cssi/SciSciGPT-SciSciNet huggingface dataset:
Hardware-Accelerated RNA Secondary-Structure Alignment

The search for homologous RNA molecules---sequences of RNA that might behave simiarly due to similarity in their physical (secondary) structure---is currently a computationally intensive task. Moreover, RNA sequences are populating genome databases at a pace unmatched by gains in standard processor performance. While software tools such as Infernal can efficiently find homologies among RNA families and genome databases of modest size, the continuous advent of new RNA families and the explosive growth in volume of RNA sequences necessitate a faster approach.This work introduces two different architectures for accelerating the task of finding homologous RNA molecules in a genome database. The first architecture takes advantage of the tree-like configuration of the covariance models used to represent the consensus secondary structure of an RNA family and converts it directly into a highly-pipelined processing engine. Results for this architecture show a 24× speedup over Infernal when processing a small RNA model. It is estimated that the architecture could potentially offer several thousands of times speedup over Infernal on larger models, provided that there are sufficient hardware resources available.The second architecture is introduced to address the steep resource requirements of the first architecture. It utilizes a uniform array of processing elements and schedules all of the computations required to scan for an RNA homolog onto those processing elements. The estimated speedup for this architecture over the Infernal software package ranges from just under 20× to over 2,350×.
The atmospheric cycle of methane

The atmospheric distribution of CH 4 is rather uniform zonally and vertically but exhibits a slight gradient with latitude in the troposphere; in the stratosphere it shows a definite decrease with altitude. The average volume mixing ratio in the troposphere is 1.4 ppm which corresponds to a total amount of 4 × 10 15 g of CH 4 present in the atmosphere. Most is of recent biologic origin. C 14 analyses show that no more than 20% is released by fossil sources. The various ecosystems producing CH 4 are discussed and the total annual production is estimated to lie between 5.5 × 10 14 g/yr and 11 × 10 14 g/yr. The corresponding turnover times for atmospheric CH4 range from 4 to 7 yr. The destruction of CH 4 takes place mainly in the troposphere, most probably through the reaction CH 4 + OH ? CH 3 + H 2 O. About 10% of the CH 4 is destroyed in the stratosphere. The CH 4 cycle is strongly coupled to the H 2 and CO cycles and contributes also on the order of 1% to the atmospheric carbon cycle. DOI: 10.1111/j.2153-3490.1974.tb01952.x
A Method for the Isolation of Purine Nucleoside Phosphorylase-Deficient Variants of Mammalian Cell Lines

A method is described for the isolation of purine nucleoside phosphorylase (PNP) deficient lines of both Novikoff hepatoma and CHO cells. This method utilizes the ability of these cell lines to grow on inosine as a carbon and energy source. Using BrdU-light selection, inosine-negative survivors appeared at a frequency of about 10−5 and PNP-deficient cells appeared at a frequency of about 10−6. The PNP-negative cell line isolated from Novikoff hepatoma cells, ino-6, was temperature sensitive for both growth and PNP activity. The low activity seen after growth at 37° was approximately 5% of the wild-type level and had a tenfold increase in the apparent Km for inosine. The extracts of the variant contained a protein that cross-reacted with antiserum made against purified rat liver PNP. This method should be useful for the isolation of PNP-deficient cells in any cell line capable of utilizing inosine for growth.
IgM and IgG antibodies to DNA, RNA, and DNA:RNA in systemic lupus erythematosus.

Abstract Sera from patients with systemic lupus erythematosus were fractionated by sucrose density gradient ultracentrifugation. Individual fractions were assayed for immunoglobulin and for antibody activity to human DNA, to reovirus RNA, and to a DNA:RNA hybrid (deoxythymidylic·riboadenylic acid, dT·rA). Antibodies to dT·rA were distributed in two peaks corresponding to 19S IgM and 7S IgG. Antibodies to DNA were predominantly IgG, whereas antibodies to RNA showed a more variable distribution. IgM antibodies to RNA were quite prominent and in some patients were the only anti-RNA antibodies detected. These results are discussed in relation to genetic and antigenic factors which determine the immunoglobulin class of anti-nucleic acid antibodies.
The effects of tungsten doping on the tin Chevrel-phase compound SnMo6S8

We have studied the effects of doping a Chevrel compound by investigating W x Sn1−x Mo6S8, wherex=0.00-0.20. An unusual peak in the dependence of the superconducting transition temperatureT c on the dopant concentration levelx has been observed. We explain the dependence ofT c onx in terms of the dependence of the electron density of states at the Fermi energy on the charge transferred from the tungsten atom to the Mo6S8 clusters.
A Novel Home Sleep Monitoring Device and Brief Sleep Intervention for Bipolar Disorder: Feasibility, Tolerability, and Preliminary Effectiveness.

