Miracle-dz/UniFAR-FTUs huggingface dataset:
A Hardware Engine for Genetic Algorithms

A genetic algorithm (GA) is an optimization method based on natural selection. Genetic algorithms have been applied to many hard optimization problems including VLSI layout optimization, boolean satis ability, power system control, fault detection, control systems, and signal processing. GAs have been recognized as a robust general-purpose optimization technique. But application of GAs to increasingly complex problems can overwhelm software implementations of GAs, causing unacceptable delays in the optimization process. This is true of any non-trivial application of GAs if the search space is large or if real-time performance is necessary. It follows that a hardware implementation of a GA is desirable for application to problems too complex for software-based GAs. Hardware's speed advantage and its ability to parallelize o er great rewards to genetic algorithms. Speedups of 1{2 orders of magnitude have been observed when frequently used software routines were implemented in hardware by way of eld-programmable gate arrays (FPGAs). Since most of the GA's operations are simple, a hardware implementation is feasible. Reprogrammability is essential in a general-purpose GA engine because certain GA modules require changeability (e.g. the function to be optimized by the GA). In hardware, reprogrammability is possible with FPGAs. Thus an FPGA-based GA is both feasible and desirable. A fully functional self-contained hardware-based genetic algorithm (the HGA) is presented here as a proof-of-concept system. It was designed using VHDL to allow for easy scalability. It is designed to act as a coprocessor with the CPU of a PC. The user programs the FPGAs which implement the function to be optimized. Other GA parameters may also be speci ed by the user. An analysis of the design is given that identi es the bottleneck of the HGA's pipeline under varying conditions. Simulation results of the HGA are also presented. A prototype HGA is described and compared to a similar GA implemented in software. In our tests, the prototype and simulations took two to ve percent as many clock cycles to run as the software-based GA. Suggested design improvements could dramatically increase the HGA's speed even further. Finally, we give other potential applications of the HGA which are feasible with current FPGA technology.
Genetic Polymorphisms in the TATA Box and Upstream Phenobarbital-Responsive Enhancer Module of the UGT1A1 Promoter Have Combined Effects on UDP-Glucuronosyltransferase 1A1 Transcription Mediated by Constitutive Androstane Receptor, Pregnane X Receptor, or Glucocorticoid Receptor in Human Liver

Transcription of UDP-glucuronosyltransferase (UGT) 1A1 is regulated by the transcription factors, constitutive androstane receptor (CAR), pregnane X receptor (PXR), glucocorticoid receptor (GR), hepatocyte nuclear factor (HNF) 1α, and HNF4α. The purpose of this study was to determine whether the genetic polymorphisms in the RNA polymerase II core promoter and the upstream phenobarbital-responsive element module (PBREM) of the UGT1A1 promoter have combined effects on UGT1A1 transcription mediated by the transcription factors. A polymorphism of A(TA)5–8TAA in the UGT1A1 TATA box and a single nucleotide polymorphism of –3279T>G in PBREM were genotyped in 98 human liver samples. Relative mRNA levels of CAR, PXR, GR, HNF1α, HNF4α, and UGT1A1 were quantified by a multiplex branched DNA technique. Correlations of mRNA levels between UGT1A1 and the transcription factors were established in liver samples with different combined genetic polymorphisms. Correlation of mRNA levels between UGT1A1 and CAR, PXR, or GR, but not HNF1α or HNF4α, was abolished in the samples with the combined genotype of TA7/7 plus –3279G/G, which was also associated with significantly lower UGT1A1 mRNA levels compared with other combined genotypes. Correlations of mRNA levels between UGT1A1 and CAR or PXR were reduced but not abolished in the samples with the combined genotype of TA6/7 plus –3279 G/G, which showed significantly lower UGT1A1 mRNA levels compared with the combined genotype of TA6/7 plus –3279T/G and other genotypes containing TA6/6. In conclusion, the combined genotypes containing A(TA)7TAA and –3279G decrease UGT1A transcription mediated by CAR, PXR, or GR but not by HNF1α or HNF4α.
Toward an understanding of risk factors for anorexia nervosa: a case-control study

