Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies.

This review summarizes reports of recurrent DNA sequence copy number amplifications in human neoplasms detected by comparative genomic hybridization. Some of the chromosomal areas with recurrent DNA copy number amplifications (amplicons) of 1p22-p31, 1p32-p36, 1q, 2p13-p16, 2p23-p25, 2q31-q33, 3q, 5p, 6p12-pter, 7p12-p13, 7q11.2, 7q21-q22, 8p11-p12, 8q, 11q13-q14, 12p, 12q13-q21, 13q14, 13q22-qter, 14q13-q21, 15q24-qter, 17p11.2-p12, 17q12-q21, 17q22-qter, 18q, 19p13.2-pter, 19cen-q13.3, 20p11.2-p12, 20q, Xp11.2-p21, and Xp11-q13 and genes therein are presented in more detail. The paper with more than 150 references and two tables can be accessed from our web site http://www.helsinki. fi/lglvwww/CMG.html. The data will be updated biannually until the year 2001.
Producing Known Complex Modulation Signals for Characterization of Coherent Optical Receivers

We introduce a family of complex modulation signals that are generated as patterns over the real and imaginary plane for characterization of coherent optical receivers. The properties of the complex signals can be predicted from first principles, enabling quantitative comparisons between measurement and theory. An optical heterodyne technique with phase-locked loops for frequency control and narrow-band lasers was used to create the known signals, providing temporal stability and ease of operation. The modulation patterns could be made arbitrarily intricate simply by selection of the heterodyne frequencies, with no hardware modifications. The technique is capable of generating signals with frequencies of more than 100 GHz. A real-time optical modulation analyzer was used to visualize the modulation patterns and illustrate their properties. In turn, we used the modulation patterns to characterize the coherent receiver within the modulation analyzer, thereby examining its demodulation algorithm, software processing, digital filtering, and detector gain balance. By working with known modulation patterns, we were able to create an error vector waveform to allow quantitative evaluation of measured signals as they spanned the complex plane.
Circadian rhythm connections to oxidative stress: implications for human health.

SIGNIFICANCE Oxygen and circadian rhythmicity are essential in a myriad of physiological processes to maintain homeostasis, from blood pressure and sleep/wake cycles, down to cellular signaling pathways that play critical roles in health and disease. If the human body or cells experience significant stress, their ability to regulate internal systems, including redox levels and circadian rhythms, may become impaired. At cellular as well as organismal levels, impairment in redox regulation and circadian rhythms may lead to a number of adverse effects, including the manifestation of a variety of diseases such as heart diseases, neurodegenerative conditions, and cancer. RECENT ADVANCES Researchers have come to an understanding as to the basics of the circadian rhythm mechanism, as well as the importance of the numerous species of oxidative stress components. The effects of oxidative stress and dysregulated circadian rhythms have been a subject of intense investigations since they were first discovered, and recent investigations into the molecular mechanisms linking the two have started to elucidate the bases of their connection. CRITICAL ISSUES While much is known about the mechanics and importance of oxidative stress systems and circadian rhythms, the front where they interact has had very little research focused on it. This review discusses the idea that these two systems are together intricately involved in the healthy body, as well as in disease. FUTURE DIRECTIONS We believe that for a more efficacious management of diseases that have both circadian rhythm and oxidative stress components in their pathogenesis, targeting both systems in tandem would be far more successful.
Antibiotics for the eradication of Propionibacterium acnes biofilms in surgical infection.

