Miracle-dz/UniFAR-FTUs huggingface dataset:
Shrinkage-based similarity metric for cluster analysis of microarray data

The current standard correlation coefficient used in the analysis of microarray data was introduced by M. B. Eisen, P. T. Spellman, P. O. Brown, and D. Botstein [(1998) Proc. Natl. Acad. Sci. USA 95, 14863–14868]. Its formulation is rather arbitrary. We give a mathematically rigorous correlation coefficient of two data vectors based on James–Stein shrinkage estimators. We use the assumptions described by Eisen et al., also using the fact that the data can be treated as transformed into normal distributions. While Eisen et al. use zero as an estimator for the expression vector mean μ, we start with the assumption that for each gene, μ is itself a zero-mean normal random variable [with a priori distribution \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} \begin{equation*}{\mathscr{N}}(0,{\tau}^{2})\end{equation*}\end{document}], and use Bayesian analysis to obtain a posteriori distribution of μ in terms of the data. The shrunk estimator for μ differs from the mean of the data vectors and ultimately leads to a statistically robust estimator for correlation coefficients. To evaluate the effectiveness of shrinkage, we conducted in silico experiments and also compared similarity metrics on a biological example by using the data set from Eisen et al. For the latter, we classified genes involved in the regulation of yeast cell-cycle functions by computing clusters based on various definitions of correlation coefficients and contrasting them against clusters based on the activators known in the literature. The estimated false positives and false negatives from this study indicate that using the shrinkage metric improves the accuracy of the analysis.
The optimal logic depth per pipeline stage is 6 to 8 FO4 inverter delays

Microprocessor clock frequency has improved by nearly 40% annually over the past decade. This improvement has been provided, in equal measure, by smaller technologies and deeper pipelines. From our study of the SPEC 2000 benchmarks, we find that for a high-performance architecture implemented in 100 nm technology, the optimal clock period is approximately 8 fan-out-of-four (FO4) inverter delays for integer benchmarks, comprised of 6 FO4 of useful work and an overhead of about 2 FO4. The optimal clock period for floating-point benchmarks is 6 FO4. We find these optimal points to be insensitive to latch and clock skew overheads. Our study indicates that further pipelining can at best improve performance of integer programs by a factor of 2 over current designs. At these high clock frequencies it will be difficult to design the instruction issue window to operate in a single cycle. Consequently, we propose and evaluate a high-frequency design called a segmented instruction window.
Efficient Category Mining by Leveraging Instance Retrieval

We focus on the problem of mining object categories from large datasets like Google Street View images. Mining object categories in these unannotated datasets is an important and useful step to extract meaningful information. Often the location and spatial extent of an object in an image is unknown. Mining objects in such a setting is hard. Recent methods model this problem as learning a separate classifier for each category. This is computationally expensive since a large number of classifiers are required to be trained and evaluated, before one can mine a concise set of meaningful objects. On the other hand, fast and efficient solutions have been proposed for the retrieval of instances (same object) from large databases. We borrow, from instance retrieval pipeline, its strengths and adapt it to speed up category mining. For this, we explore objects which are "near-instances". We mine several near-instance object categories from images. Using an instance retrieval based solution, we are able to mine certain categories of near-instance objects much faster than an Exemplar SVM based solution.
Vehicle formation analysis based on zero dynamics for road traffic system

Car-following models play an important role in the field of road traffic system, and one of its important issues is the vehicle formation. To conduct the analysis of vehicle formation, this paper introduces the concept of zero dynamics and gives a detailed analysis of the full velocity difference (FVD) model. Meanwhile, the stability analysis of FVD model based on the Lyapunov function is also discussed, and the result validates that the vehicle formation can achieve asymptotic stability. Keywords-road traffic system; vehicle formation; car-following models; zero dynamics; stability analysis
Recent Advances in Integrated Photonic Sensors

