Miracle-dz/UniFAR-FTUs huggingface dataset:
Uncoordinated regulation of stress fibers and focal adhesions by DAP kinase

Death-associated protein kinase (DAP kinase) is a proapoptotic, calcium/calmodulin-dependent serine/threonine kinase. Here, we report that DAP kinase phosphorylates the regulatory light chain of myosin II (MLC) both in vitro and in vivo, and that this phosphorylation occurs preferentially at residue Ser19. In quiescent fibroblasts, DAP kinase stabilizes stress fibers through phosphorylation of MLC, but it is dispensable for the formation of peripheral microfilament bundles. This cytoskeletal effect of DAP kinase occurs before the onset of apoptosis and does not require an intact death domain. In addition, DAP kinase is required for serum-induced stress-fiber formation, which is associated with the upregulation of its catalytic activity. Despite being both sufficient and necessary for the assembly or maintenance of stress fibers, DAP kinase is incapable of stimulating the formation of focal adhesions in quiescent cells. Moreover, it promotes the disassembly of focal adhesions but not stress fibers in cells receiving serum factors. Together, our results identify a novel and unique function of DAP kinase in the uncoupling of stress fibers and focal adhesions. Such uncoupling would lead to a perturbation of the balance between contractile and adhesion forces and subsequent cell detachment, which might contribute to its pro-apoptotic activity.
The Transition of Closely Opposed Lesions to Double-Strand Breaks during Long-Patch Base Excision Repair Is Prevented by the Coordinated Action of DNA Polymerase δ and Rad27/Fen1

ABSTRACT DNA double-strand breaks can result from closely opposed breaks induced directly in complementary strands. Alternatively, double-strand breaks could be generated during repair of clustered damage, where the repair of closely opposed lesions has to be well coordinated. Using single and multiple mutants of Saccharomyces cerevisiae (budding yeast) that impede the interaction of DNA polymerase δ and the 5′-flap endonuclease Rad27/Fen1 with the PCNA sliding clamp, we show that the lack of coordination between these components during long-patch base excision repair of alkylation damage can result in many double-strand breaks within the chromosomes of nondividing haploid cells. This contrasts with the efficient repair of nonclustered methyl methanesulfonate-induced lesions, as measured by quantitative PCR and S1 nuclease cleavage of single-strand break sites. We conclude that closely opposed single-strand lesions are a unique threat to the genome and that repair of closely opposed strand damage requires greater spatial and temporal coordination between the participating proteins than does widely spaced damage in order to prevent the development of double-strand breaks.
Genome‐Wide Analysis of Human SNPs at Long Intergenic Noncoding RNAs

Long intergenic noncoding RNAs (lincRNAs) represent a large portion of the noncoding genes in mammals and other eukaryotes but remains among the least well‐understood of genetic factors to date. Here, we systematically analyzed the human SNPs of lincRNAs at a genome level. We found a significantly lower SNP density in lincRNA regions than both their upstream and downstream flanking regions. Functional regions show lower SNP density than other regions in lincRNAs. We revealed that lincRNAs with higher expression levels and broader expression spectrum have significantly lower SNP density. Moreover, we identified lincRNAs that are under recent positive selection and revealed that these lincRNAs show distinct SNP density, expression level, and tissue specificity. Importantly, we identified a genetic variant (rs7990916:T>C) under recent positive selection at a brain‐specific lincRNA that significantly affects the structure of normal brain. Analysis of brain magnetic resonance images showed that individuals with CC genotype have significant bigger regional gray matter volume than individuals with TT genotype. Moreover, the genotype of this SNP shows different distribution in normal elders, mild cognitive impairment, and Alzheimer disease subjects, suggesting that this lincRNA may have a role in physiology and pathophysiology of human brain.
Immunological relationship among hydrogenases

