cssi/SciSciGPT-SciSciNet huggingface dataset:
Mining Gene Expression Profiles with Biological Prior Knowledge

One of the important goals in the post-genomic era is to identify the functions of genes, either individually or as group. Recently, there has been an increasing use of the Gene Ontology (GO) to analyze a list of genes identified via various statistical and/or computational methods. The main assumption behind using GO for interpreting microarray data is that the genes that belong to similar molecular functions or biological processes would display similarly tightly regulated expression patterns. Current methods utilize GO after the statistical analysis of gene expression data. In this paper, we describe a method that utilizes both gene expression values and biological knowledge simultaneously to identify the significant biological functions. The method is different from other methods in that it incorporates GO as prior knowledge into the mining of gene expression data. The method has been applied to the gene expression profiles to cell cycle experiments.
Controlling the Behaviors of Biodegradable/Bioabsorbable Polymers with Cyclodextrins

The cyclic six, seven, and eight-membered oligosaccharides α-, β-, and γ-cyclodextrins (CDs) can serve as hosts for a variety of polymer guests to form crystalline inclusion compounds (ICs), wherein the guest polymers are included in the continuous narrow channels (0.5-1.0 nm in diameter) formed by the host CD stacks. Polymers included as guests in CD-ICs are highly extended and segregated from neighboring chains by the walls of the host CD bracelets. As a consequence, when polymer-CD-ICs are treated with solvents for CDs that are non-solvents for the included polymers or with amylase enzymes, the CDs are removed and the guest polymers are coalesced into bulk samples whose structures, morphologies, and even chain conformations are different from those achieved by consolidation from their randomly coiling, entangled solutions and melts. Often these CD-IC coalesced and consequently reorganized polymer samples exhibit properties that are distinct from their normally processed bulk samples. Here we describe the CD-IC processing of several biodegradable/bioabsorbable homopolymers, copolymers, and blends made from poly (L-lactic acid), poly (e-caprolactone), and poly (β-hydroxybutyrate)s, with special emphasis placed on their improved and controllable properties. For example, the phase segregation and consequent crystallinities of their normally incompatible homopolymer blends and their block copolymers may be controlled and thus improved. In addition, co-inclusion of small molecule guests, such as drugs or anti-bacterials, in their common CD-ICs, and subsequent coalescence, yields well-mixed blends of these biodegradable/bioabsorbable polymers and the small molecule co-guests, which may lead, for example, to the improved delivery of drugs.
Assessing and improving the health-related quality of life of patients with ESRD

Impairment of the health-related quality of life (HRQOL) of patients with end-stage renal disease (ESRD) is now well documented. These impairments involve a wide variety of domains and can be assessed using an array of well-validated instruments. Incorporation of at least some of these instruments into routine patient care is important in order to measure the physical and psychological impact of a disease and its treatment on the HRQOL of patients. How this implementation can be achieved in a practical way is, however, a challenge. As more research focuses on improving the HRQOL of patients with ESRD, the systematic evaluation of HRQOL and incorporation into patient care is becoming increasingly important. Whether strategies to improve the HRQOL of patients will translate into improved patient outcomes--as evidenced by reduced mortality and hospitalizations--and lower costs, remains to be determined.
How important is echocardiography for risk stratification in follow-up of patients with chronic kidney disease?

Focusing largely on end-stage renal disease, this Viewpoint outlines some echocardiographic indices of left ventricular function, and examines their prognostic value in chronic kidney disease. Recommendations are provided for optimal indexing of estimates of left ventricular mass to body size in this population. The role of echocardiography as an outcome measure in interventional studies and in the longitudinal monitoring of cardiac risk are also briefly considered.
A dynamical systems approach based on averaging to model the macroscopic flow of freeway traffic

Abstract The flow of traffic exhibits distinct characteristics under different conditions, reflecting the congestion during peak hours and relatively free motion during off-peak hours. This requires one to use different mathematical equations to describe the diverse traffic characteristics. Thus, the flow of traffic is best described by a hybrid system, namely different governing equations for the different regimes of response, and it is such a hybrid approach that is investigated in this paper. Existing models for the flow of traffic treat traffic as a continuum or employ techniques similar to those used in the kinetic theory of gases, neither of these approaches gainfully exploit the hybrid nature of the problem. Spurious two-way propagation of disturbances that are physically unacceptable are predicted by continuum models for the flow of traffic. The number of vehicles in a typical section of the highway does not justify its being modeled as a continuum. It is also important to recognize that the basic premises of kinetic theory are not appropriate for the flow of traffic (see [S. Darbha, K.R. Rajagopal, Limit of a collection of dynamical systems: an application to modeling the flow of traffic, Mathematical Models and Methods in Applied Sciences 12 (10) (2002) 1381–1399] for a rationale for the same). A model for the flow of traffic that does not treat traffic as a continuum or use notions from kinetic theory is developed here and corroborated with real-time data collected on US 183 in Austin, Texas. Predictions based on the hybrid system model seem to agree reasonably well with the data collected on US 183.
Navigating EU Law and the Law of International Arbitration