Nowadays, optical devices and circuits are becoming fundamental components in several application fields such as medicine, biotechnology, automotive, aerospace, food quality control, chemistry, to name a few. In this context, we propose a complete review on integrated photonic sensors, with specific attention to materials, technologies, architectures and optical sensing principles. To this aim, sensing principles commonly used in optical detection are presented, focusing on sensor performance features such as sensitivity, selectivity and rangeability. Since photonic sensors provide substantial benefits regarding compatibility with CMOS technology and integration on chips characterized by micrometric footprints, design and optimization strategies of photonic devices are widely discussed for sensing applications. In addition, several numerical methods employed in photonic circuits and devices, simulations and design are presented, focusing on their advantages and drawbacks. Finally, recent developments in the field of photonic sensing are reviewed, considering advanced photonic sensor architectures based on linear and non-linear optical effects and to be employed in chemical/biochemical sensing, angular velocity and electric field detection.
Algebraic Space Time Coding in a CDMA System over a Rayleigh fading Channel

The originality of this paper consists of combining code division multiple access (CDMA) technique with Multi Input Multi Output (MIMO) antenna system. The main objective of our contribution is to improve the capacity of the existing DS-CDMA systems by supporting an increased number of users and to achieve good performance in terms of bit error rate. This new communication scheme combining the two techniques benefit from perfect codes by employing a spectrally efficient algebraic space time coding (ASTC) and spreading spectrum by using CDMA technique equipped with multi user detector (MUD) that is near far resistant. In our system each user is distinguished by its spreading code signature and its unique channel impulse response (CIR) transfer function. The MIMO-CDMA system, associated by multi user detector, improves the spectral efficiency of wireless system, combat channel fading and reduce narrowband interference. The resulting is a multi-user CDMA- ASTC solution promising high speed communication for 4G cellular wireless networks. Our study and numerical results show the utility of this new wireless communication; a significant BER versus signal to noise ratio (SNR) was achieved thus Multiple access interference (MAI) is suppressed and so supporting a large number of users.
Seizure-Induced Regulations of Amyloid-β, STEP61, and STEP61 Substrates Involved in Hippocampal Synaptic Plasticity

Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline. Pathologic accumulation of soluble amyloid-β (Aβ) oligomers impairs synaptic plasticity and causes epileptic seizures, both of which contribute to cognitive dysfunction in AD. However, whether seizures could regulate Aβ-induced synaptic weakening remains unclear. Here we show that a single episode of electroconvulsive seizures (ECS) increased protein expression of membrane-associated STriatal-Enriched protein tyrosine Phosphatase (STEP61) and decreased tyrosine-phosphorylation of its substrates N-methyl D-aspartate receptor (NMDAR) subunit GluN2B and extracellular signal regulated kinase 1/2 (ERK1/2) in the rat hippocampus at 2 days following a single ECS. Interestingly, a significant decrease in ERK1/2 expression and an increase in APP and Aβ levels were observed at 3-4 days following a single ECS when STEP61 level returned to the baseline. Given that pathologic levels of Aβ increase STEP61 activity and STEP61-mediated dephosphorylation of GluN2B and ERK1/2 leads to NMDAR internalization and ERK1/2 inactivation, we propose that upregulation of STEP61 and downregulation of GluN2B and ERK1/2 phosphorylation mediate compensatory weakening of synaptic strength in response to acute enhancement of hippocampal network activity, whereas delayed decrease in ERK1/2 expression and increase in APP and Aβ expression may contribute to the maintenance of this synaptic weakening.
RNA Chemical Probing Reagents and Protein Amino Acids: a Double-Edged Sword