Sleep disturbance is common in bipolar disorder and negatively impacts its course of illness. The purpose of this study is to assess the feasibility and tolerability of a novel EKG-based home sleep monitoring device (M1) as well as a brief (two session) psychosocial sleep intervention for individuals with bipolar disorder. The sleep intervention is individually tailored for patients with insomnia or hypersomnia and extends skills designed for non-psychiatric populations as well as includes specific considerations for sleep disturbance in bipolar disorder. We found that both the M1 device and the sleep intervention were feasible and well tolerated. Participants’ sleep duration improved after the brief sleep intervention, but their sleep was more unstable as measured by the M1. Self-reported sleepiness, sleep quality, and mood symptoms improved; however, only some measures reached statistical significance (i.e., duration of sleep, dysfunction due to sleepiness). These data suggest that the M1 device is a feasible means to obtain objective sleep quality and quantity data in individuals with bipolar disorder. A brief sleep intervention may be helpful in improving sleep in a bipolar population at risk for substantial sleep disturbance, but larger, longitudinal studies are warranted.
In vitro evaluation of sugar syrups, antibiotics, and miticides on growth of honey bee pathogen, Ascosphaera apis: Emphasis for chalkbrood prevention is on keeping bees healthy

To examine the link between chalkbrood and treatments applied to honey bee (Apis mellifera) colonies, growth of Ascosphaera apis was determined under chalkbrood-inducing conditions on agar containing crushed bee larvae as a mock infection. Treatments were tested at concentrations in the field, representative of beekeeping practice (at least in the USA). A chilling or warming stress known to heighten chalkbrood caused no growth enhancement of A. apis. Miticides had a negative effect; formic acid killed A. apis and oxalic acid reduced growth by 70 %. High-fructose corn syrups and sucrose syrup undiluted, a 50:50 mixture, alone, and with antibiotics did not alter growth of A. apis. We conclude that chalkbrood does not develop from a temperature- or treatment-induced activation of A. apis. Sugar syrups, miticides, and antibiotics point out other health problems that make bees prone to infection by A. apis. Thus, chalkbrood opportunistically infects bees under other forms of stress.
The past four decades of progress in the knowledge of gout, with an assessment of the present status.

Advances in management of acute gouty arthritis, tophaceous gout and uric acid nephrolithiasis are briefly reviewed. With respect to pathogenesis, specific enzyme abnormalities have been demonstrated in rare monogenic cases but the presumptive polygenic and multifactorial pathogenesis in most cases of primary gout remains uncertain. The hypothesis favored here is that, possibly secondary to altered glutamate catabolism, glutamine apparently is overutilized for urate overproduction by the liver, underutilized for reduced renal ammonia formation. The kidneys, modulating urinary uric acid excretion, sustain the hyperuricemia.
Study of lymphocyte and erythrocyte electrophoretic mobility by laser Doppler spectroscopy.

Abstract Laser Doppler spectroscopy, a technique that permits rapid and precise measurement of the distribution of electrophoretic mobilities in a population of suspended particles, has been applied to blood cells by using suspending medium of low ionic strength made isoosmotic with sucrose. Data on the mobilities of erythrocytes and lymphocytes, and the pH dependencies of these mobilities, appear in good agreement with those determined by classical procedures.
Closure to “Kinematic Wave Model of Urban Pavement Runoff Subject to Traffic Loadings” by Chad M. Cristina and John J. Sansalone

Closure of a discussion of a paper with the aforementioned title and authors, published in this journal (Volume 129, Number 7, July 2003) is presented. The authors agree with the discusser that there are similar formulations concerning rainfall intensity, kinematic wave time of concentration and observed time of concentration that can lead to similar results as those presented in the original paper.
Detection of oncogene mutation from neoplastic colonic cells exfoliated in feces.

Purpose: Best chances of a cure from colorectal cancer are obtained before metastatic spread. Lack of specific tests allowing early diagnosis of the tumor accounts for investigation of gene alterations involved in carcinogenesis by a noninvasive method. In the present study, K-rascodons 12 and 13 mutations were studied in neoplastic cells shed from the bowel into the stool and those contained in the tumor and normal mucosa. Moreover, healthy patients and a few others with precancerous conditions were examined. METHODS: Stool, tumor, and mucosa samples were taken from 25 patients with colorectal adenocarcinoma. Stool and mucosa samples were obtained from 11 healthy patients, and stool, pathologic bowel tissue, and normal mucosa samples were obtained from 3 patients with adenoma (1) or ulcerative colitis (2). Polymerase chain reaction amplification and restriction enzyme analysis were performed. RESULTS: K-rascodon 12 mutations were detected in both tumor and stool samples of 10 cancer patients, and no gene alterations were observed in 14 patients. In one patient with a tumor, a mutation was shown in only the tumor tissue. The agreement rate in tumor and stool analysis was 96 percent. A normal pattern of K-rascodons 12 and 13 was observed in the bowel mucosa. All stool and mucosa samples from healthy patients were not altered in K-ras.Agreement was registered between samples taken from patients with preneoplastic lesions. CONCLUSIONS: These preliminary findings show a high rate of accuracy in the investigation of K-rasalterations in the colorectal cells shed into the feces, suggesting that such an approach could be used to study other gene alterations and, prospectively, to identify early colorectal cancers.
Toward a better understanding of the hierarchical nature of police organizations: Conception and measurement

Abstract The present article proposes a reconceptualization of police organizational hierarchy as a multidimensional construct. This notion of a multidimensional police hierarchy was derived from the sociological literature of stratification and the prior management literature of organizational hierarchy. It is proposed here that police employees are stratified based upon the differential allocation of various resources (such as rewards and formal power) and attributes (such as skills). This differential allocation stratifies employees into five different hierarchies. This article describes these five hierarchies and suggests how they might be measured, at both the individual and comparative/organizational levels. Finally, the possible interrelations among these hierarchies is discussed as well as three management issues concerning this multidimensional conception of police hierarchy.
County-level socioeconomic status and survival after HIV diagnosis, United States.