The European Union and international arbitration are two robust legal regimes that have managed to develop largely in accordance with their own respective ‘first principles’, and they have accordingly thrived. This article initially explains why that has been the case. But the era of parallelism between the regimes has ended, and rather suddenly. This article identifies the two principal fronts on which tensions between EU law and international arbitration law have emerged. Interestingly, both commercial and investment arbitration are implicated. A first front entails a conflict between the European Court of Justice's (ECJ's) expansive notions of EU public policy and two well-established axioms of international commercial arbitration law: first, that public policy must be construed narrowly when invoked as a ground for annulling an award or denying it recognition and enforcement; and second, that parties in arbitration are expected to raise all substantive arguments pertinent to their claims or defences in the course of the arbitral proceedings and not reserve them for post-award relief from a disappointing award. A second front finds EU Member States invoking their obligations under EU law as a defence – sometimes jurisdictional, sometimes substantive – in investor-State tribunals. The paradigm argument is that EU law mandates withdrawal of an illegal state aid in reliance on which an investor entered that market. This article examines two prevailing methodologies for addressing these tensions, in arbitral tribunals themselves as well as in reviewing courts. It concludes that many such tensions – particularly those along the first front – may be resolved through accommodation techniques well-established in other areas of the law. Others, particularly those arising in the investor-State context, resist resolution in that way and are requiring decision-makers to face the uncomfortable prospect of making one of these legal regimes cede ground to the other. The ECJ and investor-State tribunals are understandably inclined to prioritise the regimes differently, with the ultimate outcome falling to member state courts which owe allegiance to both regimes.
Antioxidant activity of α-tocopherol and Trolox in different lipid substrates : Bulk oils vs oil-in-water emulsions

This study was aimed at evaluating the antioxidant effectiveness of α-tocopherol and its water-soluble analogue, Trolox, in different lipid systems. The oxidative stability of lipids in bulk and emulsion systems at 37 °C decreased in the order corn oil triglycerides > methyl linoleate > linoleic acid. In both bulk and emulsified linoleic acid, Trolox was a better inhibitor of hydroperoxide formation and decomposition than α-tocopherol. However, in bulk methyl linoleate and corn oil triglycerides, although Trolox was a better inhibitor of hydroperoxide formation, in emulsions, α-tocopherol was a better inhibitor of both the formation and decomposition of hydroperoxides. In emulsified methyl linoleate and corn oil, the partition coefficients of Trolox between lipids and water at high concentrations were not affected by Tween 20, and the antioxidant activity of Trolox decreased because it partitioned into the water phase and Tween 20 micelles. In contrast, in linoleic acid emulsified with Tween 20, the forma...
Enterohepatic circulation of tetracycline in rats.

Abstract The absorption of tetracycline hydrochloride excreted in the bile of rats was evaluated using the in situ intestinal preparation. For comparative purposes, the absorption of the drug from an aqueous solution having the same pH as that of the bile was also determined. After 4 hr, the amounts of tetracycline absorbed from the bile and aqueous solutions were 72.92 and 77.34%, respectively. There was no significant difference in the amount of drug accumulated in the gut tissue. The disappearance of the drug from the intestinal lumen was biexponential, and the kinetic parameters appeared to be similar. It was concluded that tetracycline excreted in the bile is readily absorbed from the rat intestine. Accordingly, biliary excretion does not seem to account for a significant elimination of this antibiotic from the body.
Seasonal periodicity of the saprolegniaceae in the south-eastern United States

The Saprolegniaceae of the south-eastern United States can be divided into two species groups with regard to seasonal periodicity of occurrence and variation in abundance. One group, composed of species characterized by centric and subcentric oospores, exhibits a marked seasonal periodicity, whereas the second group, consisting of species forming eccentric oospores, shows no discernible periodicity pattern. Comparison of these findings with those reported by various workers in other parts of the world indicates that these relationships between periodicity and oospore type may be universal. Observations made in south Georgia and north Florida suggest that temperature is a major environmental factor determining the periodicity patterns of the Saprolegniaceae in these areas. However, no definite conclusions may be drawn from the information available. Speculations as to the general geographical distribution of the Saprolegniaceae in the northern hemisphere are presented, based on an interpretation of previous studies in the light of the findings reported from south Georgia. It appears that species forming centric and subcentric oospores (regardless of their generic affinity) comprise the major portion of water mould populations in northern areas, becoming less common as one moves south. In contrast, species forming eccentric oospores seem to be the major water mould constituents in southern areas, becoming less abundant to the north. The paucity of occurrence and distribution information in the tropics makes it impossible to test this premise adequately.
The 5′-flanking region of the mouse muscle nicotinic acetylcholine receptor β subunit gene promotes expression in cultured muscle cells and is activated by MRF4, myogenin and myoD

