Miracle-dz/UniFAR-FTUs huggingface dataset:
Gate-Level Netlist Reverse Engineering Tool Set for Functionality Recovery and Malicious Logic Detection

Reliance on third-party resources, including thirdparty IP cores and fabrication foundries, as well as wide usage of commercial-off-the-shelf (COTS) components has raised concerns that backdoors and/or hardware Trojans may be inserted into fabricated chips. Defending against hardware backdoors and/or Trojans has primarily focused on detection at various stages in the supply chain. Netlist reverse engineering tools have been investigated as an alternative to existing chip-level reverse engineering methods which can help recover functional netlists from fabricated chips, but fall short of detecting malicious logic or recovering high-level functionality. In this work, we develop a netlist reverse engineering tool-set which recovers high-level functionality from the netlist, thereby aiding malicious logic detection. The tool-set performs state register identification, control logic recovery and datapath tracking, which facilitates validation of encrypted/obfuscated hardware IP cores. Relying on 3-SAT algorithms and topology-based computational methods, we demonstrate that the developed tool-set can handle netlists of various complexities.
A bi-population based scheme for an explicit exploration/exploitation trade-off in dynamic environments

Optimisation in changing environments is a challenging research topic since many real-world problems are inherently dynamic. Inspired by the natural evolution process, evolutionary algorithms (EAs) are among the most successful and promising approaches that have addressed dynamic optimisation problems. However, managing the exploration/exploitation trade-off in EAs is still a prevalent issue, and this is due to the difficulties associated with the control and measurement of such a behaviour. The proposal of this paper is to achieve a balance between exploration and exploitation in an explicit manner. The idea is to use two equally sized populations: the first one performs exploration while the second one is responsible for exploitation. These tasks are alternated from one generation to the next one in a regular pattern, so as to obtain a balanced search engine. Besides, we reinforce the ability of our algorithm to quickly adapt after cnhanges by means of a memory of past solutions. Such a combination aims to restrain the premature convergence, to broaden the search area, and to speed up the optimisation. We show through computational experiments, and based on a series of dynamic problems and many performance measures, that our approach improves the performance of EAs and outperforms competing algorithms.
Bivalirudin versus heparin in patients treated with percutaneous coronary intervention: a meta-analysis of randomised trials.

AIMS Current recommendations on the use of bivalirudin in patients treated with percutaneous coronary intervention (PCI) are mostly based on trials comparing bivalirudin versus heparin plus planned glycoprotein IIb/IIIa inhibitor (GPI). Whether bivalirudin is also superior to heparin alone is still not well established. This meta-analysis investigates the efficacy and safety of bivalirudin versus heparin in patients treated with PCI without planned use of GPI. METHODS AND RESULTS Scientific databases and websites were searched for randomised controlled trials. The primary efficacy and safety outcomes were the 30-day incidence of death and major bleeding, respectively. The secondary outcomes were the 30-day incidence of myocardial infarction (MI), definite stent thrombosis (ST), urgent target vessel revascularisation (TVR), and overall death at the longest available follow-up. Odds ratio (OR) and 95% confidence interval (95% CI) served as summary statistics. Ten trials were identified including a total of 18,065 PCI patients randomised to bivalirudin (n=9,033) versus heparin (n=9,032). At 30 days, bivalirudin versus heparin showed a comparable risk of death (1.09 [0.83-1.41], p=0.54), and MI (1.10 [0.83-1.46], p=0.50) with a trend towards a higher risk of urgent TVR (1.37 [0.96-1.96], p=0.08). The risk of major bleeding was lower with bivalirudin (0.57 [0.40-0.80], p=0.001) and the bleeding reduction was more evident when high doses of heparin were used as comparator (p for interaction <0.001). The risk of definite ST (2.09 [1.26-3.47], p=0.005) and, in particular, the risk of acute ST (3.48 [1.66-7.28], p<0.001) was increased by bivalirudin. CONCLUSIONS Patients undergoing PCI randomised to therapy with either bivalirudin or heparin display a similar mortality. Bivalirudin as compared to heparin appears to reduce the risk of major bleeding at the expense of a higher risk of acute ST.
Delivery of large molecules via poly(butyl cyanoacrylate) nanoparticles into the injured rat brain