Purpose To estimate relative survival (RS) after human immunodeficiency virus (HIV) diagnosis, by race/ethnicity and county-level socioeconomic status (SES). Methods We estimated 5-year RS by age, race/ethnicity, transmission category, sex, diagnosis year, CD4 count, and by county-level SES variables from the U.S. Census. Data, from the national HIV/AIDS Reporting System, were for HIV-infected persons ages ≥13 years (diagnosis during 1996–2003 and follow-up through 2005). We calculated RS proportions by using a maximum likelihood algorithm and modeled the relative risk of excess death (RR) using generalized linear models, with poverty as a random effect. Results For men, RS was worse in counties with larger proportions of people living below the 2000 U.S. poverty level (87.7% for poverty of ≥20% vs. 90.1% for poverty of 7.1% vs. 90.5% where unemployment Conclusions RS was worse in lower SES areas. To help address the impact of county-level SES, resources for HIV testing, care, and proven economic interventions should be directed to areas with concentrations of economically disadvantaged people.
Plane-stress crack-tip fields for power-law hardening orthotropic materials

Plane stress mode I near-tip fields in orthotropic materials are examined. Plastic orthotropy is described by Hill's quadratic yield function and the strain hardening behavior is given by an appropriate generalization of a uniaxial tensile power-law stress-strain relation. Pronounced changes in the pattern of the angular variations of crack-tip fields have been observed with the degree of plastic orthotropy and the amount of strain hardening. Possible shapes and sizes of plastic zones (as inferred from effective stress contours) are presented for high- and low-hardening materials and a wide range of plastic orthotropy. The shape of the plastic zone for a particular case of plastic orthotropy agreed remarkably well with the zone of intense straining induced by an appropriately orientated crack within a graphite/epoxy laminate.
Laboratory sand column study of encapsulated buffer release for potential in situ pH control

Abstract Encapsulation technology is being investigated as a method for controlling pH in situ at contaminated groundwater sites where pH may limit remediation of organic contaminants. This study examined the effectiveness of using KH2PO4 buffer encapsulated in a pH-sensitive coating to neutralize pH in laboratory sand columns (1.5-l) under a simulated groundwater flow rate and characterized the pattern of capsule release in the flow-through system. Denitrification was used in the columns to increase the pH of the pore water. Each of three columns was equipped with three miniature mesh wells to allow contact of the buffer with column pore water, but capsules (15 g) were inserted into only one column (amended). The two other columns served as amendment (no buffer) and abiotic (no denitrification) controls. Oxidation–reduction potential, dissolved organic and inorganic carbon, NH4+, NO3−+NO2−, PO43−, and pH were measured in the influent, two side ports, and effluent of the columns over time. Near complete conversion of 80 mg N/l of nitrate and 152 mg/l of ethanol per day resulted in a mean pH increase from 6.2 to 8.2 in the amendment control column. The amended column maintained the target pH of 7.0±0.2 for 4 weeks until the capsules began to be depleted, after which time the pH slowly started to increase. The capsules exhibited pulses of buffer release, and were effectively dissolved after 7.5 weeks of operation. Base-neutralizing capacity contributed by the encapsulated buffer over the entire study period, calculated as cation equivalents, was 120 mM compared to 8 mM without buffer. This study demonstrates the potential for this technology to mediate pH changes and provides the framework for future studies in the laboratory and in the field, in which pH is controlled in order to enhance organic contaminant remediation by pH-sensitive systems.
Bicuculline application affects discharge patterns, rate-intensity functions, and frequency tuning characteristics of bat auditory cortical neurons.

This study examined the effect of bicuculline application on the auditory response properties in the auditory cortex of the big brown bat, Eptesicus fuscus. All auditory cortical neurons studied discharged either 1–2 or 3–7 impulses to 4 ms sound stimuli. Cortical neurons with high best frequencies tended to have high minimum thresholds. Bicuculline application increased the number of impulses and shortened the response latencies of all cortical neurons as well as changing the discharge patterns of half of the cortical neurons studied. Bicuculline application raised the rate–intensity functions but lowered the latency–intensity functions to varying degrees. Threshold–frequency tuning curves (FTCs) were either V-shaped, upper threshold or double-peaked. Threshold–FTCs and impulse–FTCs were mirror-images of each other. Bicuculline application expanded and raised the impulse–FTCs but lowered the threshold–FTCs, resulting in significantly decreased Qn values. Threshold–FTCs of cortical neurons determined within an orthogonally inserted electrode were very similar and expanded FTCs during bicuculline application were also very similar. Possible mechanisms for the contribution of GABAergic inhibition to shaping these response properties of cortical neurons are discussed.
Predatory feeding behavior of a marine copepod, Labidocera trispinosa 1

