Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA‐mediated specificity of DNA packaging into hybrid lambda/phi 29 proheads.

A small RNA (pRNA, 174 nt) is known to be essential for DNA packaging in bacteriophage phi 29. However, in an in vitro DNA packaging system based on hybrid lambda/phi 29 proheads (made up of head proteins from phage lambda and connectors from phage phi 29), the specificity of DNA packaging is lost, and different RNA molecules fulfil the requirements for DNA packaging, albeit with less efficiency than phi 29 pRNA. Competition assays with RNAs from different sources have shown that phi 29 connectors bind preferentially pRNA. An increase in the efficiency of phi 29 DNA packaging into hybrid proheads induced by phi 29 pRNA is observed because, when phi 29 pRNA is incubated with hybrid proheads, phi 29 DNA is packaged more efficiently than other DNAs of similar length. Furthermore, when hybrid proheads carrying phi 29 pRNA are incubated with a mixture of DNAs from different sources, phi 29 DNA is selectively packaged, thus indicating that phi 29 pRNA determines the specificity of DNA packaging.
Flexible and Reconfigurable Time-Domain Demultiplexing of Optical Signals at 160 Gb/s

We present experimental results showing reconfigurable switching of four 40-Gb/s tributary channels in a 160-Gb/s data signal using Fourier-domain temporal pulse shaping and all-optical processing. Arbitrary combinations of multiple tributary channels are switched out of a high-speed data-modulated signal. The performance is characterized using a fast optical sampling oscilloscope and bit-error-rate measurements.
A collaborative study of genetic linkage of bipolar manic‐depressive illness and red/green colorblindness : A PROJECT OF THE BIOLOGICAL PSYCHIATRY COLLABORATIVE PROGRAM OF THE WORLD HEALTH ORGANIZATION

A study of linkage of bipolar manic‐depressive illness to the protan/deutan colorblindness region of the X‐chromosome was performed on 16 informative families, in a WHO collaborative study (eight families from Brussels, six from Bethesda, one each from Basel and Copenhagen). Overall, the series did not support close linkage, but is possibly suggestive of loose linkage. but is possibly suggestive of loose linkage. The possibility of genetic heterogeneity of bipolar manic‐depressive illness, with one form linked to colorblindness, is considered.
Mantle transition zone discontinuities beneath the Indochina Peninsula: Implications for slab subduction and mantle upwelling

While the northward indentation of the Indian into Eurasian plates has been intensively investigated, its oblique subduction beneath the Indochina Peninsula (ICP) and the role it played on mantle structure and dynamics remain enigmatic. In this first regional‐scale receiver function study of the mantle transition zone (MTZ) discontinuities beneath the ICP and its surrounding areas, we stack ∼12,000 receiver functions recorded at 33 stations using a non–plane wave common‐conversion‐point stacking technique. Systematic spatial variations of MTZ thickness with departures between −21 and +24 km from the globally averaged value are revealed, providing independent evidence for the presence of slab segments in the MTZ beneath the central and a slab window beneath the western ICP. The results also support the existence of broad mantle upwelling adjacent to the eastern edge of the slab segments, which might be responsible for the widespread Cenozoic volcanisms and pervasively observed upper mantle low velocities in the area.
The Changing Landscape in the Treatment of Metastatic Castration-Resistant Prostate Cancer: Where are we in 2017?

At the June 26, 2000 Human Genome Announcement Speech at the White House, President Clinton praised the completion of the initial working draft sequence of the entire 3.2-Gb haploid human genome, stating: “It will revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases. ” The announcement was universally hailed as a historic achievement for some hopes for galloping advances in the diagnosis and treatment of genetic disease. Two years later in April 2003, the Human Genome Project (HGP) was officially declared finished. The finished human genome map was published in
Age of Islet Autoantibody Appearance and Mean Levels of Insulin, but Not GAD or IA-2 Autoantibodies, Predict Age of Diagnosis of Type 1 Diabetes