OBJECTIVES Propionibacterium acnes is increasingly recognized as a cause of delayed infection after spinal instrumentation or shunting for hydrocephalus. Biofilm development by this organism has recently been demonstrated. We therefore investigated the effect of two different courses of three antibiotics (penicillin, rifampicin and linezolid) on mature P. acnes biofilms in vitro. Outcomes were eradication or regrowth after withdrawal of antibiotics, simulating successful treatment and relapse. METHODS P. acnes biofilms were grown on titanium discs for 6 days until mature, then exposed to the antibiotics for either 7 or 14 days before sonication and culture. Further, discs were similarly exposed, but after each course, they were reincubated for a further 9 days to check for regrowth. RESULTS Penicillin, linezolid and linezolid plus rifampicin eradicated P. acnes biofilms after 14 days, but only penicillin had this effect after 7 days. 'Relapse' was prevented only by 14 day courses of penicillin or linezolid plus rifampicin, but not by linezolid alone. CONCLUSIONS For P. acnes spinal instrumentation infections, either penicillin or linezolid plus rifampicin might be equally effective. For shunt infections, as penicillin does not give therapeutic cerebrospinal fluid concentrations, rifampicin plus linezolid might be the treatment of choice. Linezolid alone appears not to be as effective as penicillin against P. acnes biofilms.
Antigenic structure and variation in an influenza virus N9 neuraminidase

We previously determined, by X-ray crystallography, the three-dimensional structure of a complex between influenza virus N9 neuraminidase (NA) and the Fab fragments of monoclonal antibody NC-41 [P. M. Colman, W. G. Laver, J. N. Varghese, A. T. Baker, P. A. Tulloch, G. M. Air, and R. G. Webster, Nature (London) 326:358-363, 1987]. This antibody binds to an epitope on the upper surface of the NA which is made up of four polypeptide loops over an area of approximately 600 A2 (60 nm2). We now describe properties of NC-41 and other monoclonal antibodies to N9 NA and the properties of variants selected with these antibodies (escape mutants). All except one of the escape mutants had single amino acid sequence changes which affected the binding of NC-41 and which therefore are located within the NC-41 epitope. The other one had a change outside the epitope which did not affect the binding of any of the other antibodies. All the antibodies which selected variants inhibited enzyme activity with fetuin (molecular weight, 50,000) as the substrate, but only five, including NC-41, also inhibited enzyme activity with the small substrate N-acetylneuramin-lactose (molecular weight, 600). These five probably inhibited enzyme activity by distorting the catalytic site of the NA. Isolated, intact N9 NA molecules form rosettes in the absence of detergent, and these possess high levels of hemagglutinin activity (W.G. Laver, P.M. Colman, R.G. Webster, V.S. Hinshaw, and G.M. Air, Virology 137:314-323, 1984). The enzyme activity of N9 NA was inhibited efficiently by 2-deoxy-2,3-dehydro-N-acetylneuraminic acid, whereas hemagglutinin activity was unaffected. The NAs of several variants with sequence changes in the NC-41 epitope lost hemagglutinin activity without any loss of enzyme activity, suggesting that the two activities are associated with separate sites on the N9 NA head.
Drought Induces Distinct Growth Response, Protection, and Recovery Mechanisms in the Maize Leaf Growth Zone1[OPEN]

Drought inhibits cell division and expansion in the maize leaf growth zone by reducing antioxidant levels and increases photosynthetic capacity to allow for enhanced growth upon recovery. Drought is the most important crop yield-limiting factor, and detailed knowledge of its impact on plant growth regulation is crucial. The maize (Zea mays) leaf growth zone offers unique possibilities for studying the spatiotemporal regulation of developmental processes by transcriptional analyses and methods that require more material, such as metabolite and enzyme activity measurements. By means of a kinematic analysis, we show that drought inhibits maize leaf growth by inhibiting cell division in the meristem and cell expansion in the elongation zone. Through a microarray study, we observed the down-regulation of 32 of the 54 cell cycle genes, providing a basis for the inhibited cell division. We also found evidence for an up-regulation of the photosynthetic machinery and the antioxidant and redox systems. This was confirmed by increased chlorophyll content in mature cells and increased activity of antioxidant enzymes and metabolite levels across the growth zone, respectively. We demonstrate the functional significance of the identified transcriptional reprogramming by showing that increasing the antioxidant capacity in the proliferation zone, by overexpression of the Arabidopsis (Arabidopsis thaliana) iron-superoxide dismutase gene, increases leaf growth rate by stimulating cell division. We also show that the increased photosynthetic capacity leads to enhanced photosynthesis upon rewatering, facilitating the often-observed growth compensation.
Development of a prediction formula of Parkinson disease severity by optical coherence tomography