We examined the immunological cross-reactions of 11 different hydrogenase antigens with 9 different hydrogenase antibodies. Included were antibodies and antigens of both subunits of the hydrogenases of Bradyrhizobium japonicum and Thiocapsa roseopersicina. The results showed a strong relationship among the Ni-Fe dimeric hydrogenases. The two subunits of Ni-Fe dimeric hydrogenases appeared immunologically distinct: specific interactions occurred only when antibodies to the 60- and 30-kilodalton subunits reacted with the 60- and 30-kilodalton-subunit antigens. The interspecies cross-reactions suggested that at least one conserved protein region exists among the large subunits of these enzymes, whereas the small subunits are less conserved. Antibodies to the Fe-only bidirectional hydrogenase of Clostridium pasteurianum reacted with the Desulfovibrio vulgaris bidirectional hydrogenase. Surprisingly, antibodies to the clostridial uptake hydrogenase did not react with any of the Fe-only bidirectional hydrogenases but did react with several of the Ni-Fe dimeric hydrogenases. The two hydrogenases from C. pasteurianum were found to be quite different immunologically. The possible relationship of these findings to the structure and catalytic functions of hydrogenase are discussed.
EMFi-Based Ultrasonic Sensory Array for 3D Localization of Reflectors Using Positioning Algorithms

This paper describes a first prototype of an airborne ultrasonic array that combines pulse-compression techniques with positioning algorithms in order to achieve accurate determination of the position of the reflectors placed in front of the array. The new sensory system is based on an array with four independently controlled emitters and a receiver. The emitters are made of ferroelectrets as active material, leveraging their features to produce broadband air-coupled ultrasonic transducers at low cost. The ultrasonic emissions are encoded with an orthogonal Kasami sequence for each transducer, making possible to transmit simultaneously from each one. Furthermore, one of the main novelties of the proposal is that reflectors are located by means of a spherical trilateration algorithm that uses the time-of-flight of the ultrasonic signals from each transmitter to the receiver, bounced back by the reflector.
A noninvasive computerized tail-cuff system for measuring blood pressure in mice.

We have validated a noninvasive computerized tail-cuff system for measuring blood pressure in mice. The system was designed to perform all functions automatically, including a programmable routine of cuff inflation and deflation, analysis and assignment of pulse rate and blood pressure, and recording of data electronically. To evaluate this system over a range of blood pressures, we gave groups of mice enalapril or NG-nitro-L-arginine methyl ester in their drinking water. For each of these groups, an equal number of control mice were given nothing in their drinking water. Tail-cuff blood pressures were recorded as the means of blood pressures determined on at least 3 days after at least 7 days of training. Tail-cuff enalapril and control group means were measured both 3 and 4 months after enalapril (or no drug) was begun; the group means at 3 months were not significantly different from the group means at 4 months. These results demonstrate that the system gives reproducible results. After the tail-cuff measurements were completed, intra-arterial blood pressures were attempted in all mice under unrestrained, unanesthetized conditions, and individual mouse (n = 22) blood pressures with the use of the two methods were compared. The blood pressures from individual mice by tail-cuff and intra-arterial methods were highly correlated (r = .86, P < .01). The means for the four mouse groups were also highly correlated (r = .98, P < .02). (ABSTRACT TRUNCATED AT 250 WORDS)
The Human Reduced Folate Carrier Gene Is Regulated by the AP2 and Sp1 Transcription Factor Families and a Functional 61-Base Pair Polymorphism*

Recently, our laboratory reported an intricate regulation of the human reduced folate carrier (hRFC) gene, involving multiple promoters and noncoding exons. We localized promoter activity to a 452-bp GC-rich region upstream of noncoding exon A, including a 47-bp basal promoter with a CRE/AP-1-like consensus element that bound the bZip family of DNA-binding proteins (e.g.CREB-1 and c-Jun). We now report that three nearly identical tandem repeats (49–61 bp) in the hRFC-A upstream region are involved in regulating promoter activity. By in vitro binding assays, multiple transcription factors (e.g. AP2 and Sp1/Sp3) bound this region. When AP2 was cotransfected with the hRFC-A reporter construct into HT1080 cells, promoter activity increased 3-fold. In Drosophila SL2 cells, Sp1 transactivated promoter A and showed synergism with CREB-1. However, c-Jun was antagonistic to the effects of Sp1. A sequence variant in the hRFC-A repeated region was identified, involving an exact duplication of a 61-bp sequence. This variant had an allelic frequency of 78% in 72 genomic DNAs and resulted in a 63% increase in promoter activity. These results identify important regions in the hRFC-A promoter and critical roles for AP2 and Sp1, in combination with the bZip transcription factors. Moreover, they document a functionally novel polymorphism that increases promoter activity and may contribute to interpatient variations in hRFC expression and effects on tissue folate homeostasis and antitumor response to antifolates.
Hardware implementation of compressive sensing for image compression