OBJECTIVE We evaluated predictors of progression to diabetes in children with high-risk HLA genotypes and persistent islet autoantibodies. RESEARCH DESIGN AND METHODS The Diabetes Autoimmunity Study in the Young (DAISY) followed 2,542 children with autoantibodies measured to GAD, IA-2, and insulin. RESULTS Persistent islet autoantibodies developed in 169 subjects, and 55 of those progressed to diabetes. Children expressing three autoantibodies showed a linear progression to diabetes with 74% cumulative incidence by the 10-year follow-up compared with 70% with two antibodies and 15% with one antibody (P < 0.0001). Both age of appearance of first autoantibody and insulin autoantibody (IAA) levels, but not GAD or IA-2 autoantibodies, were major determinants of the age of diabetes diagnosis (r = 0.79, P < 0.0001). CONCLUSIONS In the DAISY cohort, 89% of children who progressed to diabetes expressed two or more autoantibodies. Age of diagnosis of diabetes is strongly correlated with age of appearance of first autoantibody and IAA levels.
Models for improved tractability and accuracy in dependency parsing

Automatic syntactic analysis of natural language is one of the fundamental problems in natural language processing. Dependency parses (directed trees in which edges represent the syntactic relationships between the words in a sentence) have been found to be particularly useful for machine translation, question answering, and other practical applications. For English dependency parsing, we show that models and features compatible with how conjunctions are represented in treebanks yield a parser with state-of-the-art overall accuracy and substantial improvements in the accuracy of conjunctions. For languages other than English, dependency parsing has often been formulated as either searching over trees without any crossing dependencies (projective trees) or searching over all directed spanning trees. The former sacrifices the ability to produce many natural language structures; the latter is NP-hard in the presence of features with scopes over siblings or grandparents in the tree. This thesis explores alternative ways to simultaneously produce crossing dependencies in the output and use models that parametrize over multiple edges. Gap inheritance is introduced in this thesis and quantifies the nesting of subtrees over intervals. The thesis provides O( n6) and O(n 5) edge-factored parsing algorithms for two new classes of trees based on this property, and extends the latter to include grandparent factors. This thesis then defines 1-Endpoint-Crossing trees, in which for any edge that is crossed, all other edges that cross that edge share an endpoint. This property covers 95.8% or more of dependency parses across a variety of languages. A crossing-sensitive factorization introduced in this thesis generalizes a commonly used third-order factorization (capable of scoring triples of edges simultaneously). This thesis provides exact dynamic programming algorithms that find the optimal 1-Endpoint-Crossing tree under either an edge-factored model or this crossing-sensitive third-order model in O(n 4) time, orders of magnitude faster than other mildly non-projective parsing algorithms and identical to the parsing time for projective trees under the third-order model. The implemented parser is significantly more accurate than the third-order projective parser under many experimental settings and significantly less accurate on none.
One-dimensional I test and direction vector I test with array references by induction variable

In this paper, theoretical aspects to demonstrate the accuracy of the Interval Test (the I test and the direction vector I test) to be applied for resolving the problem stated above is presented. Also, it is proved from the proposed theoretical aspects that under a specific direction vector there are integer-valued solutions for one-dimensional arrays with subscripts formed by induction variable and under other specific direction vectors there are no integer-valued solutions. Experiments with benchmarks, cited from Parallel loop, Vector loop and TRFD (Perfect benchmark), reveal that our framework can properly enhance the precision of data dependence analysis for one-dimensional arrays with subscripts mentioned above.
Algebra and Query Language for A Historical Data Model

We propose a «state» oriented view of historical databases. We propose an algebra for historical relations which contains classical as well as some new operators. The operators are simple to comprehend, unlike in other research proposals. Were are also able to formulate a completeness criteria for the proposed model. Finally, we extend the popular SQL query language for use with historical databases. Again, the extensions are consistent with the simple basis of standard SQL
AMPA and Kainate Receptors Each Mediate Excitotoxicity in Oligodendroglial Cultures

