cssi/SciSciGPT-SciSciNet huggingface dataset:
Changes in bone mineral and bone formation rates during pregnancy and lactation in rats

Changes in bone chemistry, cortical bone morphometry, and periosteal and trabecular bone formation rates were determined during pregnancy and lactation in rats. Data were obtained using chemical, static morphometric, and fluorochrome-based histomorphometric methods in pregnant or lactating animals and compared with age-matched, unmated controls. There were significant increases in bone weight, ash weight, calcium content, and femoral cross-sectional area by late pregnancy and decreases in these same parameters during lactation. There were also decreases in bone mass and increases in surface:volume ratios of trabecular bone during lactation. There were increases in femoral periosteal and endosteal perimeters associated with the reproductive cycle. Bone formation and appositional rates at the periosteal and endosteal surfaces were elevated during pregnancy, particularly evident at midpregnancy. Periosteal bone formation rates declined during lactation, but trabecular bone formation rates increased. These results indicate that during pregnancy there are increases in bone formation rates contributing to the increases in skeletal mass. During lactation in rats, reductions in skeletal mass are accompanied by increases in bone turnover, particularly evident in trabecular bone.
Part-time Residency in Pediatrics: Description of Current Practice

Objective. To determine current national utilization levels of part-time pediatric residency and to identify reasons for pursuing training on a part-time basis. Design. Data were obtained through (1) a survey regarding part-time residency mailed to all accredited pediatric residency programs, (2) the American Medical Association Fellowship and Residency Interactive Electronic Database, and (3) the American Academy of Pediatrics postgraduate level 3 survey, 2003. Results. Of the 190 accredited pediatric residency programs surveyed, 156 (82%) responded; 18 (12%) of these programs had ≥1 part-time resident during academic years 2000–2003. Nationally, 43 of 6609 residents represented in the survey (0.7%) undertook some of their training on a part-time basis. All programs prorated salaries in proportion to time percentage, 10 (71%) continued full benefits for part-time residents, and 15 (88%) used a reduced call schedule. Although multiple reasons were given for part-time status, including travel (16%), research (14%), advanced degrees (9%), personal illness (9%), and family illness (5%), 67% cited child care as 1 reason. Length of residency was extended by an average of 15 months (range: 4–36 months). Analysis of the American Medical Association Fellowship and Residency Interactive Electronic Database showed that 45 (24%) of 190 programs advertise part-time slots. Conclusions. Although numerous pediatric programs advertise part-time positions, few residents actually held such positions during a 3-year period. There is variability among programs in how benefits and call schedules are managed. Part-time positions are chosen for multiple reasons, but the most common reason is to care for children. Pediatric residency programs can use this information to meet resident needs.
Designing Swellable Beads of Alginate and Gelatin for Controlled Release of Pesticide (Cypermethrin)

In the present study biopolymeric beads of sodium alginate and gelatin were prepared by employing CaCl2 as a crosslinking agent. A series of such microspheres of different compositions were prepare...
The extended life span of Drosophila melanogaster eye-color (white and vermilion) mutants with impaired formation of kynurenine

Animal and human studies suggest that aging is associated with increased formation of kynurenine (KYN) from tryptophan (TRY). The rate-limiting factors of TRY–KYN metabolism are transmembrane transport of TRY, and activity of enzyme, TRY 2,3-dioxygenase (TDO2). Eye-color mutants, white (w1118) (impaired TRY transport) and vermilion (v48a and v2) (deficient TDO activity), were compared with wild-type Oregon-R (Ore-R) strain of Drosophila melanogaster. Female 1-day-old adult flies maintained on a standard medium, and acclimatized to 12-h light:12-h dark cycle were collected, and then regularly transferred to fresh medium every 3–4 days. The number of dead flies was recorded at the time of transfer. Forty flies were studied in each experimental group. The life span of w1118 (mean = 45.5 days), and v48a (mean = 47.6 days) and v2 (mean = 43.8 days), were significantly longer than of wild-type Ore-R flies (27.1 days) (p < 0.001, Logrank test). There were no differences in life span between w1118 and v48a and v2 mutants. Present results suggest that prolongation of life span may be associated with slow rate of KYN formation from TRY.
Concurrent processing in nonlinear column stability

A concurrent processing algorithm is developed for materially nonlinear stability analysis of imperfect columns with biaxial partial rotational end restraints. The algorithm for solving the governing nonlinear ordinary differential equations is implemented on a multiprocessor computer called the “finite element machine”, developed at the NASA Langley Research Center. Numerical results are obtained on up to nine concurrent processors. A substantial computational gain is achieved in using the parallel processing approach.
Optimal Fault-Secure Scheduling

We consider here two basic fault-secure scheduling problems for multiprocessor systems. First, given the number of processors in the system and a set of computational tasks of unit length expressed as a complete binary tree, a scheduling algorithm is proposed such that the total execution time is a minimum and no undetected single error result will be delivered. Second, given a deadline and a computation tree, another algorithm is given which generates a fault-secure scheduling using a minimum number of processors. We show that two previous approaches are special cases of these algorithms. We also discuss the way to modify our scheduling to ensure a given fault latency requirement. Finally, extensions that cover multiple errors, non-unit length tasks and computation graphs of arbitrary binary trees are discussed.
Protein Structure: Born to be beta