Abstract The expression of the nicotinic acetylcholine receptor (AChR) in vertebrate striated muscle is regulated both during development by nerve-evoked muscle activity and by local factors released or associated with the nerve ending. The expression pattern of AChR is achieved by coordinate regulation of four embryonic subunit mRNAs, alpha, beta, gamma and delta. We have taken the approach of identifying the similarities and differences among cis-acting regulatory elements of AChR genes to gain a better understanding of these mechanisms. Thus, to begin to define DNA sequences necessary for the transcriptional regulation of the mouse beta AChR gene, we have analyzed its 5'-flanking region. Primer extension and RNAase protection analyses showed that transcription initiates at one major and two minor sites, all of which are close to the translational initiation site. Using plasmids in which segments of the 5'-flanking region were linked to the bacterial chloramphenicol acetyltransferase (CAT) gene, we have demonstrated that 150 bp of the 5'-flanking region is active in C2 myotubes but not C2 myoblasts or NIH3T3 fibroblasts. This region contains a putative binding site for myoD, and when linked to CAT was transactivated by the muscle regulatory factors myoD, myogenin, and MRF4. Thus, a 150 bp sequence of the beta-subunit gene contains information necessary for developmental specificity and responsiveness to myogenic factors.
The Changing Occupational Structure of Large Metropolitan Areas: Implications for the High School Educated

: This article examines employment trends in broad occupational categories during the 1986 to 1999 period for a group of 50 large United States metropolitan areas. After describing the secular trends, I estimate a cross-sectional model to quantify the effects of local industry mix and labor-saving technology on the occupational employment distribution in these urban areas. Despite quite heterogeneous occupational employment distributions among the 50 MSAs, I find a strikingly uniform decline in the share of mid-skilled administrative support and precision production, craft and repair occupations appropriate for high school graduates and growth in the share of high-skilled managerial and professional occupations, suggesting skill and wage polarization. The regression analysis indicates that the share of mid-skilled employment in large metropolitan areas is positively associated with the output shares of the durable manufacturing and finance, insurance and real estate (FIRE) industries and negatively associated with the introduction of labor-saving technologies in these industries. I conclude by reviewing local policy initiatives that may improve labor market outcomes for high school graduates.
Caffeine contractures in denervated frog muscle

Caffeine contracture tension, effect of caffeine on the resting membrane potential, and caffeine influx in normal and denervated frog sartorius muscle have been investigated. Peak caffeine contracture tension is increased after denervation at all caffeine concentrations. The percentage increases in tension are highest for lower caffeine concentrations. The caffeine concentration required for half maximum tension is decreased from about 3.6 mM in control muscles to 2.6 mM in denervated muscles. Caffeine at 3.5 mM produces a depolarization of about 6 mV in control muscles and 16 mV in denervated muscles. The large contracture tensions observed in denervated muscles are not due to the greater depolarization produced by the drug in denervated muscles since innervated muscles depolarized to the same level by external K+ do not enhance caffeine contracture tension. Both control and denervated muscles are highly permeable to caffeine. The increases in sarcoplasmic reticulum development (Moscatello et al. 1965) and calcium content (Picken and Kirby 1976) promoted by denervation may explain the larger tension elicited by caffeine in denervated muscles.
Challenges to Doing Sexual Violence Work

Sexual assault victims experience a number of effects as a result of their victimization. Sexual assault crisis workers are assigned the responsibility of trying to minimize the negative consequences of sexual assault. In their efforts to serve sexual assault victims, it is likely that certain problems make it difficult to adequately help victims. This study considers how 43 sexual assault crisis workers (27 directors of sexual assault crisis centers and 16 workers) define the challenges of serving sexual assault victims. Major challenges reported included a lack of awareness about sexual assault, victim blaming, and a lack of resources. Implications are provided.
Static timing analysis using backward signal propagation

In this paper, we address the problem of signal pruning in static timing analysis (STA). Traditionally, signals are propagated through the circuit and are pruned, such that only the signal with the latest arrival time at each node is propagated forward. This sig-nal pruning is a key to the linear run time of STA. However, it was previously observed that a signal with the latest arrival time may not be the most critical signal, as an earlier signal with a larger transition time can result in a longer delay in the down-stream logic. Hence, arrival time based pruning can result in an optimistic delay, incorrect critical paths, and discontinuities of the delay dur-ing circuit optimization. Although algorithms were proposed to remedy this issue, they rely on propagation of multiple signals and have an exponential worst-case complexity. In this paper, we pro-pose a new timing analysis algorithm, which uses a two pass tra-versal of the circuit. In the initial backward traversal, we construct delay tables which record the required time at a node as a function of the transition time at that node. This is followed by a forward traversal where signals are pruned not based on arrival times but based on slack. The proposed algorithm corrects the accuracy problems of the arrival time based pruning while at the same time maintaining the linear run time of STA. We implemented our algo-rithm and demonstrated its accuracy and efficiency.
Pattern synthesis for arbitrary arrays using an adaptive array method