Recent studies indicate that oligodendrocytes are vulnerable to excitotoxic insults mediated by glutamate receptors. The present study was carried out to characterize the type of glutamate receptors triggering cell death in optic nerve oligodendrocyte cultures. Acute activation of either AMPA or kainate receptors was toxic to oligodendrocytes, an effect that was prevented by CNQX. However, exposure to agonists of the NMDA and metabotropic glutamate receptors did not impair cell viability. Dose-response curves showed that toxicity was mediated by three distinct populations of receptors: an AMPA-type receptor and high- and low-affinity kainate-type receptors. Expression and immunocytochemical studies suggested that the glutamate receptor subunits give rise to the native receptors in each population. In all instances, Ca(2+) entry was a major determinant of glutamate receptor excitotoxicity. However, its influence varied for each receptor subtype. These results indicate that aberrantly enhanced activation of AMPA and/or kainate receptors may be involved in demyelinating diseases.
Transition between virtual environment and workstation environment with projective head mounted display

The construction of virtual worlds often requires the user to use various tools in different environments to create several types of elements which have geometrical properties and behavioral characteristics. Due to the inconveniences associated with this task, a compound environment for the task of constructing virtual worlds was proposed. This environment contains both the popular workstation as well as a surrounding virtual world. To realize this compound environment, a Projective Head Mounted Display (PHMD) prototype was developed, which effectively minimized the difficulty of going and coming between workstation and virtual environments. The PHMD was also able to address the problem that is common to traditional HMDs which involve false images. The concept and development behind the PHMD and the compound environment are discussed, and the prototype PHMD and the prototype application examples are constructed.
An Integrated Lean-Methods Approach to Hospital Facilities Redesign

Abstract Lean production methods for eliminating waste and improving processes in manufacturing are now being applied in healthcare. As the author shows, the methods are appropriate for redesigning hospital facilities. When used in an integrated manner and employing teams of mostly clinicians, the methods produce facility designs that are custom-fit to patient needs and caregiver work processes, and reduce operational costs. The author reviews lean methods and an approach for integrating them in the redesign of hospital facilities. A case example of the redesign of an emergency department shows the feasibility and benefits of the approach.
Association between blood lactate levels, Sequential Organ Failure Assessment subscores, and 28-day mortality during early and late intensive care unit stay: A retrospective observational study*

Objectives:To evaluate whether the level and duration of increased blood lactate levels are associated with daily Sequential Organ Failure Assessment (SOFA) scores and organ subscores and to evaluate these associations during the early and late phases of the intensive care unit stay. Design:Retrospective observational study. Setting:Mixed intensive care unit of a university hospital. Patients:134 heterogeneous intensive care unit patients. Interventions:None. Measurements and Main Results:We calculated the area under the lactate curve above 2.0 mmol/L (lactateAUC>2). Daily SOFA scores were collected during the first 28 days of intensive care unit stay to calculate initial (day 1), maximal, total and mean scores. Daily lactateAUC>2 values were related to both daily SOFA scores and organ subscores using mixed-model analysis of variance. This was also done separately during the early (<2.75 days) and late (>2.75 days) phase of the intensive care unit stay. Compared with normolactatemic patients (n = 78), all median SOFA variables were higher in patients with hyperlactatemia (n = 56) (initial SOFA: 9 [interquartile range 4–12] vs. 4 [2–7]; maximal SOFA: 10 [5–13] vs. 5 [2–9]; total SOFA: 28 [10–70] vs. 9 [3–41]; mean SOFA: 7 [4–10] vs. 4 [2–6], all p < .001). The overall relationship between daily lactateAUC>2 and daily SOFA was an increase of 0.62 SOFA-points per 1 day·mmol/L of lactateAUC>2 (95% confidence interval, 0.41–0.81, p < .00001). During early intensive care unit stay, the relationship between lactateAUC>2 and SOFA was 1.01 (95% confidence interval, 0.53–1.50, p < .0005), and during late intensive care unit stay, this was reduced to 0.50 (95% confidence interval, 0.28–0.72, p < .0005). Respiratory (0.30, 0.22–0.38, p < .001) and coagulation (0.13, 0.09–0.18, p < .001) subscores were most strongly associated with lactateAUC>2. Conclusions:Blood lactate levels were strongly related to SOFA scores. This relationship was stronger during the early phase of intensive care unit stay, which provides additional indirect support for early resuscitation to prevent organ failure. The results confirm that hyperlactatemia can be considered as a warning signal for organ failure.
Benzoate-Coenzyme A Ligase from Thauera aromatica: an Enzyme Acting in Anaerobic and Aerobic Pathways