Abstract The β -sheet-forming propensities of amino acids have been measured in a new model system. The origins of observed variations in the propensities are unclear, but the results provide a useful tool for protein design.
Long-term potentiation: evidence against an increase in transmitter release probability in the CA1 region of the hippocampus

It is widely accepted that N-methyl-D-aspartate (NMDA)-receptor-dependent long-term potentiation (LTP) in the CA1 region of the hippocampus is triggered postsynaptically, but there is considerable debate as to the site at which the increase in synaptic strength is expressed. The irreversible open-channel blocking action of the NMDA receptor antagonist MK-801 has been used to test whether the probability of transmitter release (Pr) is increased during LTP. Although the rate of decline of the amplitude of the NMDA receptor-mediated excitatory postsynaptic current (EPSC) in the presence of MK-801 strongly depends on Pr, the rate of decline of the EPSC evoked at synapses expressing LTP is identical to that observed at synapses not expressing LTP. These findings are difficult to reconcile with models in which the expression of LTP is due to an increase in Pr.
Development and Perforation of the Occluding Plate in Oviducts of Young Turkey Females as Related to Laying of the First Egg

Abstract RELATIVELY little information is available in the literature on the development and subsequent perforation of the oviduct occluding plate prior to or in conjunction with laying of the first egg by young turkey females. Greenwood (1935) has described the process of perforation of the oviduct in the domestic fowl. Kar (1947a) traced the early developmental stages in formation of the occluding plate and concluded (Kar, 1947b) perforation of the oviduct is controlled by estrogenic activity of the ovary. Asmundson et al. (1946) made observations to determine when the vagina opened in young turkey females and described the appearance of the occluding plate. They estimated the interval between opening of the vagina and laying the first egg at about two weeks in brightly lighted pens (2 foot candle—f.c.) and three weeks in medium lighted pens (0.3 to 1.0 f.c.). The observations reported in the present study were undertaken to provide…
Identification and characterization of pyrrolidine diastereoisomers as potent functional agonists and antagonists of the human melanocortin-4 receptor

A series of trans-4-phenylpyrrolidine-3-carboxamides were synthesized and characterized as potent ligands of the human melanocortin-4 receptor. Interestingly, a pair of diastereoisomers 13b displayed potent functional agonist and antagonist activity, respectively. Thus, the 3S,4R-pyrrolidine 13b-1 possessed a Ki of 1.0 nM and an EC50 of 3.8 nM, while its 3R,4S-isomer 13b-2 exhibited a Ki of 4.7 and an IC50 of 64 nM. Both compounds were highly selective over other melanocortin receptor subtypes. The MC4R agonist 13b-1 also demonstrated efficacy in a diet-induced obesity model in rats.
Excitation of the ground state band of 19F by 13.9 MeV proton scattering

Abstract The preferential excitation of the ground state rotational band of the 19 F nucleus has been observed in an experiment with 13.9 MeV protons. The angular distributions are fitted with the adiabatic approximation rotational optical model.
Advances and challenges in NDE sensors

The industrial world continues to demand greater efficiency and effectiveness from the inspection processes using Nondestructive Evaluation (NDE) techniques. NDE sensors form the heart of any inspection system and could be one of the most important contributor to effective and reliable inspections in the industrial world. One important and frequently adopted approach by researchers in the NDE community is to innovate in the NDE sensors area. The industrial world of engineering structures and components is reasonably complex and extremely broad in terms of materials used, shapes, designs, defects to be detected, operating conditions, etc. The reasons for focusing on the sensors side is multifold; most important being the fact that in the entire system, it is the closest in proximity to the object being inspected and thus can contribute significantly. In addition many of the advances taking place in a host of enabling technologies such as electronics, communication, signal processing, computers, manufacturing, modeling/simulation tools, etc, have accelerated and motivated the design and development of new NDE sensors which can meet today's tough demands.
Schedule-induced polydipsia under conditions of restricted access to water

Abstract Schedule-induced polydipsia has been observed when access to water is restricted to later portions of the inter-pellet interval. This argues against low probability of reinforcement being the sole controlling factor of this phenomenon and suggests that other factors, such as post-prandial and dry-mouth, may also play a role in schedule-induced polydipsia. This experiment investigates the role of these other factors in a schedule-induced polydipsia situation where access to water is limited. Water was made available during two 10-sec periods of each inter-pellet interval. In the last phase of the experiment, a 5-min pre-session access period was given. Two animals consumed water during both availability periods and also during the pre-session period, while a third animal drank only during the first post-pellet water presentation. The results extend the generality of schedule-induced polydipsia under conditions of limited access to water.
Urea Placement and Nitrification Inhibitor Effects on Growth and Nitrogen Accumulation by No-Till Winter Wheat

