bluuebunny/crossref_metadata_2025 huggingface dataset:
Compression of DNA sequence reads in FASTQ format
Authors: Deorowicz Sebastian , Grabowski Szymon
Published: January 2011

Motivation: Modern sequencing instruments are able to generate at least hundreds of millions short reads of genomic data. Those huge volumes of data require effective means to store them, provide quick access to any record and enable fast decompression.

Results: We present a specialized compression algorithm for genomic data in FASTQ format which dominates its competitor, G-SQZ, as is shown on a number of datasets from the 1000 Genomes Project (www.1000genomes.org).

Availability: DSRC is freely available at http:/sun.aei.polsl.pl/dsrc.

Contact:  sebastian.deorowicz@polsl.pl

Supplementary information:  Supplementary data are available at Bioinformatics online.
Biological assessment of robust noise models in microarray data analysis
Authors: Posekany A. , Felsenstein K. , Sykacek P.
Published: January 2011

Motivation: Although several recently proposed analysis packages for microarray data can cope with heavy-tailed noise, many applications rely on Gaussian assumptions. Gaussian noise models foster computational efficiency. This comes, however, at the expense of increased sensitivity to outlying observations. Assessing potential insufficiencies of Gaussian noise in microarray data analysis is thus important and of general interest.

Results: We propose to this end assessing different noise models on a large number of microarray experiments. The goodness of fit of noise models is quantified by a hierarchical Bayesian analysis of variance model, which predicts normalized expression values as a mixture of a Gaussian density and t-distributions with adjustable degrees of freedom. Inference of differentially expressed genes is taken into consideration at a second mixing level. For attaining far reaching validity, our investigations cover a wide range of analysis platforms and experimental settings. As the most striking result, we find irrespective of the chosen preprocessing and normalization method in all experiments that a heavy-tailed noise model is a better fit than a simple Gaussian. Further investigations revealed that an appropriate choice of noise model has a considerable influence on biological interpretations drawn at the level of inferred genes and gene ontology terms. We conclude from our investigation that neglecting the over dispersed noise in microarray data can mislead scientific discovery and suggest that the convenience of Gaussian-based modelling should be replaced by non-parametric approaches or other methods that account for heavy-tailed noise.

Contact:  peter.sykacek@boku.ac.at

Availability:  http://bioinf.boku.ac.at/alexp/robmca.html.
Remifentanil Degradation in Umbilical Cord Blood of Preterm Infants
Authors: Welzing Lars , Ebenfeld Sabine , Dlugay Verena , Wiesen Martin H. J. , Roth Bernhard , Mueller Carsten
Published: January 2011

Background

No pharmacokinetic data about remifentanil in preterm infants exist, although remifentanil is increasingly used in this especially vulnerable subgroup of pediatric patients. Unfortunately, ethical restrictions in the volume of blood that can be withdrawn for kinetic sampling nearly prohibit pharmacokinetic studies in preterm infants.

Methods

Because remifentanil is rapidly metabolized by nonspecific blood esterases, we collected umbilical cord serum of preterm and term infants to investigate whether the activity of nonspecific blood esterases depends on gestational age. Umbilical cord serum, buffer solution, ascorbic acid, and remifentanil were mixed in a glass vial placed in a shaking water bath at 37°C. Subsequently, serum samples were subjected to liquid chromatography-mass spectrometry-based analysis of remifentanil and its metabolite GR90291 after 0, 30, 60, 100, and 150 min.

Results

We analyzed umbilical cord serum samples of 34 preterm infants (24-36 gestational weeks) and six term infants. The degradation rates of remifentanil to its major metabolite GR90291 were comparable in preterm and term infants. The overall median degradation half-life of remifentanil was 143 ± (interquartile range) 47 min (minimum, 76 min; maximum, 221 min) without significant differences between very preterm infants (less than 28 gestational weeks) and term infants. The remifentanil concentration remained stable in control runs without serum.

Conclusions

Our study demonstrates that very preterm infants exhibit a high nonspecific esterase activity in umbilical cord blood that is comparable with that of term infants. These results support clinical experiences that remifentanil is rapidly metabolized by preterm infants without prolonged side effects.
Latex Sensitization
Authors: Draisci Gaetano , Zanfini Bruno A. , Nucera Eleonora , Catarci Stefano , Sangregorio Raffaella , Schiavino Domenico , Mannocci Alice , Patriarca Giampiero
Published: January 2011

Background

Previous studies have reported a greater frequency of sensitization to latex in the female population and a higher incidence of anaphylactic reactions to latex during cesarean section. In this study, the authors investigated the prevalence of latex sensitization in obstetric patients compared with nonpregnant subjects.

Methods

Two hundred ninety-four healthy pregnant women who were at term with a singleton fetus and scheduled for caesarean section (group A) were compared with 294 healthy nulliparous women with childbirth potential undergoing gynecologic surgery (group B). Before surgery, patients completed a questionnaire, and venous blood samples were collected to measure specific immunoglobulin E serum concentrations with a fluorescent enzyme immunoassay test. Skin-prick tests were performed if adverse reactions occurred during surgery. Latex allergy was diagnosed on the basis of immunoglobulin E results and/or positive skin-prick tests.