The behavior of Labidocera feeding on early devclopmcntal stages of five common species of planktonic calanoid copepods was investigated to determine its species-specific impact on a mixed copepod community. Feeding rates on individual prey were not affected by prey density or the availability of alternate prey; threshold feeding behavior was not observed. Capture rates of naupliar prey of all species increase as a function of their size even though larger nauplii appear better able to avoid capture. In general, the ability of Labidocera to capture individuals of a prey species decreases abruptly after the prey develop to the copcpodid stages. As a consequence of the limited susceptibility of copepodid stages to capture by Labidocera and higher feeding rates on larger nauplii, the predatory impact of Lnbidocera is greatest on the largest of the prey species.
Bank reserve adjustment process and the use of reserve carryover as a reserve management tool: A comment

Abstract In an article published in this Journal, Spindt and Tarhan (1984) estimate a weekly model of the reserve adjustment behavior of several large money center banks during 1969–1979. Their study is unique because of its use of micro data, and because most previous studies of bank reserve management do not submit their models to an empirical test. However, Spindt and Tarhan's empirical results provide contradictory evidence on the fit of their model. This paper explains that the empirical results may be due to a constraint that Spindt and Tarhan impose on some of the estimated coefficients of the model rather than the nature of the model itself.
Strong transitivity, rationality and weak monotonicity in fuzzy pairwise comparisons

Strong transitivity and weak monotonicity are two important axioms in the theory of value and utility measurement. In this paper we define strong transitivity and weak monotonicity for fuzzy pairwise comparisons matrices. Using the requirements of strong transitivity, we develop a metric for measuring the degree of strong transitivity in fuzzy pairwise comparisons. We further demonstrate that a matrix which satisfies the metric of strong transitivity will satisfy the weak monotonicity axiom as well.
Outcomes of Open Carpal Tunnel Release at a Minimum of Ten Years

Background: There is little research on the long-term outcomes of open carpal tunnel release. The purpose of this retrospective study was to determine the functional and symptomatic outcomes of patients at a minimum of ten years postoperatively. Methods: Two hundred and eleven patients underwent open carpal tunnel release from 1996 to 2000 performed by the same hand fellowship-trained surgeon. Follow-up with validated self-administered questionnaire instruments was conducted an average of thirteen years after surgery. The principal outcomes included the Levine-Katz symptom and function scores, ranging from 1 point (best) to 5 points (worst), and satisfaction with the results of surgery. The patients self-reported current comorbidities. Results: After a mean follow-up of thirteen years (range, eleven to seventeen years), 92% (194) of 211 patients were located. They included 140 who were still living and fifty-four who had died. Seventy-two percent (113) of the 157 located, surviving patients responded to the questionnaire. The mean Levine-Katz symptom score (and standard deviation) was 1.3 ± 0.5 points, and 13% of patients had a poor symptom score (≥2 points). The mean Levine-Katz function score was 1.6 ± 0.8 points, and 26% had a poor function score (≥2 points). The most common symptom-related complaint was weakness in the hand, followed by diurnal pain, numbness, and tingling. The least common symptoms were nocturnal pain and tenderness at the incision. Eighty-eight percent of the patients were either completely satisfied or very satisfied with the surgery. Seventy-four percent reported their symptoms to be completely resolved. Thirty-three percent of men were classified as having poor function compared with 23% of women. Two (1.8%) of 113 patients underwent repeat surgery. Conclusions: At an average of thirteen years after open carpal tunnel release, the majority of patients are satisfied and free of symptoms of carpal tunnel syndrome. Level of Evidence: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Moving cheaply: energetics of walking in the african elephant

Large animals have a much better fuel economy than small ones, both when they rest and when they run. At rest, each gram of tissue of the largest land animal, the African elephant, consumes metabolic energy at 1/20 the rate of a mouse; using existing allometric relationships, we calculate that it should be able to carry 1 g of its tissue (or a load) for 1 km at 1/40 the cost for a mouse. These relationships between energetics and size are so consistent that they have been characterized as biological laws. The elephant has massive legs and lumbers along awkwardly, suggesting that it might expend more energy to move about than other animals. We find, however, that its energetic cost of locomotion is predicted remarkably well by the allometric relationships and is the lowest recorded for any living land animal.
BEN: a novel domain in chromatin factors and DNA viral proteins.