Reduced forage production, grain yield, and visual N deficiency symptoms in no-till winter wheat (Triticum aestivum L.) prompted this study. Our objectives were to determine the effect of urea placement and two nitrification inhibitors-nitrapyrin [2-chloro-6 (trichloromethyl) pyridine] (NP) and dicyandiamide (DCD)-on aerial dry matter and N accumulation. A 4-yr field study was conducted on a Renfrow silt loam soil (fine-silty, mixed thermic Udertic Paleustoll) silt loam near El Reno, OK. The seven treatments included urea fertilizer (60 kg N ha - with and without the two inhibitors, surface broadcast or banded 3 to 4 em below the seed row, and an unfertilized control. Aerial dry matter accumulation during autumn was higher for banded urea plus DCD (22%) and broadcast urea plus DCD (25%), than for broadcast urea without an inhibitor. Whole plant N content during autumn also was higher for banded urea plus DCD (28%) than for broadcast urea without an inhibitor. Neither inhibitor nor placement affected total dry matter accumulation measured at tillering, but differences were noted at spike emergence, grainfill, and final harvest. At spike emergence in 1991, when climatic conditions were favorable for early season wheat growth, N content was greater for broadcast urea plus nitrapyrin than for broadcast urea or banded urea without inhibitor. At final harvest, both DCD treatments exhibited greater N content than all other N treatments. In 1993, when climatic conditions were favorable for leaching, DCD was effective in slowing nitrification and increasing N uptake, regardless of fertilizer placement. Our results suggest that fall application of DCD with urea can potentially increase autumn forage production and N content, thus prolonging the grazing season or accommodating increased stocking rates.
MR imaging and sonography of early prostatic cancer: pathologic and imaging features that influence identification and diagnosis.

The purpose of this study was to correlate findings at MR imaging and transrectal sonography with histopathologic findings after surgery in patients with prostatic cancer, to identify the pathologic characteristics of prostatic cancer that improved detection with MR imaging and transrectal sonography, and to identify the imaging characteristics that correlated with detection of true cancers.Data from MR imaging in 320 patients and from transrectal sonography in 343 patients who were enrolled in the Radiological Diagnostic Oncology Group multiinstitutional study of imaging in prostatic cancer were correlated with results of radical prostatectomy. Only cancers 5 mm or greater in at least one dimension were evaluated pathologically. The locations of lesions and the linear dimensions and volumes of individual lesions and the prostate gland were evaluated pathologically and with imaging studies. The appearance of lesion margins on images and the degree of differentiation of lesions seen on pathologic examinati...
A multidimensional birth process and its application to some problems in the dynamics of biological populations.

This paper is a sequel to a paper by the author entitled “Restricted Transition Probabilities and Their Applications to Some Problems in the Dynamics of Biological Populations” (Bull. Math. Biophysics, 1966,28, 315–331). The paper is divided into two parts. In part one some aspects of the maximum size attained by the population during a finite time interval are studied for the case the stochastic process underlying the evolution of the population is a birth process. Two interesting by-products emerge from the study presented in part one; namely a combinatorial method of finding solutions to the Kolmogorov differential equations in special cases, and secondly, a set of criteria for the optimum allocation of genotypes in the host population of a host-pathogen system. The optimum allocation of genotypes in the host population is a problem of practical importance in controlling plant pathogens. In part two the theory of restricted transition probabilities developed in the companion paper is applied in finding the distribution of the time to the appearance of the first mutation for the case of a two dimensional birth process. The distribution of the time to the appearance of the first mutation is of importance in understanding the role mutation plays in the evolution of a population, particularly in the pathogen population of a host-pathogen system.
How to beat critical slowing down: 1990 update

Abstract We discuss the problem of critical slowing-down (CSD) in Monte Carlo simulations, and review recent progress in devising collective-mode algorithms that reduce or eliminate CSD. Emphasis is on cluster and embedding algorithms; multigrid and Fourier acceleration are also discussed briefly.
T-cell adhesion to endothelial cells in systemic lupus erythematosus

To investigate the pathogenesis of the lymphopenia in systemic lupus erythematosus (SLE), we examined the adhesion of these T cells to endothelial cells (EC). T cells from 10 lymphopenic patients with active SLE showed significantly reduced adhesion to unstimulated and interleukin-1 (IL-1)-stimulated human EC monolayers when compared with T cells from age, sex, and race matched normal control individuals. Percentage decreases from control values (Δ) in the measured percentage of T cells adherent to unstimulated and IL-1-stimulated EC were 36.4% (P<0.025) and 34.0% (P<0.005), respectively. Percentage adhesion of phorbol ester-treated T cells of SLE patients was also reduced compared with similarly treated T cells of control patients; the decrease was 22.8% (P<0.025). No abnormality was detected in the adhesion to EC of T cells from patients with asthma who were receiving corticosteroids, suggesting that the abnormality in the SLE T cells was related to the disease process itself. The reduced adhesion of the circulating T cells may be a consequence of the withdrawal from the blood of more strongly adherent cells in the course of the inflammatory response. The loss of strongly adherent lymphocytes may contribute to the lymphopenia of SLE.
Subjected words: African linguistics and the colonial encounter