Results

The prevalence of latex sensitization was higher in group A than in group B (15/294, 5.1% vs. 5/294, 1.7%; P < 0.05). A significant difference in specific immunoglobulin E serum concentration was noted between pregnant and nonpregnant patients who had a positive fluorescent enzyme immunoassay test (median serum concentration: 1.93 kilounits/l; interquartile range = 2.28 vs. 0.78 kilounits/l; interquartile range = 1.07; P less than 0.05). Two patients in group A experienced an anaphylactic reaction to latex. Statistical analysis disclosed no association between latex sensitization and accepted risk factor for latex allergy.

Conclusions

The authors report a higher prevalence of latex sensitization in the obstetric population than in nonpregnant subjects undergoing gynecologic surgery.
Antibiotic resistance mechanisms of Vibrio cholerae
Authors: Kitaoka Maya , Miyata Sarah T. , Unterweger Daniel , Pukatzki Stefan
Published: January 2011

As the causative agent of cholera, the bacteriumVibrio choleraerepresents an enormous public health burden, especially in developing countries around the world. Cholera is a self-limiting illness; however, antibiotics are commonly administered as part of the treatment regimen. Here we review the initial identification and subsequent evolution of antibiotic-resistant strains ofV. cholerae. Antibiotic resistance mechanisms, including efflux pumps, spontaneous chromosomal mutation, conjugative plasmids, SXT elements and integrons, are also discussed. Numerous multidrug-resistant strains ofV. choleraehave been isolated from both clinical and environmental settings, indicating that antibiotic use has to be restricted and alternative methods for treating cholera have to be implemented.
Optimal management of β thalassaemia intermedia
Authors: Taher Ali T. , Musallam Khaled M. , Cappellini Maria Domenica , Weatherall David J.
Published: January 2011

Our understanding of the molecular and pathophysiological mechanisms underlying the disease process in patients with β thalassaemia intermedia (TI) has substantially increased over the past decade. The hallmark of disease process in patients with TI includes ineffective erythropoiesis, chronic haemolytic anaemia, and iron overload. There are a number of options currently available for managing patients with TI including splenectomy, transfusion therapy, iron chelation therapy, modulation of fetal haemoglobin production, and several other agents targeting specific clinical complications. Limited studies assessed the efficacy and safety of these modalities; hence, there are currently no clear guidelines for managing patients with TI. Until solid evidence‐based guidelines are available, individualised treatment should be entertained.
Evapotranspiration and plant–atmospheric coupling in a Brachiaria brizantha pasture in the Brazilian savannah region
Authors: Meirelles M. L. , Franco A. C. , Farias S. E. M. , Bracho R.
Published: January 2011

The savannah of central Brazil occupies 208 million ha, of which about 54 million ha have been converted to cultivated pasture. The aim of this study was to provide the dynamics of evapotranspiration (ET) in a Brachiaria brizantha cultivated pasture in the Brazilian Savannah region at the beginning of the rainy season and determine biological and environmental factors that influence ET by using the decoupling approach. A meteorological station and an eddy covariance system were placed at the studied site. The above‐ground biomass production of the B. brizantha pasture responded rapidly to the onset of the rainy season. Leaf area index (LAI) increased from 0·4 to 1·1 between 15 November and 3 December, with a corresponding increase in live biomass. Average ET during the study period was 2·6 ± 0·9 mm. Daily ET was significantly correlated with maximum vapour pressure deficit and precipitation. The average of daytime decoupling factor obtained over 2 d without rain was 0·50 ± 0·06. The B. brizantha pasture deployed in this region showed an intermediate coupling which takes ET to be influenced by both atmospheric conditions and by the available radiation at the canopy.
Broad‐scale latitudinal patterns of genetic diversity among native European and introduced house sparrow (Passer domesticus) populations
Authors: SCHREY A. W. , GRISPO M. , AWAD M. , COOK M. B. , McCOY E. D. , MUSHINSKY H. R. , ALBAYRAK T. , BENSCH S. , BURKE T. , BUTLER L. K. , DOR R. , FOKIDIS H. B. , JENSEN H. , IMBOMA T. , KESSLER‐RIOS M. M. , MARZAL A. , STEWART I. R. K. , WESTERDAHL H. , WESTNEAT D. F. , ZEHTINDJIEV P. , MARTIN L. B.
Published: January 2011

Introduced species offer unique opportunities to study evolution in new environments, and some provide opportunities for understanding the mechanisms underlying macroecological patterns. We sought to determine how introduction history impacted genetic diversity and differentiation of the house sparrow (Passer domesticus), one of the most broadly distributed bird species. We screened eight microsatellite loci in 316 individuals from 16 locations in the native and introduced ranges. Significant population structure occurred between native than introduced house sparrows. Introduced house sparrows were distinguished into one North American group and a highly differentiated Kenyan group. Genetic differentiation estimates identified a high magnitude of differentiation between Kenya and all other populations, but demonstrated that European and North American samples were differentiated too. Our results support previous claims that introduced North American populations likely had few source populations, and indicate house sparrows established populations after introduction. Genetic diversity also differed among native, introduced North American, and Kenyan populations with Kenyan birds being least diverse. In some cases, house sparrow populations appeared to maintain or recover genetic diversity relatively rapidly after range expansion (<50 years; Mexico and Panama), but in others (Kenya) the effect of introduction persisted over the same period. In both native and introduced populations, genetic diversity exhibited large‐scale geographic patterns, increasing towards the equator. Such patterns of genetic diversity are concordant with two previously described models of genetic diversity, the latitudinal model and the species diversity model.
Clopidogrel dilemma for orthopaedic surgeons
Authors: Steele Mitchell J. , Fox John S. , Fletcher John P. , Grigg Leeanne E. , Bell Gordon
Published: January 2011

Background:  Patients medicated with clopidogrel who require orthopaedic surgery present a particular challenge. Whether in an emergency or elective situation the orthopaedic surgeon must balance the risks of ceasing clopidogrel versus the risk of increased bleeding that dual antiplatelet therapy generates.