Poly(n-butyl-2-cyanoacrylate) (PBCA) nanoparticles have been successfully applied to deliver small-molecule drugs to the central nervous system (CNS). However, it is unclear whether PBCA nanoparticles can be used as the delivery system for large molecules to potentially treat traumatic brain injury (TBI). In this study, we tested the capacity of PBCA nanoparticles in passing through the blood–brain barrier (BBB) and transporting large molecules into normal and injured brains in the rat. We first synthesized PBCA nanoparticles by dispersion polymerization and then loaded the particles with either horseradish peroxidase (HRP, 44 kDa) or enhanced green fluorescent protein (EGFP, 29 kDa), which were further coated with polysorbate 80. Next, the polysorbate 80-coated HRP or EGFP-loaded PBCA nanoparticles were intravenously injected into the normal and brain-injured rats. We found that, at 45 min after injection, PBCA nanoparticle-delivered HRP or EGFP was hardly detected in the normal brains of the rats, but a small amount of EGFP carried by PBCA nanoparticles was noted in the normal brains 48 h after administration, which was further confirmed by immunolocalization with anti-EGFP antibodies. In contrast, at 4 h after TBI with a circulation time of 45 min, although the penetration of HRP or EGFP alone was hampered by the BBB, the PBCA nanoparticle-delivered HRP or EGFP was widely distributed near injured sites. Together, our findings provide histological evidence that PBCA nanoparticles can be used as an efficient delivery system for large molecules to overcome the barrier in the brain with TBI.
Hepatitis G virus coinfection influences the liver histology of patients with chronic hepatitis C.

AIMS/BACKGROUND The present investigation compared the histological features of the liver of chronic hepatitis C patients who are or are not coinfected with hepatitis G virus (HGV) to determine the histological and clinical characteristics of HGV infection. SUBJECTS AND METHODS This study included 194 patients with chronic hepatitis C who visited our institution between 1993 and 1995. Detection of serum HGV RNA was performed by nested reverse transcription-polymerase chain reaction. Scores were assigned to indicate the severity of each of the following features on the liver biopsy of a patient: inflammatory cell infiltration in the periportal, parenchymal, and portal area; fibrous stage; lymphoid aggregates in the portal area; portal sclerotic change; perivenular fibrosis; pericellular fibrosis; bile duct damage; bridging necrosis; and irregular regeneration of hepatocytes (IR). RESULTS HGV RNA was detected in the sera of 18 (9.3%) of the 194 patients. The histological features of the HGV RNA-positive patients show significantly more severe bile duct damage, perivenular fibrosis, pericellular fibrosis and IR than the liver of the HGV RNA-negative patients. The biochemical results in the two groups did not significantly differ. CONCLUSION Our data suggest that chronic HGV coinfection worsens the histological features of liver disease.
ACVRL 1 germinal mosaic with two mutant alleles in hereditary hemorrhagic telangiectasia associated with pulmonary arterial hypertension

Germline mutations in genes encoding members of the transforming growth factor-β (TGF-β)/bone morphogenetic protein (BMP) superfamily are causal for two hereditary vascular disorders, hereditary hemorrhagic telangiectasia (HHT) and heritable pulmonary arterial hypertension (PAH). When the two diseases coexist, activin A receptor type II-like kinase-1 (ACVRL1 ) gene mutations are usually identified. We report a remarkable ACVRL1 germinal and somatic mosaicism characterized by the presence of two distinct mutant alleles and a non-mutant ACVRL1 allele in a woman diagnosed with PAH at the age 40. She also met the Curaçao diagnostic criteria for HHT based on additional findings of telangiectases, epistaxis and arteriovenous malformations. Mutation analysis of ACVRL1 identified two adjacent heterozygous deleterious mutations within exon 10: c.1388del (p.Gly463fsX2) and c.1390del (p.Leu464X) in a region enriched by mutation-associated DNA motifs. The mother transmitted the c.1388del to one child and the c.1390del to two children confirming germinal mosaicism. Allele-specific polymerase chain reaction analysis showed that c.1388del is the predominant mutation in lymphocytes of the index case. Haplotype analysis revealed that both mutant alleles have a common chromosomal origin which is distinct from that of the mother’s non-mutant ACVRL1 allele. These distinct mutant alleles in tissues and germline could have arisen by DNA structure-mediated events occurring in the early stages of the mother’s embryogenesis, prior to the segregation of her germline, which ultimately led to the independent transmission of each allele. These highlight the complexity of genomic events occurring during early embryogenesis and the consequences of mutational mosaicism upon pathogenic variability.
Genetics of Natural Populations. Xxviii. the Magnitude of the Genetic Load in Populations of Drosophila Pseudoobscura.