Abstract The systematic study of African languages emerged in the 19th century as a scientific field along with other European projects of information-gathering, religious proselytizing, and establishing an imperial presence on the continent. This paper considers how the conditions – ideological, social, and material – of linguistic research in the early colonial encounter influenced the resulting descriptions of African languages and the delimitation of linguistic boundaries. Frameworks and precedents from those early projects have remained influential in African linguistics, for example in the identification of ‘ethnolinguistic groups,’ in the shape of grammatical descriptions, and in the politics of orthography.
Elevated temperature fatigue behavior of SCS-6/Ti24Al11Nb

Abstract An investigation has been conducted to determine the effects of stress ratio, frequency and hold time on the elevated temperature fatigue behavior of SCS-6/Ti24Al11Nb. Load-controlled tests conducted at 650°C, and two stress ratios, 0.1 and 0.5, are compared at a frequency of 3 Hz. The baseline tests at 3 Hz are compared with data at three other frequencies: 30, 0.0083 and 0.00278 Hz. The effects of superimposed hold times were also investigated at the lowest frequency, 0.00278 Hz. Cycles to failure are compared for all the data sets, and life-fraction models were developed which take into account both the time-dependent and cyclic-dependent effects of this composite material. The model is capable of predicting cycles to failure for the frequency range investigated and is based on data resulting from the highest frequency fatigue as well as creep testing. This linear life fraction model is extended successfully to accout for hold times.
Studies on the mechanism of the lung toxicity of paraquat: comparison of tissue distribution and some biochemical parameters in rats and rabbits.

Abstract After iv injection of [14C]paraquat (20 mg/kg) tissue localization was preferential in lungs of rats as well as rabbits although the latter did not show any histopathologic or biochemical signs of lung damage. No preferential subcellular localization of [14C]paraquat was found in lungs of either species, but all subcellular levels decreased more rapidly in the rabbit than in the rat. [14C]Paraquat was not covalently bound to tissue macromolecules. In vitro measurements of lipid peroxidation, H2O2 formation and lung lysosomal stability failed to account adequately for the lung damage in the rat.
A New Look at the Dynamics of Human-Automation Trust: Is Trust in Humans Comparable to Trust in Machines?

The trust placed in automated diagnostic aids by the human operator is one of the most critical psychological factors that influences operator reliance on decision support systems. Studies examinin...
Radar Reflectivity-Ice Water Content Relationships for Use above the Melting Level in Hurricanes

Abstract Regression equations linking radar reflectivity (Ze) and ice water content (IWC) were calculated from airborne radar and particle image data that were collected above the melting level in two hurricanes. The Ze − IWC equation from the stratiform areas of Hurricane Norbert (1984) is similar to the composite equation for thunderstorm anvils derived by Heymsfield and Palmer. The Ze − IWC equation from the convective regions of Hurricane Irene (1981) has essentially the same exponent, but a significantly greater coefficient than that from Norbert. The higher density of the graupel and rounded ice in the Irene data accounts for the difference in the coefficients. The hurricane Ze − IWC relations have smaller exponents than most of those from midlatitude clouds, which indicates that small ice particles may be more prevalent in these two hurricanes than in midlatitude clouds.
Antigen-presenting cells in the female reproductive tract: influence of the estrous cycle on antigen presentation by uterine epithelial and stromal cells

The objective of the present study was to define the afferent arm of the mucosal immune system in the female reproductive tract. When uterine cells were incubated with ovalbumin-specific T cells and ovalbumin, antigen presentation by purified luminal epithelial cells and stromal cells was measured. Analysis of uterine cells from intact rats throughout the reproductive cycle indicated that antigen presentation is controlled by the female sex hormones. Antigen presentation by epithelial cells was high at diestrus (day 3), when estradiol levels are elevated, and low at estrus and diestrus (days 1 and 2). In contrast, antigen presentation by stromal cells was low at diestrus (day 3) and high at estrus and diestrus (days 1 and 2). Estradiol given to ovariectomized rats stimulated epithelial cell and inhibited stromal cell antigen presentation compared with saline controls. To determine whether uterine cells interact with other cells to facilitate antigen presentation, thymus dendritic-like cells were incubated...
Rate of Initial Entry of Ca47 and Sr85 from the Intestine into the Vascular Space.