Compressive sensing (CS) is one of the effective data compression methods where a small number of measurements of a sparse signal is required to have an exact recovery. In Compressive sensing technique, the data is acquired and compressed at the same time. CS concept allows capturing only fewer sparse and compressible signal which contains only useful information that helps to recover a proper signal. In this paper, image compression is performed with compressive sensing concept. The different basis matrices and sensing matrices are considered which satisfy the Restricted Isometric Property (RIP) and Independent and Identically Distributed (IID). The hardware implementation of CS is covered to have real-time compression for various image-based applications. The performance is observed regarding SNR, compression ratio, and correlation. The reconstruction algorithms are implemented on MATLAB platform. The obtained results show satisfactory performance for CS based image compression.
Pluggable Application Server Framework

Building a system based on variants of disparate individual components/programs is usually a challenging task. The components/programs are not designed to communicate with each other but the whole system construction does require a seamless collaboration among them. In this paper, targeting at protein structure prediction, a pluggable application server framework is presented. The framework is capable of combining various existing programs into an efficient unit and the design is devoted to provide a model which is able to integrate heterogeneous components/programs into the system quickly without modifying their codes. Based on the model, different components can be plugged into the system with easy configuration, which would lead to a self-configurable and adaptive system. A protein structure prediction server implementation was developed by applying the design model and the real implementation emphasizes the efficiency and simplicity of the system construction. The method and model are generic and can be applied to other system design as well
Hard photon production and matrix-element parton-shower merging

We present a Monte Carlo approach to prompt-photon production, where photons and QCD partons are treated democratically. The photon fragmentation function is modeled by an interleaved $\mathrm{QCD}+\mathrm{QED}$ parton shower. This known technique is improved by including higher-order real-emission matrix elements. To this end, we extend a recently proposed algorithm for merging matrix elements and truncated parton showers. We exemplify the quality of the Monte Carlo predictions by comparing them to measurements of the photon fragmentation function at LEP and to measurements of prompt photon and diphoton production from the Tevatron experiments.
Fault isolation filter with linear matrix inequality solution to optimal decoupling

In this paper we consider a model-based fault detection and isolation problem for linear time-invariant dynamic systems subject to faults and disturbances. We use an observer scheme that cancels the system dynamics and defines a residual vector signal that is sensitive only to faults and disturbances. We then design a stable fault isolation filter such that the Hinfin-norm of the transfer matrix function from disturbances to the residual is minimized (for fault detection) subject to the constraint that the transfer matrix function from faults to residual is equal to a pre-assigned diagonal transfer matrix (for fault isolation). The optimization of disturbance decoupling is accomplished via the help of linear matrix inequalities. A numerical example is also presented to illustrate the algorithm
Measurements of total and regional body composition in preschool children: A comparison of MRI, DXA, and anthropometric data

There are clear sex differences in the distribution of visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT) in adults, with males having more VAT and less SAT than females. This study assessed whether these differences between the sexes were already present in preschool children. It also evaluated which measures of body composition were most appropriate for assessing abdominal obesity in this age group.
Evaluating the effort expended to understand speech in noise using a dual-task paradigm: the effects of providing visual speech cues.