RNA chemical probing experiments are a broadly used method for revealing the structure of RNA, as well as for identifying protein binding sites. This is beneficial for expanding our understanding of biological processes governed by protein-RNA complex interactions, as well as facilitating the identification of complex inhibiting molecules. The reagents commonly used in chemical probing experiments are highly reactive, methylating or acylating atoms of flexible RNA nucleotides. The highly reactive nature of the chemical probes means that they can also react with nucleophilic amino acid side chains, and subsequently affect protein-RNA binding events. We combine MD simulations, MALDI-MS, and NMR experiments to show that commonly used RNA chemical probes react with protein amino acids and demonstrate that this effect alters protein-RNA binding interactions through binding shift assays. We discuss the implications of this phenomenon in elucidating protein-RNA interactions, and also demonstrate this as a useful means for identifying surface-exposed protein residues, omitting the need for extensive mutagenesis experiments that are critical for RNA interactions. GRAPHICAL ABSTRACT
Arthroscopically assisted anterior cruciate ligament reconstruction: comparison of bone-patellar tendon-bone versus hamstring tendon autograft.

BACKGROUND The bone-patellar tendon-bone (BPTB) and the hamstring tendons are commonly used for arthroscopially-assisted anterior cruciate ligament (ACL) reconstruction. PURPOSE To compare the results of arthroscopically-assisted ACL reconstruction using bone-patellar tendon-bone and hamstring tendons grafts in terms of postoperative knee stability, knee functions and clinical rating scale, and patient satisfaction. HYPOTHESIS There was no difference in the outcomes of the two grafts. STUDY DESIGN Retrospective non-randomized clinical trial. MATERIAL AND METHOD Two groups of patients, 45 in the BPTB group and 30 in the hamstring group, were followed for at least one year. RESULTS The two groups had similar pre-operative data except the hamstring group which had a significantly shorter duration of injury before operation (9.5 versus 18 months, p < 0.05). There was no difference in median pre-operative Lysholm knee score (74 in the BPTB group versus 75 in the hamstring group, p > 0.05) and the post-operative one (95 in the BPTB group versus 99 in the hamstring group, p > 0.05). There was also no difference in the median pre-operative HSS knee score (58 in the BPTB group versus 61 in the hamstring group, p > 0.05). Although there was a statistically significant difference in the median post-operative HSS knee score between the two groups (95 in the BPTB group versus 96 in the hamstring group, p < 0.05), this was not clinically significant since both scores were rated as an excellent result. Both groups had a significantly improved knee stability and knee functions (Lysholm and HSS knee scores). The hamstring group, however, had significantly higher patient satisfaction (88% in the BPTB group versus 93% in the hamstring group, p < 0.05). CONCLUSION Both the BPTB and the hamstring tendon grafts resulted in significantly improved knee stability and functions with high patient satisfaction. The hamstring tendon group, however, had a significantly better post-operative patient satisfaction (Visual Analog Scale, VAS).
Epigenetic and evolutionary mechanisms uniquely contribute to rescue from global change

Both adaptation and plasticity are critical for species persistence during rapid anthropogenic global change. However, we know little about how these mechanisms of resilience interact, particularly the role of epigenetic variation in long-term adaptation. We used a 25-generation selection experiment simulating future acidification, warming, and their combination to reveal how epigenetic and genetic mechanisms interact to promote resilience in a foundational copepod at the base of the marine food web. Epigenetic divergence was positively linked to gene expression divergence, indicating that epigenetic changes may facilitate phenotypic change. In contrast, genetic and epigenetic changes were negatively related, where genomic regions experiencing significant epigenetic changes had lower genetic divergence than those without. Thus, evolutionary and epigenetic changes acted in different regions of the genome during adaptation to global change conditions, due to either local inhibition of one another or distinct functional targets of selection. These results suggest that both genetic and epigenetic mechanisms underlie resilience to global change but have unique contributions. Teaser Epigenetic divergence is linked to both gene expression and genetic divergence during evolutionary rescue from global change.
Inhibition of human colonic epithelial cell proliferation in vivo and in vitro by calcium.