SummaryThe rate of initial entry of both radioactive calcium and strontium from the gastrointestinal tract into the vascular system has been determined in man by adapting an integral equation approach for use with a digital computer. A single tracer dose of Ca47 and of Sr85 was given both by the oral and intravenous route in separate studies and serial samples of plasma were obtained for radioassay. The maximal rate of initial entry of Ca47 per 15-minute interval ranged from 2.2% to 3.8% of the dose and was reached within 1 1/2 hours. This rate was sustained for about one hour and decreased thereafter with time. The rate of initial entry for Sr85 was less than that for Ca47, not exceeding 1.5% of the dose in any 15-minute interval, but was relatively more sustained from the first to the fourth hour After the fourth hour, the rates of initial entry of Sr85 and Ca47 were almost proportional.
Protracted downregulation of CX3CR1 on microglia of aged mice after lipopolysaccharide challenge

Abstract Fractalkine (CX 3 CL1) to fractalkine receptor (CX 3 CR1) interactions in the brain are involved in the modulation of microglial activation. Our recent findings indicate that there is microglial hyperactivity in the aged brain during an inflammatory challenge. The underlying cause of this amplified microglial response in the aged brain is unknown. Therefore, the purpose of this study was to determine the degree to which age-associated impairments of CX 3 CL1 and CX 3 CR1 in the brain contribute to exaggerated microglial activation after intraperitoneal (i.p.) injection of lipopolysaccharide (LPS). Here we show that CX 3 CL1 protein was reduced in the brain of aged (18–22 mo) BALB/c mice compared to adult (3–6 mo) controls. CX 3 CL1 protein, however, was unaltered by LPS injection. Next, CX 3 CR1 levels were determined in microglia (CD11b + /CD45 low ) isolated by Percoll density gradient separation at 4 and 24 h after LPS injection. Flow cytometric and mRNA analyses of these microglia showed that LPS injection caused a marked decrease of CX 3 CR1 and a simultaneous increase of IL-1β at 4 h after LPS injection. While surface expression of CX 3 CR1 was enhanced on microglia of adult mice by 24 h, it was still significantly downregulated on a subset of microglia from aged mice. This protracted reduction of CX 3 CR1 corresponded with a delayed recovery from sickness behavior, prolonged IL-1β induction, and decreased TGFs expression in the aged brain. In the last set of studies BV2 microglia were used to determine effect of TGFs on CX 3 CR1. These results showed that TGFβ enhanced CX 3 CR1 expression and attenuated the LPS-induced increase in IL-1β expression.
Noncompaction of the ventricular myocardium in Melnick‐Needles syndrome

A 4-year-old asymptomatic boy was referred for evaluation after being diagnosed with Melnick-Needles syndrome. Echocardiography demonstrated noncompaction of the left ventricular myocardium as an isolated cardiac finding. Though other structural cardiac defects were reported previously in this syndrome, this is the first report of this rare cardiac anomaly in this likewise rare syndrome. We postulate that this occurrence represents a primary disorder of early fetal development. Patients with Melnick-Needles syndrome should be evaluated for noncompaction of the ventricular myocardium and its potential cardiovascular dysfunction.
Electrical detection of charge-current-induced spin polarization due to spin-momentum locking in Bi2Se3

Topological insulators exhibit metallic surface states populated by massless Dirac fermions with spin-momentum locking, where the carrier spin lies in-plane, locked at right angles to the carrier momentum. Here, we show that a charge current produces a net spin polarization via spin-momentum locking in Bi2Se3 films, and this polarization is directly manifested as a voltage on a ferromagnetic contact. This voltage is proportional to the projection of the spin polarization onto the contact magnetization, is determined by the direction and magnitude of the charge current, scales inversely with Bi2Se3 film thickness, and its sign is that expected from spin-momentum locking rather than Rashba effects. Similar data are obtained for two different ferromagnetic contacts, demonstrating that these behaviours are independent of the details of the ferromagnetic contact. These results demonstrate direct electrical access to the topological insulators’ surface-state spin system and enable utilization of its remarkable properties for future technological applications. The spin-momentum locking in a topological insulator can be detected directly through electrical measurements.
Empirical evidence of cognitive vulnerability for depression among children and adolescents: A cognitive science and developmental perspective

We summarize and integrate research on cognitive vulnerability to depression among children and adolescents. We first review prospective longitudinal studies of the most researched cognitive vulnerability factors (attributional style, dysfunctional attitudes, and self-perception) and depression among youth. We next review research on information processing biases in youth. We propose that the integration of these two literatures will result in a more adequate test of cognitive vulnerability models. Last, we outline a program of research addressing methodological, statistical, and scientific limitations in the cognitive vulnerability literature.
Globally, unrelated protein sequences appear random

Motivation: To test whether protein folding constraints and secondary structure sequence preferences significantly reduce the space of amino acid words in proteins, we compared the frequencies of four-and five-amino acid word clumps (independent words) in proteins to the frequencies predicted by four random sequence models. Results: While the human proteome has many overrepresented word clumps, these words come from large protein families with biased compositions (e.g. Zn-fingers). In contrast, in a non-redundant sample of Pfam-AB, only 1% of four-amino acid word clumps (4.7% of 5mer words) are 2-fold overrepresented compared with our simplest random model [MC(0)], and 0.1% (4mers) to 0.5% (5mers) are 2-fold overrepresented compared with a window-shuffled random model. Using a false discovery rate q-value analysis, the number of exceptional four-or five-letter words in real proteins is similar to the number found when comparing words from one random model to another. Consensus overrepresented words are not enriched in conserved regions of proteins, but four-letter words are enriched 1.18-to 1.56-fold in α-helical secondary structures (but not β-strands). Five-residue consensus exceptional words are enriched for α-helix 1.43-to 1.61-fold. Protein word preferences in regular secondary structure do not appear to significantly restrict the use of sequence words in unrelated proteins, although the consensus exceptional words have a secondary structure bias for α-helix. Globally, words in protein sequences appear to be under very few constraints; for the most part, they appear to be random. Contact: wrp@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Deuterium Isotope Effects on Permeation and Gating of Proton Channels in Rat Alveolar Epithelium