Method:  This paper reviews the current published evidence regarding the risks of continuing clopidogrel, the risks of discontinuing clopidogrel and associated considerations such as venous thromboprophylaxis.

Results:  Little good quality evidence exists in regard to perioperative clopidogrel for orthopaedic surgery. Available evidence across non‐cardiac and cardiac surgery were assessed and presented in regards to current practices, blood loss for orthopaedic operations, risks when continuing clopidogrel, risks of stopping clopidogrel and also the consideration of venous thromboembolism.

Conclusions:  The patients at greatest risk, when discontinuing clopidogrel therapy, are those with drug eluting stents who may be at risk of stent thrombosis. Where possible, efforts should be made to continue clopidogrel therapy through the perioperative period, taking precautions to minimize bleeding. If the risk of bleeding is too high, antiplatelet therapy must be reinstated as soon as considered reasonable after surgery. In addition, patients on clopidogrel who sustain a fall or other general trauma need to be carefully assessed because of the possibility of occult bleeding, such as into the retroperitoneal space. Until more definitive evidence becomes available, this review aims to provide a guide for the orthopaedic surgeon in dealing with the difficult dilemma of the patient on clopidogrel therapy, recommending that orthopaedic surgeons take a team approach to assess the individual risks for all patients and consider continuation of clopidogrel therapy perioperatively where possible.
Optional inferior vena cava filter use in surgical patients: a Western Australian experience
Authors: Sebunya Jonathan , Baschera Dominik , Isenegger Patrick , Zellweger Rene
Published: January 2011

Background:  The optional filter is gaining ground, supplementing anticoagulation in the management of venous thromboembolism (VTE) in high‐risk surgical patients, this despite knowledge gaps relating to its efficacy. We studied the literature and audited our experience with inferior vena cava filters to educate ourselves on this mode of VTE prophylaxis, particularly its practical implications, if any, for the surgeon.

Methods:  A retrospective clinical study on inferior vena cava filter (IVCF)‐related events in a Western Australian tertiary centre in 2008 was performed. Literature on IVCFs was reviewed.

Results:  The 118 IVCF‐related events at our centre in 2008, involved either Recovery‐G2 75(88%) or Cook‐Celect nine (11%). Of these, 78 were insertions and 36 were retrievals with four failed retrievals (10% of the attempts). Major indications for insertion included multi‐trauma 32 (38%), prothrombotic state 29 (34%), head injury/intracranial bleeding 16 (19%) and others eight (9%). The mean dwelling time was 100 days (12–349 days). The mean age was 43 and the retrieval rate was 58%.

Conclusion:  Optional filters have presented both versatility and challenge to the management of VTE in high‐risk patients. An underlying concern about the quintessential efficacy of IVCFs lingers on, while the impact of lost follow‐ups in young patients is still at large.

Class 1 studies on optional filters would add certainty to the use of this generation of filters, be a step forward in relevance from the seminal work of Decousus and garner the willingness needed to engage teamwork and institutional proactiveness against loopholes such as lost follow‐ups that can undermine the portrayed benefits of a potentially lifesaving device.
Origin and radiation of rissooidean gastropods (Caenogastropoda) in ancient lakes of Sulawesi
Authors: Zielske Susan , Glaubrecht Matthias , Haase Martin
Published: January 2011

Zielske, S., Glaubrecht, M. & Haase, M. (2010). Origin and radiation of rissooidean gastropods (Caenogastropoda) in ancient lakes of Sulawesi. —Zoologica Scripta,40, 221–237.

We investigated diversity and origin of as well as relationships among rissooidean gastropods from the ancient lakes of Sulawesi. Analyses of morphological, anatomical and genetic data (16S rRNA, COI and 18S rRNA) revealed ten new species:Sulawesidrobia perempuansp. n., which is probably parthenogenetic,Sulawesidrobia soedjatmokoisp. n.,Sulawesidrobia mahalonaensissp. n.,Sulawesidrobia ancepssp. n.,Sulawesidrobia bicolorsp. n.,Sulawesidrobia megalodonsp. n.,Sulawesidrobia abreuisp. n.,Sulawesidrobia datarsp. n.,Sulawesidrobia yunusisp. n. andSulawesidrobia towutiensissp. n. In two cases morphological and anatomical differentiation between pairs of species were not paralleled by genetic differentiation suggesting young speciation events and incomplete lineage sorting as a likely explanation. A Bayesian phylogenetic analysis including representatives of most rissooidean families placedSulawesidrobiaPonder & Haase 2005among Tateidae and thus indicated an Australasian origin of the genus. Relationships among the Sulawesian species suggested that isolated Lake Poso was colonised only once whereas the lakes of the Malili system experienced repeated colonizations.
Nicorandil ameliorates ischaemia‐reperfusion injury in the rat kidney
Authors: Shimizu Shogo , Saito Motoaki , Kinoshita Yukako , Ohmasa Fumiya , Dimitriadis Fotios , Shomori Kohei , Hayashi Atsushi , Satoh Keisuke
Published: January 2011

BACKGROUND AND PURPOSE

Nicorandil, an ATP‐sensitive potassium (KATP) channel opener and nitric oxide donor, is used in the treatment of angina and acute heart failure. Here we investigated the effects of two KATPchannel openers, nicorandil and cromakalim on ischaemia reperfusion (I‐R) injury in the kidney.