Nine patients at high risk of developing colon cancer were placed on daily p.o. supplementation of 1500 mg of calcium for 4-8 weeks. The colonic epithelial cells in six of these patients showed a statistically significant decrease in their [3H]thymidine labeling indices in tissue culture so that they resembled those of patients at low risk of developing colon cancer. The three nonresponders had similar labeling indices before and after calcium supplementation. Biopsies from each of nine high-risk patients exhibited a decrease in proliferation when they were cultured in vitro with a high level of CaCl2 (2.2 mM compared with the 0.1 mM optimum value for proliferation). Two adenomas and two carcinomas showed a different pattern of response than normal cells, exhibiting no inhibition of growth at 2.2 mM CaCl2. These data indicate that the growth inhibition induced by high levels of extracellular calcium levels is lost at a stage in tumor development before cells become malignant.
A computational model for bacteriophage ϕX174 gene expression

Bacteriophage ϕX174 has been widely used as a model organism to study fundamental processes in molecular biology. However, several aspects of ϕX174 gene regulation are not fully resolved. Here we construct a computational model for ϕX174 and use the model to study gene regulation during the phage infection cycle. We estimate the relative strengths of transcription regulatory elements (promoters and terminators) by fitting the model to transcriptomics data. We show that the specific arrangement of a promoter followed immediately by a terminator, which occurs naturally in the ϕX174 genome, poses a parameter identifiability problem for the model, since the activity of one element can be partially compensated for by the other. We also simulate ϕX174 gene expression with two additional, putative transcription regulatory elements that have been proposed in prior studies. We find that the activities of these putative elements are estimated to be weak, and that variation in ϕX174 transcript abundances can be adequately explained without them. Overall, our work demonstrates that ϕX174 gene regulation is well described by the canonical set of promoters and terminators widely used in the literature.
Neural dynamics express syntax in the time domain during natural story listening

Studies of perception have long shown that the brain adds information to its sensory analysis of the physical environment. A touchstone example for humans is language use: to comprehend a physical signal like speech, the brain must add linguistic knowledge, including syntax. Yet, syntactic rules and representations are atemporal (i.e., abstract and not bound by time), so they must be translated into time-varying signals for speech comprehension and production. Here, we test three different models of the temporal spell-out of syntactic structure against brain activity of people listening to Dutch stories: an integratory bottom-up parser, a predictive top-down parser, and a mildly predictive left-corner parser. These models build exactly the same structure but differ in when syntactic information is added by the brain – this difference is captured in the (temporal distribution of the) complexity metric ‘incremental node count’. Using temporal response function models with both acoustic and information-theoretic control predictors, node counts were regressed against source-reconstructed delta-band activity acquired with magnetoencephalography. Neural dynamics in left frontal and temporal regions most strongly reflect node counts derived by the top-down method, which postulates syntax early in time, suggesting that predictive structure building is an important component of Dutch sentence comprehension. The absence of strong effects of the left-corner model further suggests that its mildly predictive strategy does not represent Dutch language comprehension well, in contrast to what has been found for English. Understanding when the brain projects its knowledge of syntax onto speech, and whether this is done in language-specific ways, will inform and constrain the development of mechanistic models of syntactic-structure building in the brain.
Influence of the dietary protein:lipid ratio and fish oil substitution on fatty acid composition and metabolism of Atlantic salmon (Salmo salar) reared at high water temperatures

A factorial, two-way, experimental design was used for this 10-week nutritional trial, aiming to elucidate the interactive effects of decreasing dietary protein:lipid level and substitution of fish oil (FO) with rapeseed oil (RO) on tissue fatty acid (FA) composition and metabolism of large Atlantic salmon (Salmo salar L.) reared at high water temperatures (sub-optimal, summer temperatures: 11·6°C). The six experimental diets were isoenergetic and formulated to include either FO or RO (60 % of the added oil) at three dietary protein:lipid levels, specifically (1) 350 g/kg protein and 350 g/kg lipid, (2) 330 g/kg protein and 360 g/kg lipid, (3) 290 g/kg protein and 380 g/kg lipid. Final weight, specific growth rate and thermal growth coefficient were positively affected by the dietary RO inclusion at the expense of FO, while no significant effects were seen on growth due to the decreasing protein level. The oil source had a significant effect on muscle and liver FA composition. However, the changes in muscle and liver FA indicate selective utilisation or retention of individual FA and moderate reductions in tissue EPA and DHA. Pyloric caeca phospholipid FA composition was significantly affected by the two factors and, in some cases, significant interactions were also revealed. Liver and red muscle β-oxidation capacities were significantly increased due to RO inclusion, while an interactive effect of protein level and oil source was shown for white muscle β-oxidation capacity. The results could explain, at least partially, the better performance that was shown for the RO groups and the enhanced protein-sparing effect.
Adaptive evolution of sesquiterpene deoxyphomenone in mycoparasitism by Hansfordia pulvinata associated with horizontal gene transfer from Aspergillus species