The aims of this study were to assess the peripapillary retinal nerve fiber layer (RNFL) thickness in patients with Parkinson's disease (PD), to determine its correlation with disease severity, and to define a simple biomarker for predicting clinical severity. One hundred two eyes from 52 patients affected by PD were compared with 97 eyes from 50 age‐comparable controls. In all patients, peripapillary RNFL thickness was measured by optical coherence tomography (OCT). We used the Unified Parkinson's Disease Rating Scale (UPDRS) total score and measured responses in the on medication state. Eyes from patients with PD had a statistically significant decrease in average peripapillary RNFL thickness compared with control eyes (P < 0.001). This reduction was observed in every quadrant (inferior, superior, nasal [P < 0.001], and temporal [P = 0.017]) in patients with PD. Furthermore, a strong inverse correlation was found between the PD severity measured according to the UPDRS score and the average peripapillary RNFL thickness (r = −0.615; P < 0.001) and PD duration (r = −0.303; P = 0.002). From these results, we defined a regression equation that predicts the UPDRS score from the above‐mentioned variables: UPDRS = 81.6 + 29.6 * log PD duration (years) − 0.6 * RFNL thickness (μm). We observed that, as the evolution and severity of PD progress, the peripapillary RNFL layer thickness, as evaluated by OCT, gradually diminishes. These results suggest that the average peripapillary RNFL thickness measured by OCT might be useful as a biomarker to detect the early onset and progression of PD. © 2013 International Parkinson and Movement Disorder Society
Growth inhibition of human pancreatic cancer cell lines by anti‐sense oligonucleotides specific to mutated K‐ras genes

About 90% of human pancreatic cancers carry K‐ras point mutation, which may play an important role in tumorigenesis. We investigated the inhibitory effects of anti‐sense oligonucleotides targeting K‐ras point mutation on the growth of cultured human pancreatic cancer cells. Eight human pancreatic cancer cell lines were screened for K‐ras codon 12 point mutations by PCR‐RFLP analysis and direct sequencing. Then, 3 cell lines with the major types of K‐ras point mutation, i.e.,HuP‐T1, HuP‐T3 and PANC‐1, and 1 without mutation, BxPC‐3, were used for the experiments. Seventeen mer anti‐sense oligonucleotides were designed, targeting the point mutation of K‐ras codon 12, and transfected into the cells by the liposome‐mediated method. Cell‐growth activities were estimated by MTT assay. Levels of K‐ras mRNA expression were determined using quantitative RT‐PCR, and K‐ras p21 protein synthesis was evaluated with Western blotting. Mutation‐matched anti‐sense oligonucleotides effectively inhibited the growth of these pancreatic cancer cell lines, except for BxPC‐3, by suppressing K‐ras mRNA expression and K‐ras p21 protein synthesis. Moreover, mutation‐matched anti‐sense oligonucleotides showed stronger anti‐proliferative effects than did mutation‐mismatched ones. Our results suggest that anti‐sense therapy specific to point mutations of K‐ras mRNA is a practical approach to selective suppression of tumor growth, with little effect on normal cells. Int. J. Cancer 80:553–558, 1999. © 1999 Wiley‐Liss, Inc.
Enterococcus faecalis Inhibits Hyphal Morphogenesis and Virulence of Candida albicans