Background Prospective, longitudinal studies of risk factors for anorexia nervosa (AN) are lacking and existing cross-sectional studies are generally narrow in focus and lack methodological rigor. Building on two studies that used the Oxford Risk Factor Interview (RFI) to establish time precedence and comprehensively assess potential risk correlates for AN, the present study advances this line of research and represents the first case-control study of risk factors for AN in the USA. Method The RFI was used for retrospective assessment of a broad range of risk factors, while establishing time precedence. Using a case-control design, 50 women who met DSM-IV criteria for AN were compared to those with non-eating disorder DSM-IV psychiatric disorders (n=50) and those with no psychiatric disorder (n=50). Results Women with psychiatric disorders reported higher rates of negative affectivity, maternal and paternal parenting problems, family discord, parental mood and substance disorder, and physical and sexual abuse than women with no psychiatric disorder. Women with AN specifically reported greater severity and significantly higher rates of negative affectivity, perfectionism and family discord, and higher parental demands than women with other psychiatric disorders. The role of weight and shape concerns was most salient in the year preceding onset of AN. Conclusions Convergent data identifying common risk factors as well as those more severe in the development of AN are emerging to inform longitudinal risk factor and prevention studies for this disorder.
Recurrent lumbar disc herniation: A prospective comparative study of three surgical management procedures

Context: The optimal surgical treatment of recurrent lumbar disc herniation is controversial. Aim: To compare prospectively the clinical outcomes of surgical treatment of recurrent lumbar disc herniation by three different methods; discectomy alone, discectomy with transforaminal lumbar interbody fusion (TLIF), and diecectomy with posterolateral fusion (PLF), regardless of the postoperative radiological findings. Study Design: This is a prospective, randomized, comparative study. Materials and Methods: This is a prospective, randomized, comparative study on 45 patients with first time recurrent lumbar disc herniation. Patients were evaluated clinically by using the criteria of the Japanese Orthopedic Association's evaluation system for low back pain syndrome (JOA score). The patients were classified into three groups: Group A; patients who had revision discectomy alone, group B; patients who had revision discectomy with TLIF, and group C; patients who had revision discectomy with PLF. The mean follow-up period was 37 (±7.85 STD) months. Results: The mean overall recovery rate was 87.2% (±19.26 STD) and the satisfactory rate was 88.9%. Comparison between the three groups showed no significant difference with regard to the mean total postoperative JOA score, recovery rate, and satisfactory rate. However, the postoperative low back pain was significantly higher in group A than that of group B and C. Two patients in group A required further revision surgery. The incidences of dural tear and postoperative neurological deficit were higher in group A. The intraoperative blood loss and length of operation were significantly less in group A. The total cost of the procedure was significantly different between the three groups, being least in group A and highest in group B. There was no significant difference between the three groups with regard to the length of postoperative hospital stay. Conclusion: Revision discectomy is effective in patients with recurrent lumbar disc herniation. Fusion with revision discectomy improves the postoperative low back pain, decreases the intraoperative risk of dural tear or neural damage and decreases the postoperative incidence of mechanical instability or re-recurrence. TLIF and PLF have comparable results when used with revision discectomy, but PLF has significantly less total cost than TLIF.
Apurinic/apyrimidinic endonuclease APE1 is required for PACAP-induced neuroprotection against global cerebral ischemia