The voltage-activated H+ selective conductance of rat alveolar epithelial cells was studied using whole-cell and excised-patch voltage-clamp techniques. The effects of substituting deuterium oxide, D2O, for water, H2O, on both the conductance and the pH dependence of gating were explored. D+ was able to permeate proton channels, but with a conductance only about 50% that of H+. The conductance in D2O was reduced more than could be accounted for by bulk solvent isotope effects (i.e., the lower mobility of D+ than H+), suggesting that D+ interacts specifically with the channel during permeation. Evidently the H+ or D+ current is not diffusion limited, and the H+ channel does not behave like a water-filled pore. This result indirectly strengthens the hypothesis that H+ (or D+) and not OH- is the ionic species carrying current. The voltage dependence of H- channel gating characteristically is sensitive to pH0 and pHi and was regulated by pD0 and pDi in an analogous manner. shifting 40 mV/U change in the pD gradient. The time constant of H+ current activation was about three times slower (T(act) was larger) in D2O than in H2O. The size of the isotope effect is consistent with deuterium isotope effects for proton abstraction reactions, suggesting that H+ channel activation requires deprotonation of the channel. In contrast, deactivation (T(tail)) was slowed only by a factor < or = 1.5 in D2O. The results are interpreted within the context of a model for the regulation of H+ channel gating by mutually exclusive protonation at internal and external sites (Cherny, V.V., V.S. Markin, and T.E. DeCoursey. 1995. J. Gen. Physiol. 105:861-896). Most of the kinetic effects of D2O can be explained if the pKa of the external regulatory site is approximately 0.5 pH U higher in D2O.
RNA-Skim: a rapid method for RNA-Seq quantification at transcript level.

Motivation: RNA-Seq technique has been demonstrated as a revolutionary means for exploring transcriptome because it provides deep coverage and base pair-level resolution. RNA-Seq quantification is proven to be an efficient alternative to Microarray technique in gene expression study, and it is a critical component in RNA-Seq differential expression analysis. Most existing RNA-Seq quantification tools require the alignments of fragments to either a genome or a transcriptome, entailing a time-consuming and intricate alignment step. To improve the performance of RNA-Seq quantification, an alignment-free method, Sailfish, has been recently proposed to quantify transcript abundances using all k-mers in the transcriptome, demonstrating the feasibility of designing an efficient alignment-free method for transcriptome quantification. Even though Sailfish is substantially faster than alternative alignment-dependent methods such as Cufflinks, using all k-mers in the transcriptome quantification impedes the scalability of the method. Results: We propose a novel RNA-Seq quantification method, RNA-Skim, which partitions the transcriptome into disjoint transcript clusters based on sequence similarity, and introduces the notion of sig-mers, which are a special type of k-mers uniquely associated with each cluster. We demonstrate that the sig-mer counts within a cluster are sufficient for estimating transcript abundances with accuracy comparable with any state-of-the-art method. This enables RNA-Skim to perform transcript quantification on each cluster independently, reducing a complex optimization problem into smaller optimization tasks that can be run in parallel. As a result, RNA-Skim uses 100 speedup over the state-of-the-art alignment-based methods, while delivering comparable or higher accuracy. Availability and implementation: The software is available at http://www.csbio.unc.edu/rs. Contact: ude.alcu.sc@gnawiew Supplementary information: Supplementary data are available at Bioinformatics online.
Refining the Binding of the Escherichia coli Flagellar Master Regulator, FlhD4C2, on a Base-Specific Level

The Escherichia coli flagellar master regulator, FlhD4C2, binds to the promoter regions of flagellar class II genes, yet, despite extensive analysis of the FlhD4C2-regulated promoter region, a detailed consensus sequence has not emerged. We used in vitro and in vivo experimental approaches to determine the nucleotides in the class II promoter, fliAp, required for the binding and function of FlhD4C2. FlhD4C2 protects 48 bp (positions −76 to −29 relative to the σ70-dependent transcriptional start site) in the fliA promoter. We divided the 48-bp footprint region into 5 sections to determine the requirement of each DNA segment for the binding and function of FlhD4C2. Results from an in vitro binding competition assay between the wild-type FlhD4C2-protected fragment and DNA fragments possessing mutations in one section of the 48-bp protected region showed that only one-third of the 48 bp protected by FlhD4C2 is required for FlhD4C2 binding and fliA promoter activity. This in vitro binding result was also seen in vivo with fliA promoter-lacZ fusions carrying the same mutations. Only seven bases (A12, A15, T34, A36, T37, A44, and T45) are absolutely required for the promoter activity. Moreover, A12, A15, T34, T37, and T45 within the 7 bases are highly specific to fliA promoter activity, and those bases form an asymmetric recognition site for FlhD4C2. The implications of the asymmetry of the FlhD4C2 binding site and its potential impact on FlhD4C2 are discussed.
JPEG steganalysis using color correlation and training on clean images only