EXPERIMENTAL APPROACH

Right nephrectomy was performed in 8‐week‐old male Sprague‐Dawley rats and they were then divided into six groups: control group; I‐R, including 30 min of left renal ischaemia followed by 24 h of reperfusion; I‐R groups plus nicorandil 3 or 10 mg·kg−1i.p.; and I‐R groups plus cromakalim 100 or 300 µg·kg−1i.p. After reperfusion, renal function was estimated by serum creatinine (SCr), urinary albumin : creatinine ratio (ACR) and urinary β2‐microglobulin (β2‐MG). Levels of KATPchannel subtypes were investigated by Western blot. Kidney sections were stained for 4‐hydroxy‐2‐nonenal and 8‐hydroxy‐2′‐deoxyguanosine.

KEY RESULTS

Renal I‐R induced significant increases in SCr, ACR and β2‐MG levels compared with the control animals. Treatment with KATPchannel openers reduced urinary β2‐MG levels, raised by I‐R. Both KIR6.1 and KIR6.2 channels were expressed. Expression of KIR6.2 channels in the I‐R group was lower than in the control group, which was restored to normal by treatment with KATPchannel openers. Histologically, severe acute tubular damage was observed in the I‐R kidney and this damage was ameliorated by KATPchannel openers, dose‐dependently.

CONCLUSIONS AND IMPLICATIONS

ATP‐sensitive potassium channel openers protected against proximal tubule damage after I‐R injury. Nicorandil could represent a powerful additional component in the treatment of patients undergoing partial nephrectomy or renal transplantation.
CCAAT/ enhancer‐binding protein β activation by capsaicin contributes to the regulation of CYP1A1 expression, mediated by the aryl hydrocarbon receptor
Authors: Han Eun Hee , Hwang Yong Pil , Kim Hyung Gyun , Choi Jai Ho , Park Bong Hwan , Song Gye Yong , Lee Gye Won , Jeong Tae Cheon , Jeong Hye Gwang
Published: January 2011

BACKGROUND AND PURPOSE

Capsaicin, a constituent of peppers, has been linked to the suppression of tumorigenesis and carcinogenesis. The influence of capsaicin on cytochrome P450 (CYP) 1A1, which is involved in metabolism of carcinogens, and the underlying mechanisms remain unclear. Here, we examined the effect of capsaicin on CYP1A1 expression in mouse hepatoma cells.

EXPERIMENTAL APPROACH

Murine hepatoma Hepa‐1c1c7 cells were incubated with capsaicin and/or 3‐methylcholanthrene (3‐MC). Effects of capsaicin on CYP1A1 levels were determined by analysing mRNA expression, transcription activity and protein expression. Regulation of CYP1A1 was investigated by determining transcriptional factor expression, activation and binding activity with cotreatment with target signal antagonists.

KEY RESULTS

Capsaicin alone slightly induced CYP1A1 activity, mRNA expression, protein level and promoter activity. Treatment with transient receptor potential vanilloid type‐1 receptor (TRPV1) or aryl hydrocarbon receptor (AhR) antagonist decreased induction of CYP1A1 expression by capsaicin. Additionally, capsaicin significantly inhibited 3‐MC‐induced CYP1A1 mRNA and protein level and xenobiotic response element–luciferase activity. Capsaicin also inhibited 3‐MC‐induced AhR transactivation and nuclear localization of AhRs. Moreover, capsaicin increased Ca2+/calmodulin (CaM)‐dependent protein kinase (CaMK) and CCAAT/ enhancer‐binding protein β (C/EBPβ) activation, downstream of TRPV1 receptors. Capsaicin‐induced C/EBPβ activation inhibited induction of CYP1A1 mRNA and protein by 3‐MC.

CONCLUSIONS AND IMPLICATIONS

Capsaicin alone weakly induced CYP1A1 expression, and 3‐MC‐induced CYP1A1 levels were suppressed by capsaicin. Activation of C/EBPβ and inhibition of 3‐MC‐induced AhR transactivation by capsaicin contributed to the suppression of CYP1A1 expression. Capsaicin has a potential chemopreventive effect through inhibiting induction of CYP1A1 by poly aryl hydrocarbons.
Ex Ante Evaluation of Drought‐Tolerant Varieties in Eastern and Central Africa
Authors: Kostandini Genti , Mills Bradford , Mykerezi Elton
Published: January 2011