ABSTRACT The Gram-positive bacterium Enterococcus faecalis and the fungus Candida albicans are both found as commensals in many of the same niches of the human body, such as the oral cavity and gastrointestinal (GI) tract. However, both are opportunistic pathogens and have frequently been found to be coconstituents of polymicrobial infections. Despite these features in common, there has been little investigation into whether these microbes affect one another in a biologically significant manner. Using a Caenorhabditis elegans model of polymicrobial infection, we discovered that E. faecalis and C. albicans negatively impact each other's virulence. Much of the negative effect of E. faecalis on C. albicans was due to the inhibition of C. albicans hyphal morphogenesis, a developmental program crucial to C. albicans pathogenicity. We discovered that the inhibition was partially dependent on the Fsr quorum-sensing system, a major regulator of virulence in E. faecalis. Specifically, two proteases regulated by Fsr, GelE and SerE, were partially required. Further characterization of the inhibitory signal revealed that it is secreted into the supernatant, is heat resistant, and is between 3 and 10 kDa. The substance was also shown to inhibit C. albicans filamentation in the context of an in vitro biofilm. Finally, a screen of an E. faecalis transposon mutant library identified other genes required for suppression of C. albicans hyphal formation. Overall, we demonstrate a biologically relevant interaction between two clinically important microbes that could affect treatment strategies as well as impact our understanding of interkingdom signaling and sensing in the human-associated microbiome.
Lymphatic and vascular origin of Kaposi's sarcoma spindle cells during tumor development

The histogenesis of Kaposi's sarcoma (KS) tumor spindle cells (SC) remains controversial but several immunohistochemical studies favor a lymphatic origin. Twenty KS surgical biopsies were analyzed for the coexpression of LANA, CD34, LYVE‐1, D2‐40, VEGFR‐2, VEGFR3 by using double or triple immunostaining. Most of the SC in both early and late KS expressed the lymphatic markers LYVE‐1, D2‐40 and VEGFR‐3 and the blood vascular endothelial/endothelial precursor cell markers CD34 and endothelial stem cell marker VEGFR‐2. All the LANA+ SC in early and late KS were LYVE‐1+, but only 75% of these LANA+ cells were CD34+. The CD34+/LANA+ cells increased from early‐ (68.8%) to late‐stage KS (82.2%). However, approximately 18% of the LANA+ SC in early KS were CD34− but were LYVE‐1+, suggesting that resident lymphatic endothelial cells (LEC) are targeted for primary infection by human herpesvirus‐8. This LANA+/LYVE‐1+/CD34− (resident LEC) cell population clearly decreased during the development of KS from early (18.7%) to late KS (2.9%). Thus, in late stages of KS, most SC were LANA+/CD34+/LYVE‐1+. However, in both early‐ and late‐stage KS, approximately 18% of the SC were CD34+/LANA‐/LYVE‐1− and could represent newly recruited endothelial precursor cells, which become infected in the lesion and eventually undergo a phenotype switch expressing LEC markers. Our study apparently indicates that KS represents a unique variant of tumor growth with continues recruitment of tumor precursor cells as well as proliferation and decreased apoptosis of SC. © 2006 Wiley‐Liss, Inc.
Gesture-based interaction: a new dimension for mobile user interfaces

Today, smart phones with touchscreens and sensors are the predominant, fastest growing class of consumer computing devices. However, because these devices are used in diverse situations, and have unique capabilities and form factors, they also raise new user interface challenges, and at the same time, offer great opportunities for impactful HCI research. In this talk, I will focus on gesture-based interaction, an important interaction behavior enabled by touchscreens and built-in sensors, which sets mobile interaction apart from traditional graphical user interfaces. I will first talk about gesture shortcuts in the context of Gesture Search [1], a tool that allows users to quickly access applications and data on the phone by simply drawing a few gestures (http://www.google.com/mobile/gesture-search). Gesture Search flattens mobile phones' UI hierarchy by alleviating the need for navigating the interface. Gesture Search has been released and is invoked hundreds of thousands of times per day by a large user population. I will then cover several related projects that furthered our investigation into gesture shortcuts, including using gestures for target acquisition [3], crowd sourcing-based gesture recognition [5] and our early exploration on motion gestures [4, 6, 7]. Finally, I will turn to discuss multi-touch gestures for direct manipulation of an interface, the dominant class of gesture-based interaction on existing commercial devices. Multi-touch gestures are intuitive and efficient to use, but can be difficult to implement. I will discuss tools to support developers, allowing them to more easily create multi-touch interaction behaviors by demonstration [2]. These projects investigated various aspects of gesture-based interaction on mobile devices. They help open a new dimension for mobile interaction.
Selective Reminding and Free and Cued Selective Reminding in Mild Cognitive Impairment and Alzheimer Disease