We report a previously uncharacterized α-helical module, the BEN domain, in diverse animal proteins such as BANP/SMAR1, NAC1 and the Drosophila mod(mdg4) isoform C, in the chordopoxvirus virosomal protein E5R and in several proteins of polydnaviruses. Contextual analysis suggests that the BEN domain mediates protein-DNA and protein-protein interactions during chromatin organization and transcription. The presence of BEN domains in a poxviral early virosomal protein and in polydnaviral proteins also suggests a possible role for them in organization of viral DNA during replication or transcription.
Correction of the geomagnetically-induced image motion problem on the Hubble Space Telescope's Faint Object Spectrograph

During the Science Verification phase of the Hubble Space Telescope mission, it was determined that the Faint Object Spectrograph's (FOS) Red detector displayed significant image motions which correlated with orbital changes in the geomagnetic field. The Blue detector exhibited similar but less pronounced motions. The cause of this motion was determined to be inadequate magnetic shielding of the instrument's Digicon detectors. The results of these motions were decreases in onboard target acquisition accuracy, spectral resolution, and photometric accuracy. The Space Telescope Science Institute and the FOS Investigation Definition Team, set about correcting this Geomagnetically-induced Image Motion Problem (GIMP) through a real-time on-board correction scheme. This correction required modifications to almost all aspects of the HST ground system as well as additional NSSC1 flight software and the use of an existing software 'hook' in the FOS microprocessor firmware. This paper presents a detailed description of the problem, the proposed solution, and results of on-orbit testing of the correction mechanism.
Comparison of subject-reported allergy versus skin test results in a common cold trial.

BackgroundFew studies have examined the relationship between subject-reported allergy and results of allergy skin testing in large unselected or unbiased cohorts. The objective of this study was to...
Recognition of Histopathologic Patterns of Diffuse Malignant Mesothelioma in Differential Diagnosis of Pleural Biopsies

Abstract Context.—Diffuse malignant mesothelioma is generally divided into 3 basic histologic types—epithelial, biphasic, or sarcomatous. However, a great diversity of histologic patterns exists within these 3 basic histologic types. Design.—The diverse histologic patterns of diffuse malignant mesothelioma are briefly described, including infrequently encountered patterns. Results. The histologic patterns of diffuse malignant mesothelioma provide a wide variation of features for the pathologist to consider in the differential diagnosis of a pleural biopsy. Conclusion.—Pathologists should be aware of the varied histologic patterns of diffuse malignant mesothelioma when evaluating pleural biopsies.
Rotational invariance and the Pauli exclusion principle

In this article, the rotational invariance of entangled quantum states is investigated as a possible cause of the Pauli exclusion principle. First, it is shown that a certain class of rotationally invariant states can only occur in pairs. This will be referred to as the coupling principle. This in turn suggests a natural classification of quantum systems into those containing coupled states and those that do not. Surprisingly, it would seem that Fermi-Dirac statistics follows as a consequence of this coupling while the Bose-Einstein follows by breaking it. Finally, the experimental evidence to justify the above classification will be discussed. Pacs: this http URL, 5.30 d, this http URL
Developing good scientific publishing practices: one pharmaceutical company's perspective.

The scientific publishing practices of the pharmaceutical industry have been heavily criticized in recent years due to the inherent conflict of interest that arises when a pharmaceutical company pu...
Enhanced Chondrogenesis and Wnt Signaling in PTH‐Treated Fractures

Studies have shown that systemic PTH treatment enhanced the rate of bone repair in rodent models. However, the mechanisms through which PTH affects bone repair have not been elucidated. In these studies we show that PTH primarily enhanced the earliest stages of endochondral bone repair by increasing chondrocyte recruitment and rate of differentiation. In coordination with these cellular events, we observed an increased level of canonical Wnt-signaling in PTH-treated bones at multiple time-points across the time- course of fracture repair, supporting the conclusion that PTH responses are at least in part mediated through Wnt signaling. Introduction: Since FDA approval of PTH (PTH(1-34); Forteo) as a treatment for osteoporosis, there has been interest in its use in other musculoskeletal conditions. Fracture repair is one area in which PTH may have a significant clinical impact. Multiple animal studies have shown that systemic PTH treatment of healing fractures increased both callus volume and return of mechanical competence in models of fracture healing. Whereas the potential for PTH has been established, the mechanism(s) by which PTH produces these effects remain elusive. Materials and Methods: Closed femoral fractures were generated in 8-wk-old male C57Bl/6 mice followed by daily systemic injections of either saline (control) or 30 g/kg PTH(1-34) for 14 days after fracture. Bones were harvested at days 2, 3, 5, 7, 10, 14, 21, and 28 after fracture and analyzed at the tissue level by radiography and histomorphometry and at the molecular and biochemical levels level by RNase protection assay (RPA), real-time PCR, and Western blot analysis. Results: Quantitative CT analysis showed that PTH treatment induced a larger callus cross-sectional area, length, and total volume compared with controls. Molecular analysis of the expression of extracellular matrix genes associated with chondrogenesis and osteogenesis showed that PTH treated fractures displayed a 3-fold greater increase in chondrogenesis relative to osteogenesis over the course of the repair process. In addition, chondrocyte hypertrophy occurred earlier in the PTH-treated callus tissues. Analysis of the expression of potential mediators of PTH actions showed that PTH treatment significantly induced the expression of Wnts 4, 5a, 5b, and 10b and increased levels of unphosphorylated, nuclear localized -catenin protein, a central feature of canonical Wnt signaling. Conclusions: These results showed that the PTH-mediated enhancement of fracture repair is primarily asso- ciated with an amplification of chondrocyte recruitment and maturation in the early fracture callus. Associated with these cellular effects, we observed an increase in canonical Wnt signaling supporting the conclusion that PTH effects on bone repair are mediated at least in part through the activation of Wnt-signaling pathways. J Bone Miner Res 2007;22:1903-1912. Published online on August 6, 2007; doi: 10.1359/JBMR.070724
BOLT: Energy-efficient Out-of-Order Latency-Tolerant execution