This paper presents a new pattern synthesis algorithm for arbitrary arrays based on adaptive array theory. With this algorithm, the designer can efficiently control both mainlobe shaping and sidelobe levels. The element weights optimize a weighted L/sub 2/ norm between desired and achieved patterns. The values of the weighting function in the L/sub 2/ norm, interpreted as imaginary jammers as in Olen and Compton's (1990) method, are iterated to minimize exceedance of the desired sidelobe levels and minimize the absolute difference between desired and achieved mainlobe patterns. The sidelobe control can be achieved by iteration only on sidelobe peaks. In comparison to Olen and Compton's method, the new algorithm provides a great improvement in mainlobe shaping control. Example simulations, including both nonuniform linear and planar arrays, are shown to illustrate the effectiveness of this algorithm.
Fracture testing of a self-healing polymer composite

Inspired by biological systems in which damage triggers an autonomic healing response, a polymer composite material that can heal itself when cracked has been developed. In this paper we summarize the self-healing concept for polymeric composite materials and we investigate fracture mechanics issues consequential to the development and optimization of this new class of material. The self-healing material under investigation is an epoxy matrix composite, which incorporates a microencapsulated healing agent that is released upon crack intrusion. Polymerization of the healing agent is triggered by contact with an embedded catalyst. The effects of size and concentration of the catalyst and microcapsules on fracture toughness and healing efficiency are investigated. In all cases, the addition of microcapsules significantly toughens the neat epoxy. Once healed, the self-healing polymer exhibits the ability to recover as much as 90 percent of its virgin fracture toughness.
Optical and electrical characterization of natural and synthetic melanin

The optical properties of natural and synthetic melanin have been characterized for a number of laser wavelengths in the visible region. Natural melanin was prepared from hydrolyzed melanosomes isolated from normal, bovine retinal pigment epithelium. The inverse adding doubling method based on the diffusion approximation and radiative transport theory was employed to determine the absorption, scattering, and scattering anisotropy coefficients of melanin from the measurements of diffuse transmission, diffuse reflection and collimated transmission using double integrating spheres. The results obtained by the use of the inverse adding doubling method were compared to the Monte Carlo simulation technique. Characterization of melanin is now being extended to include electrical photoconductivity of melanin thin films on a semiconductor substrate.
Discrete-time MRAC schemes using sensor uncertainty compensation with application to artificial pancreas

In this paper, model reference adaptive control (MRAC) schemes are developed for discrete-time plants in the presence of sensor uncertainties. Two adaptive schemes are proposed for both known and unknown plant dynamics to account for parametrizable sensor uncertainties when reliable output measurements are not available for feedback. As an illustrative example, a simulation study is carried out for adaptive control of an artificial pancreas dynamic model with glucose sensor uncertainties, for desired blood glucose regulation.
The Influence of Initial Bipedal Stance Width on the Clinical Measurement of Unipedal Balance Time

Objective To determine the effect of varying initial bipedal stance width (ISW) on the clinical measurement of unipedal balance time (UBT). Design Observational, cross-sectional study. Setting Academic physiatric outpatient facility. Subjects Thirty-one clinic subjects with neuromuscular and/or musculoskeletal conditions known to influence mobility and 30 similarly-aged healthy subjects. Methods Demographic and clinical information were recorded. UBT was determined under 3 distinct conditions by varying bipedal intermalleolar distance: (1) ISW of 0.3 body height; (2) ISW of 0.05 body height; and (3) ISW of 0 body height. The last was accomplished by subjects assuming unipedal balance while using the hands on a horizontal surface for stabilization. Subjects lifted the contralateral foot (or hands in the case of 0 body height condition) in response to a cadenced command to minimize variation in rate of weight transfer. Main Outcome Measure UBT under each of the 3 ISW conditions. Results Mean UBT increased with decreasing ISW, and the differences were significant when comparing each ISW with the next smaller. Healthy subjects demonstrated greater UBT than clinic subjects at each ISW, but the magnitude of these group differences were similar across ISW condition. A UBT >10 seconds in the 0.3 body height ISW was the best discriminator between clinic and healthy subjects. Conclusion Because UBT varies with ISW, standardization of ISW is necessary for accurate within-subject, and between-subject, comparisons in UBT. Healthy subjects were best differentiated from clinic subjects by UBT >10 seconds in the 0.3 body height ISW condition.
Compliant Coatings: A Decade of Progress

This brief article reviews the important developments in the field of compliant coatings that took place in the past ten years. During this period progress in theoretical and computational methods somewhat outpaced that in experimental efforts. There is no doubt that compliant coatings can be designed to delay transition and to suppress noise on marine vehicles as well as other practical hydrodynamic devices. Transition Reynolds numbers that exceed by an order of magnitude those on rigid-surface boundary layers can be achieved. There is renewed evidence of favorable interactions of compliant coatings even for air flows and even for turbulent boundary layers, but more research is needed to confirm these latest results.
Monocularly deprived cats: binocular tests of cortical cells reveal functional connections from the deprived eye