Inducible DNA repair via the base-excision repair pathway is an important prosurvival mechanism activated in response to oxidative DNA damage. Elevated levels of the essential base-excision repair enzyme apurinic/apyrimidinic endonuclease 1 (APE1)/redox effector factor-1 correlate closely with neuronal survival against ischemic insults, depending on the CNS region, protective treatments, and degree of insult. However, the precise mechanisms by which this multifunctional protein affords protection and is activated by upstream signaling pathways in postischemic neurons are not well delineated. Here we show that intracerebral administration of pituitary adenylate cyclase-activating polypeptide (PACAP), an endogenously occurring small neuropeptide, induces expression of APE1 in hippocampal neurons. Induction of APE1 expression requires PKA- and p38-dependent phosphorylation of cAMP response-element binding and activating transcription factor 2, which leads to transactivation of the APE1 promoter. We further show that PACAP markedly reduces oxidative DNA stress and hippocampal CA1 neuronal death following transient global ischemia. These effects occurred, at least in part, via enhanced APE1 expression. Furthermore, the DNA repair function of APE1 was required for PACAP-mediated neuroprotection. Thus, induction of DNA repair enzymes may be a unique strategy for neuroprotection against hippocampal injury.
Effect of Organomodified Ni-Al Layered Double Hydroxide (OLDH) on the Properties of Polypropylene (PP)/LDH Nanocomposites

This work addresses the effect of organomodified layer double hydroxide (OLDH) on the properties of PP/LDH nanocomposites prepared by melt intercalation method using a single screw extruder with maleic anhydride grafted polypropylene (PP-g-MA) as a compatibilizer. For this, Ni-Al LDH was first prepared by the co-precipitation method at constant pH using their nitrate salts. The above synthesized pristine LDH was organically modified using sodium dodecyl sulphate (SDS) by the regeneration method. The structural and thermal properties of LDH and PP nanocomposites were performed by X-ray diffraction (XRD), FTIR spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). The influence of LDH loading on the mechanical and thermal properties of the nanocomposite was also investigated. The XRD results confirmed the formation of exfoliated PP/LDH nanocomposites. PP/LDH nanocomposites exhibited enhanced thermal stability relative to the pure PP. When 10% weight loss was selected as a point of comparison, the decomposition temperature of PP/LDH (5 wt%) nanocomposite was 15.3°C higher than that of pure PP. The DSC result indicated an increase in crystallization and melting temperature of the PP/LDH nanocomposites compared to pure PP. Overall, the mechanical properties of the PP/LDH nanocomposites increased with an increase in the LDH content. The maximum improvement of tensile strength, Young's modulus, flexural strength, and flexural modulus for the PP/LDH nanocomposite was found to be 11, 22.5, 28, and 22%, respectively, over neat PP. For comparison purposes, a nanocomposite with 5 wt% modified bentonite (PP/B5) was also prepared under the same operating condition and there was no significant improvement in mechanical properties (tensile strength and modulus).
Performance Characteristics Comparisons of Various Asphalt Mixture Technologies

A laboratory investigation was carried out to study the effects of various compaction technologies on moisture susceptibility, rutting resistance, and fatigue characteristics of various asphalt mixtures. The methodologies used in this study included three technologies such as common hot mix asphalt (HMA), warm mix (WMA), and half-warm mix asphalt (HWMA) technologies. In addition, in terms of WMA and HWMA mixtures, a foaming technology was used to produce the samples. The experimental design for WMA and HWMA included one aggregate moisture contents (� 0.5 % by weight of the dry mass of the aggregate), three lime contents (0 %, 1 % and 2 % lime by weight of dry aggregate), and 2 % foaming water content. For HMA, 1 % lime content and completely dried aggregate were used. Three aggregate sources (designated as A, B, and C) and one PG 64-22 binder were used in this study. A total of 9 Superpave mix designs and 21 mixtures were completed. A total of 84 indirect tensile strength (ITS) samples, 126 asphalt pavement analyzer (APA) samples, and 30 fatigue beams were tested in this research. The major properties such as gyration number, ITS, tensile strength ratio (TSR), rut depth, deformation, toughness, as well as fatigue life were measured and computed for all mixtures. The test results indicated that various compaction technologies would slightly affect the Superpave mix design and obviously have an influence on gyration number, ITS values, rut depth, flow, toughness, and fatigue life of various mixtures regardless of aggregate source and lime content. In addition, the aggregate source significantly affected the ITS and rutting resistance in this study.
Thermo-Mechanical Treatment to Improve Properties of Sisal Fibres for Composites