Results are reviewed from previous studies on genetic loads in Drosophila. A series of studies was made on Drosophila pseudoobscura to determine whether individuals carrying different combinations of chromosomes are phenotypically uniform or heterogeneous, and if heterogeneous, whether or not the heterogeneity is correlated with the effects of the component chromosomes in homozygotes. The magnitude of the genetic loads carried in the second and third chromosomes of Drosophila pseudoobscura were estimated for samples from populations living near Austin, Tex. , and Mather, Calif. The effects of the chromosomes on the viability of the homozygotes were found to differ in cultures raised at 25 and at l5 deg C. Data are tabulated. A negative correlation between viability and variability was observed for both homozygotes and heterozygotes. (C.H.)
Archaeology in the Land of Carchemish: landscape surveys in the area of Jerablus Tahtani, 2006

Abstract The first season of survey around the site of Tell Jerablus Tahtani, conducted in March and April 2006, demonstrated the existence of occupations from the Neolithic to the Early Islamic period. Tell Jerablus Tahtani was fringed to the west by a lower settlement of Late Uruk and early third millennium BC date, at which time settlement was also evident at Tell Sha'ir to the west and at Duluk near the junction with the Sajour. Tells formed the main mode of occupation during the Early and Middle Bronze Ages, but this pattern of occupation broke down during the Hellenistic through Late Antique periods when a more dispersed pattern of rural settlements and small towns developed. The landscape became progressively more “busy” during the Hellenistic through Late Antique periods, when the presence of conduits, canals and other landscape features attest to both increasingly intensive and extensive systems of land use.
Detection of respiratory events during NPSG: nasal cannula/pressure sensor versus thermistor.

Recording of respiratory airflow is an integral part of polysomnography (NPSG). It is conventionally monitored with a thermistor that measures temperature as a surrogate of flow. The subjectivity of interpreting hypopnea from this signal has prompted us to measure nasal airflow directly with a simple pneumotachograph consisting of a standard nasal cannula connected to a 2-cm H2O pressure transducer. We manually analyzed respiratory events using simultaneous thermistor and nasal cannula in 11 patients with obstructive sleep apnea syndrome (OSAS) and 9 with upper airway resistance syndrome (UARS). Definite events were scored separately for each signal when amplitude was <50% for >10 seconds. Events were also scored on the nasal cannula signal when the flattened shape of the signal suggested flow limitation, and these were tabulated separately. Definite events in one signal were tabulated by whether the other signal showed a definite event or not. In addition, nasal cannula events were compared to a more liberal thermistor criterion (any change in the signal for > or = 2 breaths). Visually, events were more easily recognized on the nasal cannula signal than on the thermistor signal. In OSAS, 1,873 definite thermistor events were detected. Of these, 99.1% were detected by nasal cannula, and 0.9% were missed. Of 3,541 definite nasal cannula events, 51.9% were detected by definite thermistor criteria; 75.0% were detected by liberal thermistor criteria; 25.0% were missed. In UARS, 123 definite thermistor events were detected. Of these, 89.4% were detected by nasal cannula and 10.6% were missed. Nine hundred and three nasal cannula events were detected. However, only 17.2% of these were detected by definite thermistor criteria; 38.6% were detected by liberal thermistor criteria; 61.4% were completely undetected by thermistor. When events identified on the nasal cannula by flow limitation alone were excluded, the thermistor detected 30.1% of events by definite criteria and 78.6% by liberal criteria, still leaving 21.4% completely undetected by the thermistor. We conclude that the nasal cannula reliably detects respiratory events seen by thermistor. Additional events (including some characterized only by flow limitation) that help define the UARS, were recognized by nasal cannula but often completely missed by thermistor. We propose that respiratory monitoring during NPSG with nasal cannula significantly improves event detection and classification over that with thermistor.
Journey Towards Agility: Where Are We Now And Where Are We Heading?