Steganalysis has becoming an emerging important technique for detecting secret messages that are embedded in a clean-image. Universal steganalysis is especially useful due to its independence of prior knowledge of the embedding procedure. However, the detection results from the majority of universal methods are largely determined by the training procedure on a mixture of clean-images and stego-images, and therefore not practically feasible. Moreover, many color steganalysis methods do not take color coefficients into special consideration and thus they can be viewed as a simple extension of the analysis for grayscale images. To capture the distinct features of the clean images, we propose a novel predictor based on the intra- and inter- color correlations of wavelet coefficients. This method achieves higher detection rates, under a blind condition that only involves clean images at the training stage.
Studies on “Liver-Specific” Antigens: I. Evaluation of the Liver Specificity of “LSP” and “LP-2”

The liver specificity of the cell membrane lipoprotein "LSP" and the cytoplasmic antigen "LP-2," contained in the 100,000 g supernatant of liver homogenates, was investigated by immuno fluorescence, light microscopic immunoenzyme techniques, immunodiffusion, and hemagglutination. Migration characteristics of "LSP" and "LP-2" components in sodium dodecyl sulfate SDS polyacrylamide gel electrophoresis were compared with those of the corresponding kidney fractions, KSP and KP-2. Contrary to other reports, this investigation gave evidence that both "LSP" and "LP-2" are not liver-specific antigens. In addition, "LP-2" was found to be a cell membrane rather than a cytoplasmic protein. Anti-"LSP" and -"LP-2" sera tested by immunofluorescence and an unlabeled antibody enzyme technique appeared to react with cell membranes but lacked organ specificity. Anti-"LP-2" sera showed little or no cytoplasmic reactivity. By immunodiffusion, anti-"LSP" serum precipitated "LSP", KSP, "LP-2," and KP-2 as well as solubilized particulate liver cell membranes. Similar observations were made by hemagglutination. Efforts to produce "LSP"- and "LP-2"-specific antisera by absorption were unsuccessful. Gel filtration chromatographic patterns of "LSP" and KSP were very similar. Analysis by SDS-polyacrylamide gel electrophoresis revealed that the relative mobility of most "LSP" and KSP as well as that of most "LP-2" and KP-2 components is identical, although some differences in banding patterns were observed. As compared to known standards, the molecular weight of both "LSP" and KSP subunits ranges from approximately 40,000 to 96,000 and that of "LP-2" and KP-2 components from 21,000 to 103,000. The relative mobility of some major "LP-2" and KP-2 bands coincided with that of specific "LSP" and KSP polypeptides. The buoyant densities of "LSP" and "LP-2" in a CsCl gradient were considerably different and were identical to those of KSP and KP-2. Cross-contamination of these antigens due to degradation or proteolysis can, therefore, be excluded. Our results indicate that "LSP" and "LP-2" are not organ-specific antigens but suggest that they may contain liver-specific components of low concentration, un detectable by the methods employed.
Training the Next Generation of Translational Science Teams

Mayo Clinic recently launched a new strategic plan campaign with the theme “Creating the Future.” While the theme is intended to inform and energize the entire Mayo enterprise, it resonates especially throughout the Mayo Clinic Center for Translational Science Activities (CTSA).
The prrF-Encoded Small Regulatory RNAs Are Required for Iron Homeostasis and Virulence of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part of P. aeruginosa's iron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem in P. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ΔprrF1,2 mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identified phuS, encoding a heme binding protein involved in heme acquisition, and vreR, encoding a previously identified regulator of P. aeruginosa virulence genes, as novel targets of prrF-mediated heme regulation. Finally, we showed that the prrF locus encoding the PrrF and PrrH sRNAs is required for P. aeruginosa virulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ΔprrF1,2 deletion mutant protects against future challenge with wild-type P. aeruginosa. Combined, these data demonstrate that the prrF-encoded sRNAs are critical regulators of P. aeruginosa virulence.
Glutamine Metabolism and Function in Relation to Proline Synthesis and the Safety of Glutamine and Proline Supplementation