Leaf mold caused by the ascomycete fungus Cladosporium fulvum is a devastating disease of tomato plants. The mycoparasitic fungus Hansfordia pulvinata is an effective biocontrol agent that parasitizes C. fulvum hyphae on leaves and secretes 13-deoxyphomenone, an eremophilane-type sesquiterpene, which was also identified as a sporulation-inducing factor in Aspergillus oryzae. Here, we identified deoxyphomenone biosynthesis (DPH) gene clusters conserved in both H. pulvinata and Aspergillus section Flavi including A. oryzae and A. flavus. Functional disruption of DPH1 orthologous genes encoding sesquiterpene cyclase in H. pulvinata, A. oryzae and its close relative A. flavus revealed that deoxyphomenone in H. pulvinata had exogenic antifungal activity against the host fungus C. fulvum and controlled endogenic sporulation in Aspergillus species. Deoxyphomenone also inhibited mycelial growth of C. fulvum and the non-host tomato pathogen Pseudocercospora fuligena. Complete DPH clusters, highly similar to those in H. pulvinata, were exclusive to Aspergillus section Flavi, while species in other Aspergillus sections contained fragmented DPH clusters. A comparative genomics analysis revealed that these DPH gene clusters share a common origin and are horizontally transferred across large taxonomic distances from an ancestor of Aspergillus to H. pulvinata. Our results suggest that, after horizontal transfer, H. pulvinata maintained the DPH cluster as the inhibitory effect of deoxyphomenone on spore germination and mycelial growth contributed to its mycoparasitism on the host fungus C. fulvum.
The acute effects of different training loads of whole body vibration on flexibility and explosive strength of lower limbs in divers

The purpose of this study was to examine the acute effects of different vibration loads (frequency and amplitude) of whole-body vibration (WBV) on flexibility and explosive strength of lower limbs in springboard divers. Eighteen male and female divers, aged 19 ± 2 years, volunteered to perform 3 different WBV protocols in the present study. To assess the vibration effect, flexibility and explosive strength of lower limbs were measured before (Pre), immediately after (Post 1) and 15 min after the end of vibration exposure (Post 15). Three protocols with different frequencies and amplitudes were used in the present study: a) low vibration frequency and amplitude (30 Hz/2 mm); b) high vibration frequency and amplitude (50 Hz/4 mm); c) a control protocol (no vibration). WBV protocols were performed on a Power Plate platform, whereas the no vibration divers performed the same protocol but with the vibration platform turned off. A two-way ANOVA 3 x 3 (protocol × time) with repeated measures on both factors was used. The level of significance was set at p < 0.05. Univariate analyses with simple contrasts across time were selected as post hoc tests. Intraclass coefficients (ICC) were used to assess the reliability across time. The results indicated that flexibility and explosive strength of lower limbs were significantly higher in both WBV protocols compared to the no vibration group (NVG). The greatest improvement in flexibility and explosive strength, which occurred immediately after vibration treatment, was maintained 15 min later in both WBV protocols, whereas NVG revealed a significant decrease 15 min later, in all examined strength parameters. In conclusion, a bout of WBV significantly increased flexibility and explosive strength in competitive divers compared with the NVG. Therefore, it is recommended to incorporate WBV as a method to increase flexibility and vertical jump height in sports where these parameters play an important role in the success outcome of these sports.