After more than 15 years since the Agile Manifesto and extensive research on agile information system development (AISD), a comprehensive body of knowledge is available and is constantly growing. AISD is considered an effective way for managing ISD projects in environments characterized by rapidly changing requirements. This study aims to shed light on theexisting knowledge on AISD by applying a structured literature review and computer aided analysis consisting of distinct text mining techniques. We plan to analyze a sample of more than 10,000 articles and provide preliminary results of a subset of 327 articles of the Senior Scholars’ Basket and selected conferences. Based on our approach, we are able to (1) evaluate key articles, authors, and journals, (2) analyze the development of AISD research in the last two decades and, most importantly, (3) identifyresearch foci of the past as well as gaps in our knowledge on AISD.
Progesterone induces activation in Octopus vulgaris spermatozoa

The purpose of the present study was to determine whether Octopus vulgaris spermatozoa are activated by progesterone stimulation. Spermatozoa were collected from the spermatophores in the Needham's sac of the male (MS) and from the spermathecae of oviducal glands of the female (FS). We used transmission (TEM) and scanning (SEM) electron microscopy to study the morphology of untreated, Ca2+ ionophore A23187 and progesterone‐treated MS spermatozoa, and untreated FS spermatozoa. We showed that ionophore and progesterone stimulation of MS spermatozoa induce breakdown of the membranes overlapping the acrosomal region, exposing the spiralized acrosome. These modifications resemble the acrosome reaction observed in other species. FS stored in the spermathecae did not show the membranes covering the acrosomal region present in the MS spermatozoa. When ionophore and progesterone treatments were performed in Ca2+‐free artificial sea water, no changes were observed, suggesting the role of external calcium in modifying membrane morphology. Lectin studies showed a different fluorescence distribution and membrane arrangement of FS‐untreated spermatozoa with respect to the MS, suggesting that spermatozoa transferred in the female genital tract after mating, are stored in a pre‐activated state. The plasma membrane of the untreated MS and FS spermatozoa was labelled with Progesterone‐BSA‐FITC, indicating the presence of plasma membrane progesterone receptor. Taken together these data suggest that progesterone induces an acrosome‐ like reaction in MS spermatozoa similar to that induced by calcium elevation. In addition progesterone may play a role in the pre‐activation of spermatozoa stored in the female tract, further supporting the hypothesized parallelism between cephalopods and vertebrates. Mol. Reprod. Dev. 59:97–105, 2001. © 2001 Wiley‐Liss, Inc.
Intracellular Distribution of Myelin Protein Gene Products Is Altered in Oligodendrocytes of the taiep Rat

Hypomyelination and subsequent demyelination of the taiep rat CNS are thought to result from the abnormal accumulation of microtubules (MTs) in oligodendrocytes that disrupts intracellular transport of components needed to form and maintain the myelin sheath. In this study, myelin gene expression was evaluated in mutant and age-matched controls to determine if MT abnormalities affect the distribution of myelin proteins and their mRNAs. Immunohistochemical analysis of taiep brains and spinal cords revealed a gradual decrease in levels of several myelin proteins including myelin basic protein (MBP), proteolipid protein (PLP), myelin-associated glycoprotein (MAG), and 2',3'-cyclic nucleotide 3'-phosphodiesterase. Accompanying early declines in MAG and PLP, accumulations of immunoreactive products were detected within oligodendrocytes, consistent with a defect in protein trafficking. Northern blot analysis indicated that diminishing protein levels could not be attributed to changes in transcriptional activity, except for MBP of which mRNA levels decreased with age. Cellular localization of MBP mRNA by in situ hybridization further revealed that transcripts were concentrated within oligodendrocyte cell bodies instead of uniformly distributed throughout processes. These results demonstrate that changes in expression and intracellular localization of myelin gene products are concurrent with increases in MT mass in taiep oligodendrocytes and support our hypothesis that cytoskeletal defects prevent the normal transport of elements required for the formation and maintenance of the myelin sheath.
Panoramic video stabilization based on rotational damping filter

