kinetochore-microtubule attachments, which favor chromosome segregation errors and provide a possible explanation for high rates of aneuploidy in human eggs.
Revision of the failed pedicle screw in osteoporotic lumbar spine: biomechanical comparison of kyphoplasty versus transpedicular polymethylmethacrylate augmentation.

OBJECTIVES In this study, we aimed to compare of kyphoplasty versus transpedicular polymethylmethacrylate (PMMA) augmentation biomechanically in the revision of the failed pedicle screw in osteoporotic lumbar spine. MATERIALS AND METHODS Bone mineral density (BMD) of lumbar vertebrae collected from four bovines were measured. Each vertebra was decalcified with hydrochloric acid solution to obtain osteoporotic specimens. Primary polyaxial pedicle screws were inserted into the pedicles and pulled out until they failed. The pullout strength results of all specimens were recorded. Revision pedicle screws were randomly inserted into the same pedicles by either pedicle hole PMMA augmented (group 1) or kyphoplasty (Xvoid™) PMMA augmented pedicle screws (group 2). The pullout strength results of all specimens were re-recorded. RESULTS The mean BMD significantly decreased from 1.686 ± 227.9 g/cm(2) to 1.432 ± 157.1 g/cm(2) following decalcification (p<0.001). In group 1, the mean pullout strength of primary screws significantly decreased from 3443 ± 1086 N/m(2) to 2088 ± 924 N/m(2) following pedicle screw augmentation (p=0.006). In group 2, the mean pullout strength of primary screws decreased from 3702 ± 1063 N/m(2) to 3664 ± 1057 N/m(2) following kyphoplasty augmentation (p=0.934). Pedicle screw augmentation group achieved significantly lower pullout strength values than kyphoplasty pedicle hole augmentation group (p=0.002). CONCLUSION Although pedicle hole PMMA augmentation is the gold standard for the failed screws in an osteoporotic bone, kyphoplasty augmented pedicle screw seems to be more effective method increasing the pullout strength.
Social media within sustainable product development: an exploratory multiple case study on the perception of social media usability in the new product development process

Social media can be a useful tool in order to interact with customers and open up innovation efforts. Our case studies of firms aim to outline if, how and why social media is utilised in their product development processes. Our results show that the use of social media within product development is limited among our respondents, mainly due to limited resources in combination with a low amount of customers. The results show that a low number of customers impede the ability to realise the possible gains of using social media to facilitate communication among a large number of users. Additional challenges are perceived to be the difficulty in controlling content, measuring gains and dealing with security issues. There is no consensus among the respondents with regard to social media's perceived future potential within product development; some are quite hesitant, other companies anticipate increased potential in the future.
Histone Deacetylases 5 and 9 Govern Responsiveness of the Heart to a Subset of Stress Signals and Play Redundant Roles in Heart Development

ABSTRACT The adult heart responds to stress signals by hypertrophic growth, which is often accompanied by activation of a fetal cardiac gene program and eventual cardiac demise. We showed previously that histone deacetylase 9 (HDAC9) acts as a suppressor of cardiac hypertrophy and that mice lacking HDAC9 are sensitized to cardiac stress signals. Here we report that mice lacking HDAC5 display a similar cardiac phenotype and develop profoundly enlarged hearts in response to pressure overload resulting from aortic constriction or constitutive cardiac activation of calcineurin, a transducer of cardiac stress signals. In contrast, mice lacking either HDAC5 or HDAC9 show a hypertrophic response to chronic β-adrenergic stimulation identical to that of wild-type littermates, suggesting that these HDACs modulate a specific subset of cardiac stress response pathways. We also show that compound mutant mice lacking both HDAC5 and HDAC9 show a propensity for lethal ventricular septal defects and thin-walled myocardium. These findings reveal central roles for HDACs 5 and 9 in the suppression of a subset of cardiac stress signals as well as redundant functions in the control of cardiac development.
Use of posterior predictive assessments to evaluate model fit in multilevel logistic regression

Assessing the fit of a model is an important final step in any statistical analysis, but this is not straightforward when complex discrete response models are used. Cross validation and posterior predictions have been suggested as methods to aid model criticism. In this paper a comparison is made between four methods of model predictive assessment in the context of a three level logistic regression model for clinical mastitis in dairy cattle; cross validation, a prediction using the full posterior predictive distribution and two “mixed” predictive methods that incorporate higher level random effects simulated from the underlying model distribution. Cross validation is considered a gold standard method but is computationally intensive and thus a comparison is made between posterior predictive assessments and cross validation. The analyses revealed that mixed prediction methods produced results close to cross validation whilst the full posterior predictive assessment gave predictions that were over-optimistic (closer to the observed disease rates) compared with cross validation. A mixed prediction method that simulated random effects from both higher levels was best at identifying the outlying level two (farm-year) units of interest. It is concluded that this mixed prediction method, simulating random effects from both higher levels, is straightforward and may be of value in model criticism of multilevel logistic regression, a technique commonly used for animal health data with a hierarchical structure.