The cross section variation, mechanical properties and moisture absorption of vegetable sisal fibres compressed at temperatures of 120, 160 and 200 °C were determined and compared with values obtained in non-compressed fibres. The thermo-mechanical treatment carried out resulted in a relevant increasing of fibre stiffness (elastic modulus) and decreasing of fibre moisture absorption.
Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates—assumed to be related to autotrophic metabolisms—were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.
A New Channel Coding Approach for Random Access with Bursty Traffic

This paper extends Information Theoretic analysis to packe t random access systems with bursty traffic. A new channel coding approach for coding within each data packet i s proposed with built-in support for bursty traffic phenomena, such as message underflow, and for random access m echanism, such as packet collision detection. The coding approach does not require joint communication ra te determination either between the transmitters or between the transmitters and the receiver. Its performance limitation is characterized by an achievable region defined in terms of communication rates, such that reliable packet r ecovery is supported for all rates within the region and reliable collision detection is supported for all rates outside the region. For random access communication over a discrete-time memoryless channel using a class of ran dom coding schemes, it is shown that the maximum achievable rate region of the introduced coding approach eq uals the Shannon information rate region without a convex hull operation. Further connections between the ach ievable rate region and the Shannon information rate region are explained.
Physiological and proteomic characterization of manganese sensitivity and tolerance in rice (Oryza sativa) in comparison with barley (Hordeum vulgare).

BACKGROUND AND AIMS Research on manganese (Mn) toxicity and tolerance indicates that Mn toxicity develops apoplastically through increased peroxidase activities mediated by phenolics and Mn, and Mn tolerance could be conferred by sequestration of Mn in inert cell compartments. This comparative study focuses on Mn-sensitive barley (Hordeum vulgare) and Mn-tolerant rice (Oryza sativa) as model organisms to unravel the mechanisms of Mn toxicity and/or tolerance in monocots. METHODS Bulk leaf Mn concentrations as well as peroxidase activities and protein concentrations were analysed in apoplastic washing fluid (AWF) in both species. In rice, Mn distribution between leaf compartments and the leaf proteome using 2D isoelectric focusing IEF/SDS-PAGE and 2D Blue native BN/SDS-PAGE was studied. KEY RESULTS The Mn sensitivity of barley was confirmed since the formation of brown spots on older leaves was induced by low bulk leaf and AWF Mn concentrations and exhibited strongly enhanced H2O2-producing and consuming peroxidase activities. In contrast, by a factor of 50, higher Mn concentrations did not produce Mn toxicity symptoms on older leaves in rice. Peroxidase activities, lower by a factor of about 100 in the rice leaf AWF compared with barley, support the view of a central role for these peroxidases in the apoplastic expression of Mn toxicity. The high Mn tolerance of old rice leaves could be related to a high Mn binding capacity of the cell walls. Proteomic studies suggest that the lower Mn tolerance of young rice leaves could be related to Mn excess-induced displacement of Mg and Fe from essential metabolic functions. CONCLUSIONS The results provide evidence that Mn toxicity in barley involves apoplastic lesions mediated by peroxidases. The high Mn tolerance of old leaves of rice involves a high Mn binding capacity of the cell walls, whereas Mn toxicity in less Mn-tolerant young leaves is related to Mn-induced Mg and Fe deficiencies.
See Clinical Perspective