This study presents a model to estimate potential benefits of drought‐tolerant varieties of maize, sorghum and millet in Kenya, Uganda and the Amhara region of Ethiopia. In addition to the benefits from mean yield increases, the model takes into account risk benefits associated with yield‐stabilising varieties. Ex ante estimates provided for different drought zones and for different household types within drought zones of each country suggest that drought resistance generates substantial benefits from both mean yield improvements and yield variance reductions for both consumers and small, medium and large producers.
The Incidence of EU Per‐Hectare Payments on Farmland Rental Rates: A Spatial Econometric Analysis of German Farm‐Level Data
Authors: Breustedt Gunnar , Habermann Hendrik
Published: January 2011

This article analyses determinants for 2001 farmland rental prices from 3,819 farms in Germany. Based on specification tests we estimate a general spatial model to account for both spatial relationships among rental prices of neighbouring farmers and spatially autocorrelated error terms. A €1 per hectare higher rental price in a farmer’s neighbourhood coincides with a €0.72 higher rental price paid by the farmer. The marginal incidence of EU per‐hectare payments paid for eligible arable crop land on rental rates amounts to €0.38 for each additional €1 of premium payments. Regional livestock density, which is indirectly influenced by different policies, is also a major determinant of rental prices. Results are confirmed by sensitivity analyses. Consequently, German farmland rental rates are heavily influenced by agricultural policy instruments and therefore, these policies exhibit substantial distributional effects.
The impact of land reallocation on technical efficiency: evidence from China
Authors: Zhang Yanjie , Wang Xiaobing , Glauben Thomas , Brümmer Bernhard
Published: January 2011

China's rural reforms expose farm households to an increased risk of administrative land reallocation and adjustment. This study explores the impact of land reallocation on technical efficiency, based on a panel data set from rural households in Zhejiang, Hubei, and Yunnan provinces between 1995 and 2002. Our research indicates that the development of a land rental market could serve as a substitute for administrative land reallocation in optimizing the distribution of land resources. The results from the stochastic frontier production function show that land reallocation does have effects on technical efficiency. The different signs for different provinces indicate that the impact of land reallocation on technical efficiency is an empirical issue and depends on the specific institutional settings and the overall economic environment in each province.
Double‐stranded RNA induces melanocyte death via activation of Toll‐like receptor 3
Authors: Yu Ning , Zhang Shujie , Sun Tao , Kang Kefei , Guan Ming , Xiang Leihong
Published: January 2011

Abstract:  As cutaneous pigment‐producing cells, melanocytes can become targets of primary and secondary immune response as can be seen in diseases like vitiligo and Vogt–Koyanagi–Harada (VKH) syndrome. Viral infections have previously been implicated as a possible precipitating factor in the destruction of melanocytes in these disorders. During viral replication, double‐stranded RNA (dsRNA) is produced as an intermediate metabolite, which induces antiviral and inflammatory responses through Toll‐like receptor 3 (TLR3) in cells of innate immune system. The functional responses of melanocytes to dsRNA, however, remain unclear. Herein, we demonstrated that human melanocytes expressed TLR3 at a constitutive and inducible level. Stimulation with poly(I:C), a synthetic dsRNA analogue, triggered apoptosis of melanocytes. The apoptosis‐inducing effect was shown by RNA interference to be largely dependent on TLR3, but occurred independently of NF‐κB activation since treatment with specific NF‐κB inhibitor Bay 11‐7082 failed to prevent the process. In contrast, IFN‐β neutralizing Ab blocked the apoptosis‐inducing effect of dsRNA, indicating the involvement of IFN‐β autocrine signalling. Furthermore, studies on the intracellular signal transduction pathways revealed that dsRNA induces the activation of p38, ERK1/2 and JNK1/2 in melanocytes. Using specific inhibitors, we demonstrated that activation of p38 and ERK1/2 controlled both IFN‐β secretion and IFN‐β mediated cell death. Taken together, these data suggest that viral dsRNA stimulates TLR3 in human melanocytes and triggers the cellular apoptosis through autocrine of IFN‐β.
Hypothyroidism caused by phenobarbital affects patterns of estrous cyclicity in rats
Authors: Li Yumei , Kumazawa Toshihiko , Ishiguro Tsukasa , Kawakami Yuriko , Nishitani Hiromi , Tagawa Yoshiaki , Matsumoto Yukiharu
Published: January 2011

We found that repeated treatment with phenobarbital (PB), a thyroid modulator, resulted in a persistent estrous stage in the present study. Although the effects of PB in blocking the surge release of luteinizing hormone (LH), inducing anovulation and prolonging the diestrous period has been well established, there is still no research describing the appearance of persistent estrous states in normal cycling rats dosed with PB. To further study this phenomenon, female rats exhibiting regular estrous cycle were administered an oral dose of PB for 14 consecutive days. Consecutively, vaginal smears were observed and rats from all the groups were sacrificed and serum hormone levels for prolactin, progesterone, estradiol, triiodothyronin (T3), thyroxine (T4) and thyroid stimulating hormone (TSH) were measured. Pituitary, thyroid, liver, uteri and ovaries were excised, weighed and further subjected to histological observations. We found that PB induced irregular estrous cycles, especially persistent estrus in rats. Histopathologically, the persistent estrous stages are characterized by persistent vaginal cornification in the vagina, cystic follicles and anovulation in the ovaries. Endocrinologically, serum T3 and T4 levels were significantly lower, and TSH was higher in treated‐female rats compared to control females. The serum estradiol level and the estradiol/progesterone ratio tend to increase in treated‐females. Furthermore, PB‐treated animals with irregular estrous cycle were reduced by T4 replacement. Our data indicate that treatment with PB resulted in hypothyroidism and irregular estrous cycle, particularly a persistent estrous stage in normal cycling female rats.
A New Connection Structure Between Hydrogen Nozzle and Sphere Head in a Hydrofining Reactor
Authors: Jiang Wenchun , Wang Z. B. , Gong J. M. , Li G. C.
Published: January 2011