LT (latency tolerant) execution is an attractive candidate technique for future out-of-order cores. LT defers the forward slices of LLC (last-level cache) misses to a slice buffer and re-executes them when the misses return. An LT core increases ILP without physically scaling the issue queue and register file and increases MLP without additional software threads that can reduce cache performance. Unfortunately, proposed LT designs are not energy efficient. They require too many additional structures and they defer and re-execute too many instructions to justify their performance gains. In this paper, we address these inefficiencies. We introduce a microarchitecture called BOLT (Better Out-of-Order Latency-Tolerance) that implements LT as an alternative use of SMT (Simultaneous Multi-Threading). We also present a new slice buffer organization and traversal scheme that increases performance and reduces overhead by pruning instances of useless and redundant LT. Collectively, these modifications turn out-of-order LT into a technique that improves performance in an energy-efficient way.
A random-permutations-based approach to fast read alignment

Read alignment is a computational bottleneck in some sequencing projects. Most of the existing software packages for read alignment are based on two algorithmic approaches: prefix-trees and hash-tables. We propose a new approach to read alignment using random permutations of strings. We present a prototype implementation and experiments performed with simulated and real reads of human DNA. Our experiments indicate that this permutations-based prototype is several times faster than comparable programs for fast read alignment and that it aligns more reads correctly. This approach may lead to improved speed, sensitivity, and accuracy in read alignment. The algorithm can also be used for specialized alignment applications and it can be extended to other related problems, such as assembly. More information: http://alignment.commons.yale.edu
Clock layout for high-performance ASIC based on weighted center algorithm

A new clock distribution scheme is investigated using weighted center algorithm. The algorithm is based on optimum matching of the closest clock terminals and recursively building a clock tree which connects all the clock terminals. The novel feature of the authors' approach is simultaneous minimizing of the clock skew and the total clock tree wire length, and suitable for any design style. Experimental results on the MCNC industrial benchmarks show that this approach is practical and promising. >
MIMO capacity results for Rician fading channels

The capacity of a multiple antenna system in Rician fading is considered under the assumption that channel state information (CSI) is available only at the receiver and that the transmitter has knowledge of the statistical properties of the fading process though not the instantaneous CSI. Tight upper and lower bounds for the capacity of such a system are derived and a new input signalling scheme that significantly outperforms the existing choices is also proposed. It is shown that by exploiting the knowledge of Rician-ness at the transmitter, a much higher capacity can be achieved for a multiple antenna system in Rician fading. The derived capacity bounds have been evaluated explicitly to provide numerical results in some representative situations.
Conducting a Qualitative Culture Study of Pediatric Palliative Care

While conducting a grounded theory study of Chinese American and Mexican American families' experiences in pediatric palliative care, we encountered a number of unanticipated challenges regarding project development, Institutional Review Boards, recruitment, data collection, and data analysis. In this article, we describe our experiences, strategies, and insights for the benefit of other researchers and clinicians in the field.
The Communications/Transportation Tradeoff

Probed is the available evidence on whether the astonishing rapid development of communications technologies in the present centruy has to date, or is likely in the near future to reduce the demand for transportation. The author finds that there certainly appear to be transportation-communication tradeoffs, but that their apparent consequences to date have been profoundly to alter the nature of transportation demand rather than reduce overall volume. It would appear that transportation will remain a central arena of public policy for a good many years to come, but likewise that communications innovations are likely to have continuing najor effects on the evolution of transportation demand patterns.
Effect of Enhanced Dietary Nitrogen on Reproductive Maturation of the Termite Zootermopsis angusticollis (Isoptera: Termopsidae)

We determined the effect of enhanced dietary nitrogen on the ovarian maturation of female primary and neotenic reproductives of the termite Zootermopsis angusticollis Hagen. Supplementing the wood diet of newly paired reproductives with a 0.05% uric acid solution resulted in both primaries and neotenics gaining less body mass. This may have occurred because the increased nitrogen content of their food allowed reproductives to consume less wood to meet their dietary needs, thereby reducing the mass of their gut contents. An abundance of exogenous nitrogen may have also stimulated females to excrete excess uric acid rather than store it, further reducing mass gain. Nitrogen supplementation resulted in significant increases in ovariole number and fecundity for neotenic females but not primary females. These results suggest that although enhancing dietary nitrogen may release newly molted neotenics from nutritional limitations on their fecundity, dietary enhancement with 0.05% uric acid does not significantly effect the reproductive development of recently dealated primaries. Possible reasons for each reproductive form’s response to enhanced dietary nitrogen are discussed.
Sex and menopause differences in response to tadalafil: 6-minute walk distance and time to clinical worsening