Animals that are deprived of vision in one eye during a vulnerable phase of development lose visual function of the eye. Although this phenomenon has been studied extensively, little is known about the mechanism of disconnection of the deprived eye from visual cortex. One fundamental question is whether input remains from that eye. We have examined the hypothesis that there is functional input from a deprived eye to visual cortex that cannot be observed with standard alternate tests of each eye. We have employed a robust visual stimulation procedure in which large sinusoidal gratings are presented to each eye, as well as to both eyes together, at varying relative phases or retinal disparities. Monocular and binocular stimulation was used to test kittens unilaterally deprived for brief, intermediate, or long periods. A fourth group of kittens was studied as normal controls. Standard methods were used to record from single cells in the striate cortex. After initial qualitative exploration of receptive fields, all testing and analysis were quantitative. As expected, monocular tests revealed that, for most cells, the deprived eye was ineffective, i.e., did not activate the unit. This effect was increasingly pronounced as the length of deprivation was increased. However, binocular tests revealed that a large fraction of these cells (30-40%) was clearly influenced by and therefore functionally connected to the deprived eye. This interaction was phase-selective, or suppressive and not selective for phase. There was no indication that the connections that remained were of a specific type, i.e., excitatory or inhibitory. Therefore, excitation and inhibition appear equally resistant to the effects of monocular deprivation. However, with long-term deprivation, we find minimal evidence of functional input from the deprived eye. We conclude that the effects of monocular deprivation occur over a considerably longer time period than was previously thought.
Quasi-static behavior of MOS devices in the freeze-out regime

The quasi-static CV curves (low-frequency C-V curves) measured in the freeze-out regime of MOS transistors result in peaks near the accumulation or inversion regions depending on the direction of the voltage sweep. In this paper, we report a study of these peaks in n- and p-channel CMOS transistors within and outside compensating wells. The peaks in the quasi-static CV curves are attributed to the capture of minority carriers near inversion by the interface states and the capture of majority carriers by the interface states near accumulation. >
A high resolution sigma-delta modulator with extended dynamic range

The authors introduce a third-order cascaded sigma-delta modulator that uses a modified cascaded architecture and reduced gain in the first integrator to increase the dynamic range. An experimental modulator fabricated in a 1-/spl mu/m CMOS technology attains 17-bit performance for a 25-kHz signal bandwidth using a single 5-V supply. With an oversampling ratio of 128 and a clock frequency of 6.4 MHz, the modulator achieves a 104-dB dynamic range and a peak signal-to-noise plus distortion ratio (SNDR) of 98 dB.
Reliability research on micro- and nano-electromechanical systems: a review

Research on micro/nano-electro-mechanical system (MEMS/NEMS) reliability is of crucial importance, due to the fact that we are facing an era in which MEMS and emerging NEMS are expected to have a major impact on our lives. Over the last decade, significant efforts have gone into the reliability study of MEMS/NEMS. Failure roots in micro- and nano-scales can be addressed by mechanical, electrical, chemical, thermal factors, or combinations of them, which can occur during different manufacturing and post-manufacturing phases. This paper reviews and integrates the reliability issues of MEMS and NEMS in different phases of their life cycles including design, manufacturing, logistics, and operation. This paper surveys the common failure modes and mechanisms (i.e., wear, degradation, adhesion, stiction, deformation, packaging, contamination, and electrical failure modes), the reliability aspects of design and manufacturing, as well as reliability evaluation and testing techniques for MEMS/NEMS. An extensive collection of papers were selected and integrated to cover various studies in this area, in order to provide an intuition and insight for researchers who are interested in reliability research of MEMS/NEMS. Systematic literature search shows the lack of research in system-level and probabilistic reliability analysis for MEMS/NEMS.
Trust and relational capital

Trust can be viewed at the same time as an instrument both for an agent selecting the right partners in order to achieve its own goals, and for an agent of being selected from other potential partners in order to establish with them a cooperation/collaboration and to take advantage from the accumulated trust. In this paper we will analyze trust as the agents' relational capital. Starting from the classical dependence network with potential partners, we introduce the analysis of what it means for an agent to be trusted and how this condition could be strategically used from it for achieving its own goals, that is, why it represents a form of power. The idea of taking another agent's point of view is especially important if we consider the amount of studies in social science that connect trust with social capital related issues. Although there is a big interest in literature about `social capital' and its powerful effects on the wellbeing of both societies and individuals, often it is not clear enough what is it the object under analysis. Individual trust capital (relational capital) and collective trust capital not only should be disentangled, but their relations are quite complicated and even conflicting. To overcome this gap, we propose a study that first attempts to understand what trust is as capital of individuals. In which sense "trust" is a capital. How this capital is built, managed and saved. In particular, how this capital is the result of the others' beliefs and goals. Then we aim to analytically study the cognitive dynamics of this object.
Not to Invade: A Better Strategy?