This paper presents a study of the residual stress in the welding connection between hydrogen nozzle and spherical head in a hydrofining reactor. A sequential coupling finite element program is developed to analyze the residual stress in nozzle-to-sphere connection. The results show that large residual stresses are generated in the weld and weld/parent interface during the welding of hydrogen nozzle. Large axial stress is generated on the internal surface of hydrogen nozzle due to the angular deformation, which has a great effect on hydrogen induced cracking (HIC) and stress corrosion cracking (SCC). Based on the residual stress distribution character, a new connection structure between hydrogen nozzle and head is developed. A stressless flanging is proposed to insert into the nozzle to isolate the residual stresses, which can be useful to prevent HIC and SCC. To cover all the residual stresses effectively, the arc length of flanging should be not less than 80 mm.
Experimental evaluation of an adaptive Joule–Thomson cooling system including silicon-microfabricated heat exchanger and microvalve components
Authors: Zhu Weibin , Park Jong M. , White Michael J. , Nellis Gregory F. , Gianchandani Yogesh B.
Published: January 2011

This article reports the evaluation of a Joule–Thomson (JT) cooling system that combines two custom micromachined components—a Si/glass-stack recuperative heat exchanger and a piezoelectrically actuated expansion microvalve. With the microvalve controlling the flow rate, this system can modulate cooling to accommodate varying refrigeration loads. The perforated plate Si/glass heat exchanger is fabricated with a stack of alternating silicon plates and Pyrex glass spacers. The microvalve utilizes a lead zirconate titanate actuator to push a Si micromachined valve seat against a glass plate, thus modulating the flow passing through the gap between the valve seat and the glass plate. The fabricated heat exchanger has a footprint of 1×1 cm2 and a length of 35 mm. The size of the micromachined piezoelectrically actuated valve is about 1×1×1 cm3. In JT cooling tests, the temperature of the system was successfully controlled by adjusting the input voltage of the microvalve. When the valve was fully opened (at an input voltage of −30 V), the system cooled down to a temperature as low as 254.5 K at 430 kPa pressure difference between inlet and outlet at steady state and 234 K at 710 kPa in a transient state. The system provided cooling powers of 75 mW at 255 K and 150 mW at 258 K. Parasitic heat loads at 255 K are estimated at approximately 700 mW.
Retrieval Practice Produces More Learning than Elaborative Studying with Concept Mapping
Authors: Karpicke Jeffrey D. , Blunt Janell R.
Published: January 2011

Two different ways of thinking through texts are compared for learning value.
Comparison of the k-nearest neighbor technique with geographical calibration for estimating forest growing stock volumeThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Yim Jong Su , Kim Young Hwan , Kim Sung Ho , Jeong Jin Hyun , Shin Man Yong
Published: January 2011

National Forest Inventories (NFIs) have been used in many countries to assess forest resources at the national level. To facilitate the estimation of forest growing stock volume at more regional scales, the k-nearest neighbor (k-NN) technique was applied in this research to obtain estimates for unmeasured areas by using NFI field data and optical satellite data. The NFI field data were assigned to data sets of three different sample sizes to evaluate the effect of sample size on the accuracy of k-NN estimates. In small-area estimation, calibration techniques, in which samples surveyed outside a county of interest are employed to produce estimates for the county, are often adopted due to the lack of sample observations for the county of interest. Thus, the k-NN estimates, forest growing stock volume and areal proportions by forest types, were compared with estimates obtained from field data with and without calibration. The results indicated that the accuracy of k-NN estimates could be improved as sample size increased. Also, the k-NN technique provided acceptable estimates for small-area estimation. Although there was no significant difference with the calibration approach (p > 0.18), k-NN has potential for small-area estimation and is useful to generate thematic maps of forest attributes.
Model-based inference for biomass estimation in a LiDAR sample survey in Hedmark County, NorwayThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Ståhl Göran , Holm Sören , Gregoire Timothy G. , Gobakken Terje , Næsset Erik , Nelson Ross
Published: January 2011

In forest inventories, regression models are often applied to predict quantities such as biomass at the level of sampling units. In this paper, we propose a model-based inference framework for combining sampling and model errors in the variance estimation. It was applied to airborne laser (LiDAR) data sets from Hedmark County, Norway, where the model error proportion of the total variance was found to be large for both scanning (airborne laser scanning) and profiling LiDAR when biomass was estimated. With profiling LiDAR, the model error variance component for the entire county was as large as 71% whereas for airborne laser scanning, it was 43% of the total variance. Partly, this reflects the better accuracy of the pixel-based regression models estimated from scanner data as compared with the models estimated from profiler data. The framework proposed in our study can be applied in all types of sample surveys where model-based predictions are made at the level of individual sampling units. Especially, it should be useful in cases where model-assisted inference cannot be applied due to the lack of a probability sample from the target population or due to problems of correctly matching observations of auxiliary and target variables.
Estimating forest edge length from forest inventory sample dataThis article is one of a selection of papers from Extending Forest Inventory and Monitoring over Space and Time.
Authors: Kleinn Christoph , Kändler Gerald , Schnell Sebastian
Published: January 2011