Pulmonary arterial hypertension (PAH) is a female-predominant disease, but there are little data on treatment response by sex and menopausal status. In this retrospective analysis of the Pulmonary Arterial Hypertension and Response to Tadalafil (PHIRST) randomized clinical trial, we assessed treatment response between the sexes by examining change in 6-minute walk distance (6MWD) and time to clinical worsening (TCW). We examined the effect of menopausal status on the same treatment measures. 6MWD was recorded before and after 16 weeks of treatment with tadalafil or placebo in the PHIRST study cohort of 340 subjects (264 females, 76 males). A univariate analysis was used to assess the effect of sex on change in 6MWD and TCW. Multivariate linear regression and Cox proportional hazards models were built for 6MWD and TCW, respectively. Women were subdivided by age as a surrogate for menopausal status. The linear trend test and the log-rank test were performed on change in 6MWD and TCW by age. For tadalafil-treated patients, a significant difference in change in 6MWD by sex (mean: 48.6 m for males vs. 34.7 m for females; P = 0.01) was found, but it was not significant in multivariate analysis (P = 0.08). There was a trend toward a female age-dependent effect in change in 6MWD; the premenopausal group showed the greatest improvement. A significant sex- or age-dependent effect on TCW was not present. In conclusion, this retrospective analysis of the PHIRST trial suggests that men and premenopausal women may experience greater functional improvement when treated with tadalafil than older women, but there was no consistent sex or menopausal effect on TCW.
Growth of Nanomaterials by Screw Dislocation

Controlling the morphology of nanomaterials is important for their fundamental study and practical application. Especially one-dimensional nanowires, nanorods, and nanotubes and two-dimensional nanoplates possess interesting physical and chemical properties due to their structural anisotropy. The key to obtaining these morphologies is to break the symmetry of crystal growth to promote anisotropic growth. In this chapter we discuss the catalyst- and template-free screw-dislocation-driven nanomaterial growth mechanism, in which an axial screw dislocation creates self-perpetuating growth steps upon intersecting with the crystal surface and enables anisotropic crystal growth under low supersaturation conditions. The presence of screw dislocations not only alters the growth kinetics of nanomaterials, but also distorts the crystal lattice and generates a strain field, both of which lead to morphology variation of the nanomaterials. The structural characteristics associated with dislocation-driven growth can be readily detected using transmission electron microscopy techniques. A review is presented on a wide range of nanomaterials formed under various conditions whose growth has been confirmed to be driven by screw dislocations, demonstrating the generality of this mechanism. A framework for rationally synthesizing anisotropic nanomaterials via dislocation-driven growth is provided. This will enable large-scale, low-cost production of nanomaterials for various applications.
Mechanism of preventing doxorubicin-induced mitochondrial toxicity with cardiolipin-targeted peptide, SS-31 (966.1)

Doxorubicin (DOX) is an effective chemotherapeutic that intercalates DNA and inhibits topoisomerase II in cancer cells. However, clinical use of DOX is limited by its cardiac toxicity, resulting fr...
Electroneutral uptake and electrogenic secretion of a fluorescent bile salt by rat hepatocyte couplets

The role of membrane voltage as a driving force for the hepatic uptake and secretion of fluorescent bile salts has been examined in isolated hepatocyte couplets. The present study demonstrates that the fluorescent bile salt derivative (N-[7-(nitrobenz-2-oxa- 1,3-diazol-4-yl)]-7-amino-3 alpha, 12 alpha-dihydroxy-5-cholan-24-oyl)-2-aminoethanesulfonate (7 beta-NBD-NCT) is taken up into hepatocytes by a saturable process with a Kt of 2.7 microM. Uptake rate was reduced by only 22% after total Na+ replacement and was independent of transmembrane potential difference over a range of -135 to +25 mV. In contrast, secretion into the canalicular space was strongly dependent on membrane voltage over the range from -34 to 0 mV in a manner consistent with electrodiffusion of an anion. Fitting the secretion time course to that predicted by electrodiffusion demonstrated that only approximately 50% of total secretion can result from electrodiffusion. Studies in isolated perfused liver confirmed this observation that depolarization caused a decrease in bile salt secretion rate. These results demonstrate that 7 beta-NBD-NCT is transported by a neutral uptake process at the sinusoidal membrane and is secreted across the canalicular membrane in part by electrogenic transport. This suggests that voltage changes could be a common pathway resulting in impaired organic anion secretion in diverse cholestatic syndromes.
Renegotiating the Inheritance: Strategizing Social Program Targeting in Latin America