Tracheostomy ventilation has been the traditional means of respiratory support for patients who need long-term respiratory support or when mask noninvasive ventilation (NIV) is no longer effective. However, in recent years diurnal mouthpiece NIV has been used to avoid tracheostomy.[1][1],[2][2] In
Meaning, God, and prayer: Physical and metaphysical aspects of social support

This paper highlights unique aspects of social support in a religious context, with an emphasis on the practice of prayer. We first discus presuppositions that drive work in the area including (1) adoption of a “medical model” of evaluation and (2) the corollary influence of existential chauvinism. We next outline how religious groups differ from others with respect to the provision of meaning, the position of a deity, and the practice of prayer. Examining the latter facet in detail, we explore possible ways in which prayer is related to physical behaviors (e.g., folding hands, bowing head, closing eyes) that may promote and intensify internal experiences of social support independent of the actual content of the prayer itself.
A comparison of combined p-value methods for gene differential expression using RNA-seq data

Detection of differentially expressed (DE) genes across conditions within RNA-Seq datasets yields insight into the differences in biological processes at work in these conditions. Most methods available for discovering DE genes use statistical methods that model the data based on counting reads that map to individual genes. However, the distribution of reads across different regions of a gene can be heterogeneous. Summarizing reads at the gene level may provide inaccurate results. If genes are broken down into smaller regions, such as exons or even smaller fragments, and DE analysis is performed on those regions, the significance of the overall region can be determined using combined p-values which may improve the accuracy of detecting DE genes. We therefore conducted analysis to consider the performance of widely-used methods for combining p-values using publicly available RNA-Seq data. The combined p-value methods include: Fisher's, Z-transform, Weighted Z-test, Minimum P-value, Logit, and Weighted-sum methods. On liver and kidney data, the Weighted Z-test performs the best, detecting the highest number of truly DE genes. The effect of weights assigned in the Weighted Z-test enables this approach to outperform Fisher's method. On the MAQC datasets, our analysis indicates these methods perform similarly with a slight edge to the Weighted Z-test and Fisher's method in detecting true DE genes. However, the Weighted-sum clearly performs best in detecting true non-DE genes. Furthermore, these methods appear to have an inverse relationship in their performance in detecting DE genes versus non-DE genes in the MAQC datasets. These results indicate issues in properly combining high and low p-values, which may be due to a lack of independence between tests. Thus, a modified Fisher's method may provide more accurate results in these circumstances.
Attenuation of activity-induced increases in cerebellar blood flow in mice lacking neuronal nitric oxide synthase

We used mice deficient in neuronal nitric oxide (NO) synthase (nNOS) to specifically investigate the role of neuronal NO in the increase of cerebellar blood flow (BFcrb) produced by neural activati...
Parallel protein secondary structure prediction schemes using Pthread and OpenMP over hyper-threading technology

Protein secondary structure prediction has a fundamental influence on today's bioinformatics research. In this work, tertiary classifiers for the protein secondary structure prediction are implemented on Denoeux Belief Neural Network (DBNN) architecture. Hydrophobicity matrix, orthogonal matrix, BLOSUM62 matrix and PSSM matrix are experimented separately as the encoding schemes for DBNN. Hydrophobicity matrix, BLOSUM62 matrix and PSSM matrix are applied to DBNN architecture for the first time. The experimental results contribute to the design of new encoding schemes. Our accuracy of the tertiary classifier with PSSM encoding scheme reaches 72.01%, which is almost 10% better than the previous results obtained in 2003. Due to the time consuming task of training the neural networks, Pthread and OpenMP are employed to parallelize DBNN in the Hyper-Threading enabled Intel architecture. Speedup for 16 Pthreads is 4.9 and speedup for 16 OpenMP threads is 4 in the 4 processors shared memory architecture. Both speedup performance of OpenMP and Pthread is superior to that of other research. With the new parallel training algorithm, thousands of amino acids can be processed in reasonable amount of time. Our research also shows that Hyper-Threading technology for Intel architecture is efficient for parallel biological algorithms.
A UV Resonance Raman Study of Hairpin Dimer Helices of d(A-G)10 at Neutral pH Containing Intercalated dA Residues and Alternating dG Tetrads