P atients with pulmonary arterial hypertension (PAH) develop right heart failure (RHF) because of a progressive increase in right ventricular (RV) pressure overload. 1 Although it is known for some years that RV systolic adaptation is of clinical importance, it has just recently became clear that RV diastolic stiffness increases and may contribute to disease progression in PAH. 2,3 In addition, we have previously shown that RV diastolic stiffness was closely associated with a doubling in sarcomere-derived cardio-myocyte stiffness and increased myocardial fibrosis in end-stage PAH patients. Changes in myofibril stiffness are closely regulated by the giant elastic protein titin. 5 Titin stiffness can be regulated via both post-transcriptional and post-translational modifications. Post-transcriptional modification includes a shift from the compliant N2BA isoform to the stiffer N2B isoform. 6 Post-translational modification is mainly regulated via phosphoryla-tion of titin by the protein kinases A (PKA), G, and C. Titin phosphorylation by PKA 7 and protein kinase G 8 reduce myo-fibril stiffness, whereas protein kinase C–mediated titin phos-phorylation results in increased RV diastolic stiffness. We have previously demonstrated that in end-stage PAH, no alterations in titin isoform composition are observed, 2 whereas PKA-mediated titin phosphorylation was significantly reduced. Background—The purpose of this study was to determine the relative contribution of fibrosis-mediated and myofibril-mediated stiffness in rats with mild and severe right ventricular (RV) dysfunction. Methods and Results—By performing pulmonary artery banding of different diameters for 7 weeks, mild RV dysfunction (Ø=0.6 mm) and severe RV dysfunction (Ø=0.5 mm) were induced in rats. The relative contribution of fibrosis-and myofibril-mediated RV stiffness was determined in RV trabecular strips. Total myocardial stiffness was increased in trabeculae from both mild and severe RV dysfunction in comparison to controls. In severe RV dysfunction, increased RV myocardial stiffness was explained by both increased fibrosis-mediated stiffness and increased myofibril-mediated stiffness, whereas in mild RV dysfunction, only myofibril-mediated stiffness was increased in comparison to control. Histological analyses revealed that RV fibrosis gradually increased with severity of RV dysfunction, whereas the ratio of collagen I/III expression was only elevated in severe RV dysfunction. Stiffness measurements in single membrane-permeabilized RV cardiomyocytes demonstrated a gradual increase in RV myofibril stiffness, which was partially restored by protein kinase A in both mild and severe RV dysfunction. Increased expression of compliant titin isoforms was observed only in mild RV dysfunction, whereas titin phosphorylation was reduced in both mild and severe RV dysfunction. Conclusions—RV myocardial stiffness is …
Repair Index in Examination of Nuclear Changes in the Buccal Mucosa of Smokers: A Useful Method for Screening of Oral Cancer

Background: Smoking is one of the major risk factors for cancers, especially in the oral cavity. Nuclear changes occur in the early stages of cancer. The aim of this study was therefore to investigate nuclear changes and calculate a “repair index” for the buccal mucosa of smokers. Material and Methods: This historical cohort study was conducted by selecting samples including smokers and non-smokers. In addition, the smoker group were divided into 2 subgroups with a smoking history of >10 and ≤10 years. Buccal mucosa smears were obtained and Papanicolaou staining was employed to detect nuclear changes. Micronuclei, karyorrhexis and karyolysis were assessed and eventually a repair index was calculated. Statistical analysis was performed using the t-test. Results: In the 60 samples studied, differences were significant in smopkers vs. nonsmokers for micronuclei, (P=0.002) but not karyorrhexis or karyolysis. (P=0.789 and P=0.578, respectively). Also, the repair index demonstrated no statistically significant variation (P=0.107). Comparison of the two subgroups of smokers demonstrated that the frequency of micronuclei in those with a history >10 years was significantly higher and the RI was significantly lower than with ≤10 years (P=0.0001 and 0.04, respectively). While karyorrhexis and karyolysis were also higher in the longer exposure individuals the differences were not significant (P=0.07 and 0.78, respectively). Conclusion: Among the nuclear changes investigated, micronuclei proved the more reliable indicator to assess the adverse effects of smoking on the oral mucosa, becoming prominent with increase in smoking history. In addition, while a “repair index” may have benefits for assessment of nuclear damage caused by smoking, further research is necessary in this field.