Under what conditions do leaders design less politicized social programs in countries with weak party systems? While political leaders acknowledge “good policy, good votes” in social policy design and administration, the direction of redistributive targeting carries electoral implications. Upon entering office, leftist leaders such as Hugo Chavez of Venezuela and Luiz Inacio Lula da Silva of Brazil inherited similar opportunities to design policies of social inclusion and mobilize political participation from a vast and growing group of individuals excluded from traditional social welfare policy and dissatisfied with neoliberal policy changes. To understand how leaders design policies that varied in how they target traditionally excluded populations in Latin American countries, I examine how representative institutions affect leadership mobilization strategies in social programs.I analyze political leaders’ strategic choices in the design and implementation of social programs. I find that redistributive politics illuminates institutional factors that affect social policy choice. The variation in redistributive policy design is a product of horizontal accountability and program oversight affects distribution. I illustrate this variation with survey data from LAPOP and case studies examining programs intended to break intergenerational cycles of poverty – Bolsa Familia in Brazil and Misiones Ribas, Robinson and Sucre in Venezuela.
Effect of preliminary training and signal duration on the maintenance of an avoidance response

The effect of a combination escape-avoidance procedure and an avoidance-only procedure on the maintenance of discriminative avoidance responses in a lever-pressing apparatus under increasingly stringent conditions was examined. Ss trained under a combination escape-avoidance procedure maintained a higher response rate despite a high response/shock correlation than Ss trained under avoidance-only.
Reproductive Biology of the Cigarette Beetle, Lasioderma serricorne 2. Ovarian Development and Female Sexual Maturity,,

The ovaries of Lasioderma serricorne (F.) females are comprised of 12–20 telotrophic ovarioles (6–10 per ovary). Ovarian development was measured on an arbitrary scale from 0 to 7. The first 3 stages, 0–2, were characteristic of pre-imaginal specimens. Stages 3–7 were associated with adult beetles. Stage 7 was represented by mature oocytes, and at 27±2°C, 97.5% of the experimental females had attained this level of development by 4–5 days of age. In behavioral tests, females younger than 10–12 hr of adult age did not stimulate copulatory attempts by sexually mature males, whereas older females did elicit male mating behavior. Females were generally not receptive to male copulatory attempts before 56–64 hr of age. Female receptivity, as determined by the percentage of females inseminated, reached a maximum at about 4–5 days of age. Physiological (ovarian) and behavioral (mating receptivity) maturity were thus coincident at 4–6 days of age, a time at which female sex pheromone production is maximal and adult emergence from the pupal cell usually occurs.
Pulmonary radiology in the intensive care unit

The techniques of the standard chest film and the use of specialized views for specific problems are reviewed. The radiographic manifestations of the major presenting causes of acute respiratory failure are described and compared, and the evolution of the radiograph during the progression of these diseases is considered. Radiographic manifestations of commonly encountered complications in the intensive care unit are also presented.
Prediction of Abdominal Fat in Broiler Chickens Using Wing Web and Humeral Feather Tract Measurements

Abstract Correlation coefficients between abdominal fat and two skin measurements were obtained from 314 male and 347 female broiler chickens (Gallus gallus domesticus). Wing web thicknesses were measured at 49 days of age, broilers were slaughtered at 50 days of age, and humeral feather tract pinches were measured after thawing but before evisceration. Correlation coefficients between wing web thickness and abdominal fat weight were r = +.14 for males and r = +.05 for females. Correlations for humeral tract pinch with abdominal fat weight were r = +.12 and +.17 (males) and r = +.18 and +.13 (females) for tracts on left and right shoulder regions, respectively. Abdominal fat was expressed as precentage of live weight to reduce variation in weight between birds. Correlation coefficients between wing web thickness and percentage abdominal fat were r = +.09 for males and r = +.01 for females. Correlations for the humeral feather tract pinch with percentage abdominal fat were r = +.07 and +.14 (males) and r = +.10 and +.05 (females) for left and right shoulder regions, respectively. Correlation coefficients indicate that wing web and humeral feather tract thickness are not useful for estimating abdominal fat weight and percentage.
Research on the use of BrdU to track HCMV infection in HEL cells

Objective The genome of human cytomegalovirus(HCMV)was labeled with bromodeoxyuridine(BrdU)to follow the movement of HCMV in the infected HEL cells in combination with tracking of HCMV protein pp65 expression to study the process of viral replication and proliferation.Methods HEL cells were infected with HCMV(MOI=4)which was labeled with BrdU in advance.We inspected the distribution of the labeled viral nucleic acids with anti-BrdU monoclonal antibody in the infected cells at 2,4,6,24 and 48 hours post infection.At the same time point,we also inspected the expression and distribution of pp65 with anti-pp65 monoclonal antibody. Results At the five time points included in this study,immunofluorescence staining displayed the labeled viral genome first showed up in cytoplasm,then in nucleus and finally in both cytoplasm and nucleus.The expression of pp65 was absent in the beginning,then present sequentially in the nucleus and then both in the nucleus and cytoplasm.Finally giant cells and confluent cells were formed.Conclusion Labeling of double-stranded DNA with BrdU is a useful method to study the intracellular distribution of HCMV after initial infection and may serve as a tool for study of other viruses.By including the distribution of pp65 expression,this study directly observed the replication and proliferation of HCMV in HEL cells.