The structure of the oligonucleotide d(A-G)10 in 0.6 M Na+, pH 7.0 has been investigated with UV resonance Raman (UVRR) spectroscopy. Variable wavelength excitation was used to distinguish the spectral contributions of dG and dA residues. Both classes of residues show UVRR hyperchromism with increasing temperature, reflecting unstacking of the bases. The dG residues melt relatively cooperatively with a Tm of approximately 42 degrees C. Unstacking is non-cooperative for the dA residues, increasing linearly between 4 and 80 degrees C. G-tetrads at low temperature are indicated by UVRR frequency shifts of modes associated with C6=O and C2-NH2 of the dG residues, and of vibrations involving N7, all sites of H-bonding. However, there are no indications of interbase H-bonds for the dA residues, showing they do not form H-bonded tetrads. Most of the bases are oriented anti about the glycosyl bond, but at 4 degrees C a fraction of the residues are syn. These results, together with the findings by Shiber et al. [Shiber,M.C., Braswell,E.H., Klump,H. and Fresco,J.R. (1996) Nucleic Acids Res. 24, 5004-5012] that d(A-G)10 under comparable conditions has the molecular weight of a dimer, support a model in which two hairpins interact to form a helical structure with G-tetrads and intercalated dA residues.
Exponential smoothing in the telecommunications data

Abstract Exponential smoothing methods gave poor forecast accuracy in Fildes et al.'s study of telecommunications time series. We reexamine this study and show that the accuracy of the Holt and damped trend methods can be improved by trimming the time series to eliminate irrelevant early data, fitting the methods to minimize the MAD rather than the MSE, and optimizing the parameters. Contrary to Fildes et al., we show that the damped trend is more accurate than Holt's method. Because most of the telecommunications series display steady trends, we test the Theta method of forecasting and a closely related method, simple exponential smoothing with drift. The Theta method proves disappointing, but simple exponential smoothing with drift is the best smoothing method for this data, giving about the same accuracy as the robust trend.
Health status and resources of rural homeless women and children

The purpose of this research is to describe the health status and health resources for homeless women and children in a Midwestern rural community. A group of 31 rural homeless women in a shelter participated in the study by answering questions on the Rural Homeless Interview developed by the investigators. The findings revealed higher than expected rates of illness, accidents, and adverse life events, with the incidence of substance abuse and mental illness being comparable to data from other homeless populations. The data on children were limited by lack of knowledge on the part of their mothers. Some mothers reported that their children were in foster care, had been adopted, or were being cared for by others. The inability to access health and dental care was reported by half of the participants.
Magainin-like immunoreactivity in human submandibular and labial salivary glands.:

Magainins, antimicrobial peptides secreted by granular glands of frog skin, may be related to the high resistance to infections of this epithelial surface. The oral mucosa of healthy individuals is another tissue in which infection is not frequent, probably owing to the activity of potent salivary and mucosal defense mechanisms. To investigate if magainin-like factors are a component of these oral defense mechanisms, human and animal minor (mucosal) and major salivary glands were examined by immunohistochemistry, using a polyclonal rabbit anti-magainin antibody. Cryostat sections of (para) formaldehyde-fixed tissues were incubated with the antibody and then stained with fluorescein-complexed anti-rabbit IgG. Specific staining was observed in the apical portion of the cytoplasm of ductal epithelial cells of human submandibular and labial salivary glands. Diffuse staining was present in submandibular acinar cells. Bovine, rat, hamster, and mouse tissues were unreactive. The presence of magainin-like substances in human salivary gland duct cells is consistent with reports of the occurrence of other biologically active substances in salivary gland ducts.
Nucleotide sequence of the chromosome 14-encoded S182 cDNA and revised secondary structure prediction

(1995). Nucleotide sequence of the chromosome 14-encoded S182 cDNA and revised secondary structure prediction. Amyloid: Vol. 2, No. 3, pp. 188-190.
Impact of Transforming Growth Factor-β1 on Atrioventricular Node Conduction Modification by Injected Autologous Fibroblasts in the Canine Heart

Background— Atrioventricular (AV) nodal ablation for management of atrial fibrillation (AF) is irreversible and requires permanent pacemaker implantation. We hypothesized that as an alternative, implantation of autologous fibroblasts in the perinodal region would focally modify AV nodal conduction and that this modulation would be enhanced by pretreatment with transforming growth factor-β1 (TGF-β1), a stimulant of fibroblasts. Methods and Results— Skin biopsies were taken from 12 mongrel dogs, and derived fibroblasts were dissociated and grown in culture for 2 weeks. Multiple injections (0.25 mL) were made through an 8F NOGA catheter along the fast/slow AV nodal pathways as guided by an electroanatomic mapping system. Seven dogs received fibroblasts alone (1×106 cells/mL), 7 dogs received TGF-β1 (5 μg), 4 dogs received fibroblasts and TGF-β1 (1×106 cells/mL+5 μg), and 4 dogs received saline only. AV node function was assessed at baseline and after 4 weeks. Saline (80 mL) with assigned therapy (0.25 mL per...
Defensive responses of larval Manduca sexta and their sensitization by noxious stimuli in the laboratory and field