The Selective Reminding Test (SRT) and the Free and Cued Selective Reminding Test (FCSRT) are multitrial memory tests that use a common “selective reminding” paradigm that aims to facilitate learning by presenting only the missing words from the previous recall trial. While in the FCSRT semantic cues are provided to elicit recall, in the SRT, participants are merely reminded of the missing items by repeating them. These tests have been used to assess age-related memory changes and to predict dementia. The performance of healthy elders on these tests has been compared before, and results have shown that twice as many words were retrieved from long-term memory in the FCSRT compared with the SRT. In this study, we compared the tests’ properties and their accuracy in discriminating amnestic mild cognitive impairment (aMCI; n = 20) from Alzheimer disease (AD; n = 18). Patients with AD performed significantly worse than patients with aMCI on both tests. The percentage of items recalled during the learning trials was significantly higher for the FCSRT in both groups, and a higher number of items were later retrieved, showing the benefit of category cueing. Our key finding was that the FCSRT showed higher accuracy in discriminating patients with aMCI from those with AD.
A New Secure Hash Dynamic Structure Algorithm (SHDSA) for Public Key Digital Signature Schemes

This paper presents a new secure hash algorithm based on dynamic structure algorithm called secure hash dynamic structure algorithm (SHDSA). It uses a famous secure hash algorithm (SHA) given by the National Institute of Standards and Technology (NIST). All NIST SHA have fixed structure, fixed constant and fixed output length. The goal of the new Advanced Encryption Standard (AES) is to offer, at its three cryptovariable size, 128, 192 and 256 bits of security, is the need for companion hash algorithms which provide similar levels of enhanced security. The basic design of SHDSA is to have variable output length of 128,192 and 256 bits, variable number of compression functions (single, double), variable number of iterations in each compression function and variable compression function structure. With this dynamic structure, it can provide many choices for practical applications with different level of security. The SHDSA has been designed to satisfy the dynamic structure algorithm with different level of enhanced security and to resist the advanced SHA attacks. The security analysis of the SFIDSA is compared to the old SHA given by the NIST and it gives more security and excellent results as shown in our discussion. In this paper, the digital signature standard algorithm (DSSA) which is given by the NIST has been modified using the proposed SHDSA. The SHDSA can be used in many applications such as, public key cryptosystems, digital signature, digital signcryption, message authentication code and random number generators
Patients with severe acquired brain injury show increased arousal in tilt-table training.

INTRODUCTION Patients with severe acquired brain injury (ABI) are often mobilised using a tilt-table. Complications such as orthostatic intolerance have been reported. The primary objective of this study was to investigate if using a tilt-table was feasible for mobilising patients with severe ABI admitted for sub-acute rehabilitation. We also investigated change in arousal, treatment duration before termination due to orthostatic reactions and change in muscle tone. MATERIAL AND METHODS A total of 16 patients with severe ABI were included. The patients were tilted head-up, and blood pressure, heart rate, breathing frequency and eye opening were recorded before and during the intervention. Furthermore, muscle tone was recorded before and after the intervention. RESULTS Fifteen of the 16 patients did not complete the 20-min. session of tilt training due to orthostatic intolerance. There was a significant increase in the proportion of time that the patients had open eyes during treatment as compared with before treatment (p < 0.01). The mean time to occurrence of symptoms at the first, second and third tilt was 244 (standard deviation (SD) = ± 234) sec. , 277 (SD = ± 257) sec. and 155 (SD = ± 67) sec. , respectively. CONCLUSION Patients with severe sub-acute ABI show orthostatic intolerance when mobilised on a tilt-table which results in a low mobilisation intensity. However, the patients showed a significant increase in arousal during mobilisation. FUNDING No external funding was received for this study. All resources were provided by the Department of Neurorehabilitation, Traumatic Brain Injury Unit, Glostrup University Hospital. TRIAL REGISTRATION not relevant.