Forest edge length is important for landscape ecological analysis, including the analysis of fragmentation. In this paper, we estimate forest edge length using field sample data from the German National Forest Inventory as an example. The complex plot design of many large-area forest inventories allows for the estimation of forest edge length at different spatial resolutions. As expected, estimates depend on the spatial resolution: longer estimated edge lengths resulted from observations at finer spatial resolutions. From the comparison of estimated edge lengths at different spatial resolutions, conclusions about the irregularity of forest edges can be drawn: more irregular forest boundaries resulted in greater differences between the estimated lengths for different spatial resolutions. One conclusion is of particular relevance: reported forest edge length values are meaningless unless their spatial resolution is also reported. The analysis presented is an add-on to the standard estimations from a forest inventory, producing additional, ecologically meaningful information. It is contended that many more nonstandard analyses of forest inventory data are possible either immediately or with minor modifications to the plot design.
Statistical models to identify stand development stages by means of stand characteristics
Authors: Huber Markus O.
Published: January 2011

Stand development stages differ mainly in terms of stand structure, stand density, and mortality patterns. As the fulfilment of socio-economic forest functions often depends on stand structure and density, knowledge of the frequency and distribution of stand development stages is needed for optimal forest management. Development stages have been previously identified only qualitatively by experts in forest ecology, but this study developed and compared statistical models to identify development stages by means of stand characteristics. Data from the Austrian National Forest Inventory with 4761 observations of stand development stages were used as the training data set for quadratic discriminant analysis and multinomial logistic regression. The models differ only marginally in terms of the hit ratio and the overall kappa statistic (both determined by means of an independent test data set). The quadratic discriminant analysis has the advantage that the user can reduce or even avoid the influence of the group size on the group-specific model performance by using equal prior probabilities. Furthermore, the discriminant analysis showed the best model behaviour in terms of the explanatory variables and performed best in identifying the stages that were infrequent in the training data set.
Incorporating genetic variation into a model of budburst phenology of coast Douglas-fir (Pseudotsuga menziesii var. menziesii)
Authors: Gould Peter J. , Harrington Constance A. , St. Clair J. Bradley
Published: January 2011

Models to predict budburst and other phenological events in plants are needed to forecast how climate change may impact ecosystems and for the development of mitigation strategies. Differences among genotypes are important to predicting phenological events in species that show strong clinal variation in adaptive traits. We present a model that incorporates the effects of temperature and differences among genotypes to predict the timing of budburst of coast Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco). The main components of the model are (i) functions to calculate the accumulation of chilling units (CU) and forcing units (FU) during dormancy and (ii) a function defining the combinations of CU and FU needed for budburst (the possibility line). The possibility line was fit to data from 59 populations subjected to eight different winter environments. Differences among populations were incorporated into the possibility line using population coefficients that vary the FU required for budburst. Correlations among the population coefficients and variables describing local environments supported the hypothesis that genetic variation in budburst is largely an adaptation to summer drought. The new model can be used to test potential seed transfers as a strategy to mitigate some of the effects of climate change.
Regeneration ecology of sugar maple (Acer saccharum): seedling survival in relation to nutrition, site factors, and damage by insects and pathogens
Authors: Cleavitt Natalie L. , Fahey Timothy J. , Battles John J.
Published: January 2011

The possible regeneration failure of sugar maple ( Acer saccharum Marsh.) as part of their decline has been not well explored using field studies. We sought to clarify the roles of maternal effects and dynamics of early-season survival in contributing to the previously documented pattern of larger seedlings and higher seedling densities on a Ca-treated watershed (CAL) at Hubbard Brook Experimental Forest. We used a reciprocal seed planting experiment at four sites, two sites per watershed blocked by elevation. Regardless of maternity, sugar maple seedlings planted in CAL had higher survival than seedlings in the reference watershed. However, this advantage was not as clearly linked to the Ca amendment as in our previous work, probably, in part, because Ca availability has decreased over time. Maternal effects on seed chemistry and some seedling traits were detected, but these were not strong determinants of survival. Site was a good predictor of early seedling survival with litter layer depth, pathogen prevalence, and soil chemistry all contributing to the explanatory power of site. The strength of Ca,addition effects on sugar maple regeneration from seed depends on initial soil characteristics, application amounts, and interactions of the amendment with other factors such as leaf litter cycling, weather, and pathogens.
ON STRING LANGUAGES GENERATED BY SPIKING NEURALPSYSTEMS WITH ANTI-SPIKES
Authors: KRITHIVASAN KAMALA , METTA VENKATA PADMAVATI , GARG DEEPAK
Published: January 2011

An Spiking Neural P system with anti-spikes uses two types of objects called spikes and anti-spikes which can encode binary digits in a natural way. The step when system emits a spike or an anti-spike is associated with symbol 1 and 0, respectively. Here we consider these computing devices as language generators. They allow non-determinism between the rules ac→ a and ac→ ā, c ϵ ℕ, thus help to generate languages which cannot be generated using simple SN P systems.
PSYSTEMS WITH PROTEINS ON MEMBRANES: A SURVEY
Authors: PĂUN ANDREI , PĂUN MIHAELA , RODRÍGUEZ-PATÓN ALFONSO , SIDOROFF MANUELA
Published: January 2011