Sensitization of defensive responses following noxious stimulation occurs in diverse species, but no demonstration of nociceptive sensitization in insects has been reported. A set of defensive behavior patterns in larval Manduca sexta is described and shown to undergo sensitization following noxious mechanical stimulation. The striking response is a rapid bending that accurately propels the head towards sharply poking or pinching stimuli applied to most abdominal segments. The strike is accompanied by opening of the mandibles and, sometimes, regurgitation. The strike may function to dislodge small attackers and startle larger predators. When the same stimuli are applied to anterior segments, the head is pulled away in a withdrawal response. Noxious stimuli to anterior or posterior segments can evoke a transient withdrawal (cocking) that precedes a strike towards the source of stimulation and may function to maximize the velocity of the strike. More intense noxious stimuli evoke faster, larger strikes and may also elicit thrashing, which consists of large, cyclic, side-to-side movements that are not directed at any target. These are sometimes also associated with low-amplitude quivering cycles. Striking and thrashing sequences elicited by obvious wounding are sometimes followed by grooming-like behavior. Very young larvae also show locomotor responses to noxious stimuli. Observations in the field of attacks on M. sexta larvae by Cardinalis cardinalis, an avian predator, suggest that thrashing decreases the success of a bird in biting a larva. In the laboratory, noxious stimulation was found to produce two forms of sensitization. Repeated pinching of prolegs produces incremental sensitization, with later pinches evoking more strikes than the first pinch. Brisk pinching or poking of prolegs also produces conventional sensitization, in which weak test stimuli delivered to another site evoke more strikes following noxious stimulation. The degree and duration of sensitization increase with more intense noxious stimulation. The most intense stimulus sequences were found to enhance strike frequency for approximately 60 min. Nociceptive sensitization generalizes to sites distant from sites of noxious stimulation, suggesting that it involves a general, but transient, arousal of defensive responses. http://www.biologists.com/JEB/movies/jeb3271.html
Allometry of human fertility and energy use

The flux of energy and materials constrains all organisms, and allometric relationships between rates of energy consumption and other biological rates are manifest at many levels of biological organization. Although human ecology is unusual in many respects, human populations also face energetic constraints. Here we present a model relating fertility rates to per capita energy consumption rates in contemporary human nations. Fertility declines as energy consumption increases with a scaling exponent of )1 ⁄ 3a s predicted by allometric theory. The decline may be explained by parental trade-offs between the number of children and the energetic investment in each child. We hypothesize that the )1 ⁄ 3 exponent results from the scaling properties of the networked infrastructure that delivers energy to consumers. This allometric analysis of human fertility offers a framework for understanding the demographic transition to smaller family sizes, with implications for human population growth, resource use and sustainability.
Protein kinase D-mediated anterograde membrane trafficking is required for fibroblast motility.

Abstract Background: Locomoting cells exhibit a constant retrograde flow of plasma membrane (PM) proteins from the leading edge lamellipodium backward, which when coupled to substrate adhesion, may drive forward cell movement. However, the intracellular source of these PM components and whether their continuous retrograde flow is required for cell motility is unknown. Results: To test the hypothesis that the anterograde secretion pathway supplies PM components for retrograde flow that are required for lamellipodial activity and cell motility, we specifically inhibited transport of cargo from the trans-Golgi network (TGN) to the PM in Swiss 3T3 fibroblasts and monitored cell motility using time-lapse microscopy. TGN-to-PM trafficking was inhibited with a dominant-negative, kinase-dead (kd) mutant of protein kinase D1 (PKD) that specifically blocks budding of secretory vesicles from the TGN and does not affect other transport pathways. Inhibition of PKD on the TGN inhibited directed cell motility and retrograde flow of surface markers and filamentous actin, while inhibition of PKD elsewhere in the cell neither blocked anterograde membrane transport nor cell motile functions. Exogenous activation of Rac1 in PKD-kd-expressing cells restored lamellipodial dynamics independent of membrane traffic. However, lamellipodial activity was delocalized from a single leading edge, and directed cell motility was not fully recovered. Conclusions: These results indicate that PKD-mediated anterograde membrane traffic from the TGN to the PM is required for fibroblast locomotion and localized Rac1-dependent leading edge activity. We suggest that polarized secretion transmits cargo that directs localized signaling for persistent leading edge activity necessary for directional migration.
Cellular immunity in systemic lupus erythematosus.

Cellular immunity of 16 patients with systemic lupus erythematosus (SLE), as measured by the ability of their lymphocytes to proliferate in vitro following stimulation with mitogens and bacterial antigens, and by the ability of their polymorphonuclear neutrophils to reduce nitrobluetetrazolium dye, both spontaneously and upon stimulation, was found to be unimpaired by comparison with cells of 12 normal individuals. The relative frequency of responders to stimulation with human collagen and with several nuclear antigens, used over a wide range of concentrations and evaluated as a group, was significantly higher among patients with SLE. Antinuclear antibodies specific for DNA, RNA, or both, were found in all patients with SLE, but did not reflect the pattern of sensitization of lymphocytes to these antigens as measured by lymphocyte transformation.