PURPOSE Using a dual-task paradigm, 2 experiments (Experiments 1 and 2) were conducted to assess differences in the amount of listening effort expended to understand speech in noise in audiovisual (AV) and audio-only (A-only) modalities. Experiment 1 had equivalent noise levels in both modalities, and Experiment 2 equated speech recognition performance levels by increasing the noise in the AV versus A-only modality. METHOD Sixty adults were randomly assigned to Experiment 1 or Experiment 2. Participants performed speech and tactile recognition tasks separately (single task) and concurrently (dual task). The speech tasks were performed in both modalities. Accuracy and reaction time data were collected as well as ratings of perceived accuracy and effort. RESULTS In Experiment 1, the AV modality speech recognition was rated as less effortful, and accuracy scores were higher than A only. In Experiment 2, reaction times were slower, tactile task performance was poorer, and listening effort increased, in the AV versus the A-only modality. CONCLUSIONS At equivalent noise levels, speech recognition performance was enhanced and subjectively less effortful in the AV than A-only modality. At equivalent accuracy levels, the dual-task performance decrements (for both tasks) suggest that the noisier AV modality was more effortful than the A-only modality.
17β-estradiol signaling and regulation of Sertoli cell function

In this review, we will present an overview of estrogen actions in the testis from immature and adult animals, with special emphasis on signaling mechanisms involved in the 17β-estradiol regulation of Sertoli cell function from in immature rats. 17β-estradiol activates Sertoli cell proliferation in immature rats by a mechanism that involves the translocation of the estrogen receptors ESR1 and ESR2 to the plasma membrane, phosphorylation of epidermal growth factor receptor and activation of mitogen-activated protein kinase 3/1. Activation of the G protein-coupled estrogen receptor (GPER) also induces phosphorylation of mitogen-activated protein kinase 3/1 via epidermal growth factor receptor transactivation, which in turn increases expression of the antiapoptotic protein BCL2 and decreases the expression of proapoptotic protein BAX, indicating an antiapoptotic role of E2-GPER in immature rat Sertoli cells. In conclusion, ESRs and GPER can mediate rapid 17β-estradiol signaling in Sertoli cells, and modulate transcriptional events important for Sertoli cell function and maintenance of normal testis development and homeostasis. Our findings are important to clarify the role of estrogen in a critical period of testicular development and to direct further studies, which may contribute to better understand the causes of male infertility.
Specific localization of the annexin II heterotetramer in brain lipid raft fractions and its changes in spatial learning

Annexin‐II (AII) is a Ca2+‐dependent phospholipid‐binding protein that is present in both intracellular and extracellular compartments. In the present study AII immunoreactivity was found in a subpopulation of neurons in specific brain regions, including the cerebral cortex and the surface of hippocampal pyramidal neurons from adult rats. AII from synaptic membranes was detected by immunoblotting as multiple species containing the monomer (AII36) and heterotetramer (AIIt). AIIt was resistant to β‐mercaptoethanol and dithiothreitol in sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but was completely reduced to monomers (36 kDa) by two‐dimensional electrophoresis. AIIt resided exclusively in the detergent‐resistant lipid rafts concentrated in neuronal dendrites, and its recruitment to those structures was enhanced by antibody cross‐link. AII abundantly distributed on the outer leaflet of neuronal membranes and between spaces of neurons appeared to be neuronal adhesive. The formation of AIIt required synthesis of sphingolipids and cholesterol, and its stability depended on Ca2+. Increases in neuronal activities such as depolarization and learning were shown to promote formation of AIIt. Our results suggest that, via a dynamic association with dendritic lipid rafts, AII may play a role in synaptic signal transduction and remodeling. This probably involves focal adhesion and interactions with actin that are associated with brain development and memory consolidation.
Improved quantitative PCR protocols for adenovirus and CMV with an internal inhibition control system and automated nucleic acid isolation