ABSTRACT In the denitrifying member of the β-ProteobacteriaThauera aromatica, the anaerobic metabolism of aromatic acids such as benzoate or 2-aminobenzoate is initiated by the formation of the coenzyme A (CoA) thioester, benzoyl-CoA and 2-aminobenzoyl-CoA, respectively. Both aromatic substrates were transformed to the acyl-CoA intermediate by a single CoA ligase (AMP forming) that preferentially acted on benzoate. This benzoate-CoA ligase was purified and characterized as a 57-kDa monomeric protein. Based on Vmax/Km, the specificity constant for 2-aminobenzoate was 15 times lower than that for benzoate; this may be the reason for the slower growth on 2-aminobenzoate. The benzoate-CoA ligase gene was cloned and sequenced and was found not to be part of the gene cluster encoding the general benzoyl-CoA pathway of anaerobic aromatic metabolism. Rather, it was located in a cluster of genes coding for a novel aerobic benzoate oxidation pathway. In line with this finding, the same CoA ligase was induced during aerobic growth with benzoate. A deletion mutant not only was unable to grow anaerobically on benzoate or 2-aminobenzoate, but also aerobic growth on benzoate was affected. This suggests that benzoate induces a single benzoate-CoA ligase. The product of benzoate activation, benzoyl-CoA, then acts as inducer of separate anaerobic or aerobic pathways of benzoyl-CoA, depending on whether oxygen is lacking or present.
An evaluation of fruit and vegetable consumption and cigarette smoking among youth.

INTRODUCTION Research across the past 4 decades has supported a cross-sectional association between adult cigarette smoking and lower fruit and vegetable consumption (FVC), and emerging research suggests higher FVC may predict cessation. Among youth, findings are limited to a few cross-sectional studies with somewhat mixed results. Here we evaluated the FVC-smoking association among youth both cross-sectionally and longitudinally. METHODS We analyzed data from a subsample of the National Longitudinal Survey of Youth 1979: Child and Young Adult. The subsample included adolescents aged 14-18 years at baseline in the year 2004. Multivariable cross-sectional analyses assessed whether baseline FVC was associated with smoking frequency among ever-smokers (n = 578). Longitudinally, the study assessed whether baseline FVC predicted smoking progression among baseline never-smokers who tried a cigarette by 4-year follow-up (n = 388). Multivariable regression models adjusted for age, gender, race/ethnicity, parental education, and health behavior orientation. RESULTS Cross-sectionally, youth who consumed fruit ≥2 times per day were 53% less likely (RR = 0.47; p < .05) than those who typically did not consume fruit to be in a higher smoking frequency category. Longitudinally, the fruit consumption and smoking association was not significant (RR = 0.61; p = .282). There were no significant associations observed between vegetable consumption and smoking. CONCLUSIONS Fruit consumption, but not vegetable consumption, was inversely associated with smoking frequency cross-sectionally but not longitudinally. Further research is needed to provide information on the consistency of the FVC-smoking relationship among youth and may help to elucidate possible explanatory mechanisms.
Kuru: Forty Years Later, A Historical Note