Videos captured from handheld devices are commonly suffered from frame to frame jitter due to unintentional camera movements. Therefore a motion smoothing algorithm is required to produce stabilized video. In this paper a new method is proposed to stabilize panoramic videos from jitter using horizontal, vertical and rotational damping filters. Firstly speeded up robust features (SURF) are extracted from each frame of video sequence and motion estimation information is then obtained from two consecutive frames. Horizontal, vertical and rotational damping filters are applied on estimated motion to separate the intentional and unintentional motion in horizontal, vertical and rotational direction respectively. A motion compensated frame is created by translating the original frame using estimated unintentional motion information. It is evident from results that the proposed video stabilization algorithm outperforms the state-of-the-art method in terms of motion trajectories and interframe transformation fidelity for both panoramic and 3D video datasets.
Multi-objective optimization based on self-adaptive differential evolution algorithm

In this paper, our recently developed Self-adaptive Differential Evolution algorithm (SaDE) is extended to solve numerical optimization problems with multiple conflicting objectives. The performance of the proposed MOSaDE algorithm is evaluated on a suit of 19 benchmark problems provided for the CEC2007 special session (http://www.ntu.edu.sg/home/epnsugan/) on Performance Assessment of Multi-Objective Optimization Algorithms.
Neuroprotective Properties of a Novel Non-Thiazoledinedione Partial PPAR-γ Agonist against MPTP

Activation of the peroxisome proliferator activated receptor-gamma (PPAR)-γ is proposed as a neuroprotective strategy to treat neurodegenerative disorders. In this study, we examined if LSN862 (LSN), a novel non-thiazoledinedione partial PPAR-γ agonist, was neuroprotective in a mouse model of Parkinson's disease (PD) and assessed possible mechanisms of action. LSN (3, 10, or 30 mg/kg) or vehicle was orally administered daily to C57BL/6 and antioxidant response element-human placental alkaline phosphatase (ARE-hPAP) reporter mice 3 days prior to 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP; 30 mg/kg, i.p. × 5 days) or PBS administration. LSN elicited a dose-dependent preservation of dopaminergic nigrostriatal innervation that was not associated with inhibition of MPTP metabolism or activation of Nrf2-ARE, although changes in NQO1 and SOD2 mRNA were observed. A significant dose-dependent downregulation in MAC-1 and GFAP positive cells was observed in MPTP + LSN-treated mice as well as significant downregulation of mRNA expression levels of these inflammatory markers. MPTP-induced increases in PPAR-γ and PGC1α expression were ameliorated by LSN dosing. Our results demonstrate that oral administration of LSN is neuroprotective against MPTP-induced neurodegeneration, and this effect is associated with downregulation of neuroinflammation, decreased oxidative stress, and modulation of PPAR-γ and PGC1α expression. These results suggest that LSN can be a candidate alternative non-thiazoledinedione partial PPAR-γ agonist for neuroprotective treatment of PD.
Bacterial load and cytokine profile in patients with cirrhosis following therapy with proton pump inhibitors: a prospective cohort study

Background The aim of this study was to explore the presence of bacterial products and the cytokine profile in outpatients with cirrhosis before and after short-term (4-8 weeks) administration of proton pump inhibitors (PPIs). Methods Seventeen patients with cirrhosis—male/female: 12/5; age: median 59.2 years (49-65); etiology: HBV±HDV 23.5%, HCV 17.7%, alcohol 41.2%, other 17.6%; Child-Pugh score: median 7.5 (5-12); Model for End-stage Liver Disease: 10.5 (7-21); ascites (%): 3 (17.7)—attending the outpatient clinics were included. None had hepatocellular carcinoma. Indications for PPIs were: esophagitis (n=6, 35.3%), peptic ulcer (n=10, 58.6%) and other (n=1, 5.9%). Bacterial DNA in serum and the levels of endotoxin, lipopolysaccharide binding protein, transforming growth factor-β, interleukin -1β, -6, -8, -12, -10, tumor necrosis factor-α and nitric oxide were assessed at baseline (time 1) and at the end of treatment (time 2). The Wilcoxon signed rank test was used to evaluate significant differences in the parameters assayed before and after PPI administration. Results No patients developed infection during the study period. Bacterial DNA was not detected before or after treatment. No significant differences were observed between the concentrations of any indices between times 1 and 2 (P>0.05). Subgroup analysis according to Child-Pugh stage yielded similar results. Conclusion Short-term administration of PPIs had no effect on bacterial DNA, bacterial products or cytokine concentrations in patients with liver cirrhosis.