With the establishment of routine virus load (DNAemia) screening for Human adenovirus (HAdV) and Cytomegalovirus (CMV) in post‐transplant care quality standards for quantitative PCR‐assays are increasing. Established real‐time PCR assays were improved with a fully automated DNA‐extraction and with a competitive internal control DNA packaged into a lambda phage which serves as an extraction and amplification control in each sample. HAdV and CMV DNA were detected and quantified simultaneously in various types of diagnostic samples like blood, feces or respiratory tract materials. Inhibition was observed in 0.33–0.66% of over 14,000 diagnostic samples, an infrequent but nevertheless not negligible event, which is observed mainly in stool samples. CMV viral load in broncho‐alveolar lavage fluid (BALF) ranged between positive but below the quantitation limit of 1,000 copies/ml up to 1.8 × 107 copies/ml with a median of 6.0 × 103 copies/ml. Forty‐one (4.7%) BALF samples had a viral load above 5.0 × 105 copies/ml, which was proposed as a threshold for the diagnosis of pneumonia. HAdV viral loads ranged between positive but below the quantitation limit of 1,000 copies/ml to a very high concentration of 1.3 × 1011 copies/ml in stool and BALF samples. A HAdV‐DNAemia of >104 copies/ml was found only in patients with stool viral load of above 105 copies/ml. These data support the hypothesis that quantitation in diagnostic materials other than blood may give valuable diagnostic information and that further evaluation of this approach is reasonable. J. Med. Virol. 84:890–896, 2012. © 2012 Wiley Periodicals, Inc.
Quantitative 1HMRS and MRI Volumetry Indicate Neuronal Damage in the Hippocampus of Children with Focal Epilepsy and Infrequent Seizures

Summary: Purpose: Seizures induce progressive morphologic and functional changes in particular in the hippocampus, but whether and at what stage the hippocampus is affected in children with focal, temporal, nonintractable epilepsy is poorly known. We have now studied eventual metabolic and volume changes in the hippocampus of children with nonsymptomatic focal epilepsy taking antiepileptic medication (AEDs) but still having infrequent seizures.
Hardware/software cooperative caching for hybrid DRAM/NVM memory architectures

Non-Volatile Memory (NVM) has recently emerged for its nonvolatility, high density and energy efficiency. Hybrid memory systems composed of DRAM and NVM have the best of both worlds, because NVM can offer larger capacity and have near-zero standby power consumption while DRAM provides higher performance. Many studies have advocated to use DRAM as a cache to NVM. However, it is still an open problem on how to manage the DRAM cache effectively and efficiently. In this paper, we propose a novel Hardware/Software Cooperative Caching (HSCC) mechanism that organizes NVM and DRAM in a flat address space while logically supporting a cache/memory hierarchy. HSCC maintains the NVM- to-DRAM address mapping and tracks the access counts of NVM pages through a moderate extension to page tables and TLBs. It significantly simplifies the hardware design and offers several optimization opportunities for cache management in software layers. We thus propose utility-based cache filtering policies to improve the efficiency of DRAM cache. Experimental results show that HSCC improves system performance by up to 9.6X (77.2% on average) and reduces energy consumption by 34.3% on average, compared to a hardware-assisted DRAM/NVM memory system. HSCC also presents 15.4% and 14.5% performance improvement against a flat- addressable memory architecture and a Row Buffer Locality Aware (RBLA) caching policy for hybrid memories, respectively.
Nurses aged over 50 years and their experiences of shift work.

AIM The Late Career Nurse project examined views and characteristics of nurses working in New Zealand who were born before 1960. This paper focuses on the experiences of such nurses who undertake shift work. BACKGROUND The mean age of registered nurses in New Zealand has been rising steadily, and 40% are now aged 50 years or over. While there is substantial literature on the phenomenon and consequences of the ageing nursing workforce, little is known of the particular experiences of nurses aged over 50 years who work shifts. METHOD An anonymous online survey was emailed to eligible nurse New Zealand Nurses Organisation members aged over 50 years in February 2012. Quantitative and qualitative analyses of the 3273 responses received were undertaken. RESULT Over 45% of respondents worked shifts or flexible hours. While shift work suited many, others noted deleterious effects on family and social relationships, physical and mental health (notably sleep patterns and fatigue), and decreasing tolerance for shift work as they age. Poor scheduling practices were particularly detrimental. CONCLUSION AND IMPLICATIONS FOR NURSING MANAGEMENT Worldwide, workforce ageing means strategies are required to retain older nurses in the workforce. Improved scheduling practices including increasing access to flexible and part time work hours, and development of resources on coping with shift work are recommended.