Introduction Kuru (6), the first neurodegenerative human disease caused by infectious amyloids (also known as slow unconventional viruses (14, 15) or "prions") was first reported to Western medicine in 1957 by Gajdusek and Zigas (23, 24, 25, 27). The elucidation of Kuru opened a new field in human medicine and initiated more than a quarter of century of research which contributed enormously to our understanding of neurodegenerative disorders of the central nervous system. Kuru in the Fore language means to shiver or to shake from fever and cold (1, 13, 18). The Fore used the noun of the Kuru-verb to describe the always fatal plague which affected their children and adult women, rarely men (2, 3, 5, 17, 21, 26, 34). It has been and s t i l l is restricted to natives of the Fore linguistic group at Papua New Guinea's Eastern Highlands (Fig. 1) and those neighboring linguistic groups which intermarry with Fore people (Auiana, Awa, Usurufa, Kanite, Keiagana, late, Kamano, Kimi). Neighboring groups into which Kuru -affected villages did not settle through marriage or adoption, such as Anga (Kukukuku), and remote Iagaria, Kamano and Auiana people were not affected. Kuru first appeared at the turn of this century in Uwami village of Keiagana people and spread from there to the Awande in the North Fore where the Uwami had social contacts through marriage and adoption. Within 20 years it had spread further into the Kasokana and Miarasa villages of North Fore and a decade later, about 30 years before Kuru investigation started, it had reached the South Fore at the Wanikanto and Kamira villages. Kuru became endemic in all villages that it entered and became hyperendemic in the South Fore region.
Multifunctional optical MEMS sensor platform for wireless optical sensor networks

This paper reports a multifunctional optical sensor platform based on the microelectromechanical systems (MEMS) technology with the aim to miniaturize conventional bulky optical measurement systems for space-constrained applications and harsh environment. Small discrete optical components are integrated onto a printed circuit board by using optical fibers as the waveguide. Low-coherence interferometry is used for modulation and retrieval of the sensing signal. The whole optical system including the related circuit takes up a footprint of 2.2″ × 1.5″. To test the functionality, a fiber-tip pressure sensor is interrogated using this platform. The successful demonstration suggests that this platform can be used for optical measurement in the sensor node of Wireless Sensor Networks (WSNs).
Variations of heart rate variability parameters prior to the onset of ventricular tachyarrhythmia and sinus tachycardia in ICD patients. Results from the heart rate variability analysis with automated ICDs (HAWAI) registry

The HAWAI registry evaluated the role of heart rate variability in predicting the occurrence of ventricular tachycardia and fibrillation (VT/VF) and sinus tachycardia in patients with an implantable cardioverter-defibrillator (45 patients with 155 RR recordings). A significant decrease of the mean value of all RR intervals (MeanNN) was observed in the period starting 20 and 40 min prior to VT/VF and sinus tachycardia, respectively. The standard deviation of RR intervals (SDNN) and the power at low frequency (LF) were the only parameters with significant changes prior to VT/VF. For sinus tachycardia, the root mean square of successive differences of all successive RR intervals (r-MSSD) and the power at low and high frequency (HF) decreased, whereas SDNN and the power at very low frequency increased. Comparison of RR recordings preceding VT/VF and sinus tachycardia revealed significant differences of the MeanNN, SDNN, r-MSSD, LF and HF. Based on a classification and regression tree analysis, MeanNN, SDNN and r-MSSD showed a sensitivity of 94.4% and a specificity of 50.6% as predictors of VT/VF. Our results suggest that the temporal changes in heart rate before an arrhythmic event can be used to predict the occurrence of VT/VF. These parameters may be used to optimize pacing therapies designed to prevent VT/VF recurrences as well as for improving device-based discriminators for VT/VF and sinus tachycardia.
Zinc nutriture in the elderly in relation to taste acuity, immune response, and wound healing.

A comprehensive review is presented concerning the role of zinc (Zn) nutrition in taste acuity, immunity and wound recovery in the elderly. Specific attention is given to Zn in foods, Zn bioavailability, evidence of Zn deficiency, and the need for Zn in immune function. It was concluded that the mean daily Zn intake in groups of US elderly ranges from 7-13 mg. Dietary Zn intake appears to be related to energy intake. An apparently adequate Zn intake can be achieved for $1.50-2.00/day with careful food selection; hence, people spending below $1.50/day for food have limited ability to satisfy dietary Zn requirements. Further Zn bioavailability should be considered in the food selection process. Evidence suggests that some elderly individuals have a deficient Zn nutriture, but available data are insufficient to ascertain the frequency of this deficiency. Most instances of hypogensia in the elderly, however, are unrelated to Zn nutriture. Deficient Zn nutriture seems to contribute to poor healing in the elderly, but, again, the data are too few to ascertain frequency. Self-treatment with Zn greater than the RDA may be unwise. (wz)