At normal intakes, dietary glutamine and glutamate are metabolized by the small intestine and essentially all glutamine within the body is synthesized de novo through the action of glutamine synthetase. The major sites of net glutamine synthesis are skeletal muscle, lung, and adipose tissue and, under some conditions, the liver. In addition to the small intestine, where glutamine is the major respiratory fuel, other sites of net glutamine utilization include the cells of the immune system, the kidneys, and the liver. The intestine expresses pyrroline 5-carboxylate (P5C) synthase, which means that proline is an end product of intestinal glutamine catabolism. Proline can also be synthesized from ornithine and the exact contribution of the 2 pathways is not certain. Infusion of proline i.v. to increase circulating concentrations is associated with increased proline oxidation and decreased proline synthesis. In contrast, conditions of proline insufficiency, after feeding low-proline diets or in response to high rates of proline catabolism in burn patients, do not result in increased proline synthesis. Glutamine supplementation is widespread and up to 0.57-0.75 g.kg(-1).d(-1) is well tolerated. Similarly, the only study of proline supplementation, in which patients with gyrate atrophy were given 488 mg.kg(-1).d(-1), reported no deleterious side effects. In the absence of controlled trials, it is currently not possible to estimate a safe upper limit for either of these 2 amino acids.
Tomato transcriptome and mutant analyses suggest a role for plant stress hormones in the interaction between fruit and Botrytis cinerea

Fruit-pathogen interactions are a valuable biological system to study the role of plant development in the transition from resistance to susceptibility. In general, unripe fruit are resistant to pathogen infection but become increasingly more susceptible as they ripen. During ripening, fruit undergo significant physiological and biochemical changes that are coordinated by complex regulatory and hormonal signaling networks. The interplay between multiple plant stress hormones in the interaction between plant vegetative tissues and microbial pathogens has been documented extensively, but the relevance of these hormones during infections of fruit is unclear. In this work, we analyzed a transcriptome study of tomato fruit infected with Botrytis cinerea in order to profile the expression of genes for the biosynthesis, modification and signal transduction of ethylene (ET), salicylic acid (SA), jasmonic acid (JA), and abscisic acid (ABA), hormones that may be not only involved in ripening, but also in fruit interactions with pathogens. The changes in relative expression of key genes during infection and assays of susceptibility of fruit with impaired synthesis or perception of these hormones were used to formulate hypotheses regarding the involvement of these regulators in the outcome of the tomato fruit-B. cinerea interaction.
Parameters Affecting Reflectance Of Coniferous Forests In The Region Of Chlorophyll Pigment Absorption

The observed variation in the reflectance in the region of chlorophyll absorption (450 to 900 nanometers) of mature Pinus ponderosa. (Ponderosa Pine) is explained in terms of pigment concentrations and stress associated with pollutant exposure . Reflectance and chlorophyll concentrations were measured on each years growth on each of 20 trees at four sites along an ozone exposure gradient the southern Sierra Nevada. Additionally, each of these sites was characterized in terms of stand density and age. Exposure to ozone, a strong oxidant, results in chloroplast injury. Granulation of the chloroplast stroma is an early metabolic response to ozone exposure. Thus, an examination of the reflectance changes observed along the ozone gradient provide a means for quantifying the spectral changes associated with chloroplast damage and reduced photosynthetic efficency. Additionally, the spectral trends associated with increasing needle age were related to the effects of cumulative ozone exposure and changes in overall chlorophyll concentration. It was found that the within site variation of the reflectance spectra was directly related to total chlorophyll concentration; an increase in chlorophyll concentration resulted in both a shift in the "red-edge" inflection to longer wavelength and an increase in the depth of the chlorophyll absorption well. Similarly, an increase in chloroplast damage, associated with higher levels of ozone exposure, also produced shift to 10I)ger wavelengths of the "red­ edge" but a decrease in the depth of the absorption well. The absorption band broadening observed in the high ozone exposure sites is indicative of an increase in the disorder of
LAPAROSCOPIC LIVE DONOR NEPHRECTOMY: THE UNIVERSITY OF MARYLAND 3-YEAR EXPERIENCE

ABSTRACTPurpose: We determined whether the results of laparoscopic donor nephrectomy warranted expansion of the availability of the technique.Materials and Methods: Donor and recipient charts for 738 consecutive laparoscopic living donor nephrectomies have been reviewed.Results: Renal donors were 69% white race and 57% female. Age range was 18 to 74 years. Neither age nor obesity alone were exclusionary criteria. Nephrectomy was left sided in 96%. Donors with body mass index greater than 33 had longer operative times. The extraction site changed from umbilical to suprapubic during the series. Warm ischemia time was 169 seconds. Conversion to open nephrectomy occurred in 1.6% of cases and blood transfusion was required in 1.2%. Major intraoperative complications occurred in 6.8% and major postoperative complications occurred in 17.1% of cases. Hospitalization lasted 64.4 hours. Postoperative donor creatinine was 1.5 times the preoperative level. Recipient serum creatinine averaged 2.0 mg% at 1 week and 1.6...
Pull up transistor folding

A polynomial-time algorithm for the pull up transistor assignment problem is developed, and it is shown that the interval selection and interval selection with pull up transistor assignment problems are NP-hard. Heuristics for these problems are proposed and compared with that proposed by C. Lursinsap and G. Gajski (ibid., vol.7, no.8, p.887-96, 1988). >