The paper is a survey of the recent model of P systems with proteins on membranes introduced by Păun and Popa in 2006. This model can be viewed as an extension of the highly successful paper of (Păun and Păun 2002) describing P systems based on symport/antiport. The previous model represented an important change of direction from strings to objects in the area of P systems. The main drawback of the model from 2002 was the massive parallelism that is not seen in real life. The 2006 model was a step in controlling the parallelism the same way it is done in nature in symporters and antiporters: these processes take place through protein channels embedded at the level of the membrane which can only be used by a molecule at a time, thus yielding a sequentiality with respect to the number of such proteins embedded in the membrane.
LOG-GAIN STOICHIOMETRIC STEPWISE REGRESSION FOR MP SYSTEMS
Authors: MANCA VINCENZO , MARCHETTI LUCA
Published: January 2011

MP systems are a class of P systems introduced for modeling metabolic processes. Here a regression method is presented for deducing a MP system exhibiting the dynamics of an observed metabolic system. In the procedure here described the knowledge of the stoichiometry of the system is combined with the log-gain principle of MP systems and is integrated with the Least Square Estimation method and with the stepwise regression approximation.
FORMAL VERIFICATION OF P SYSTEMS USING SPIN
Authors: IPATE FLORENTIN , LEFTICARU RALUCA , TUDOSE CRISTINA
Published: January 2011

This paper presents an approach to P system verification using the Spin model checker. It proposes a P system implementation in PROMELA, the modeling language accepted by SPIN. It also provides the theoretical background for transforming the temporal logic properties expressed for the P system into properties of the executable implementation. Furthermore, a comparison between P systems verification using SPIN and NUSMV is realized. The results obtained show that the PROMELA implementation is more adequate, especially for verifying more complex models, such as P systems that model ecosystems.
P SYSTEMS AND TOPOLOGY: SOME SUGGESTIONS FOR RESEARCH
Authors: FRISCO PIERLUIGI , HOOGEBOOM HENDRIK JAN
Published: January 2011

Lately, some studies linked the computational power of abstract computing systems based on multiset rewriting to Petri nets and the computation power of these nets to their topology. In turn, the computational power of these abstract computing devices can be understood just looking at their topology, that is, information flow.

This line of research is very promising for several aspects: (i) its results are valid for a broad range of systems based on multiset rewriting; (ii) it allows to know the computational power of abstract computing devices without tedious proofs; (iii) it links computational power to topology and, in this way, it opens a broad range of questions.

In this paper we summarise the known results on this topic and we list a few suggestions for research together with the relevance of possible outcomes.
AN OBSERVER-BASED DE-QUANTISATION OF DEUTSCH'S ALGORITHM
Authors: CALUDE CRISTIAN S. , CAVALIERE MATTEO , MARDARE RADU
Published: January 2011

Deutsch's problem is the simplest and most frequently examined example of computational problem used to demonstrate the superiority of quantum computing over classical computing. Deutsch's quantum algorithm has been claimed to be faster than any classical ones solving the same problem, only to be discovered later that this was not the case. Various de-quantised solutions for Deutsch's quantum algorithm—classical solutions which are as efficient as the quantum one—have been proposed in the literature. These solutions are based on the possibility of classically simulating "superpositions", a key ingredient of quantum algorithms, in particular, Deutsch's algorithm. The de-quantisation proposed in this note is based on a classical simulation of the quantum measurement achieved with a model of observed system. As in some previous de-quantisations of Deutsch's quantum algorithm, the resulting de-quantised algorithm is deterministic. Finally, we classify observers (as finite state automata) that can solve the problem in terms of their "observational power".
Resistance and aerobic exercise protects against acute endothelial impairment induced by a single exposure to hypertension during exertion
Authors: Phillips Shane A. , Das Emon , Wang Jingli , Pritchard Kirkwood , Gutterman David D.
Published: January 2011

Resistance and aerobic exercise is recommended for cardiovascular health and disease prevention. However, the accompanying increase in arterial pressure during resistance exercise may be detrimental to vascular health. This study tests the vascular benefits of aerobic compared with resistance exercise on preventing impaired vascular function induced by a single weight lifting session that is associated with acute hypertension. Healthy, lean sedentary (SED) subjects, weight lifters, runners (>15 miles/wk), and cross trainers (chronic aerobic and resistance exercisers), underwent a single progressive leg press weight lifting session with blood pressure measurements. Brachial artery flow-mediated vasodilation (FMD; an index of arterial endothelial function) was determined using ultrasonography immediately before and after weight lifting. Sublingual nitroglycerin (0.4 mg) was used to determine endothelium-independent dilation after weight lifting. All subjects were normotensive with similar blood pressure responses during exercise. Baseline FMD was lower in runners (5.4 ± 0.5%; n = 13) and cross trainers (4.44 ± 0.3%; n = 13) vs. SED (8.5 ± 0.8%; n = 13; P = 0.037). Brachial FMD improved in conditioned weight lifters (to 8.8 ± 0.9%; P = 0.007) and runners (to 7.6 ± 0.6%; P < 0.001) but not cross trainers (to 5.3 ± 0.6%; P = NS) after acute hypertension. FMD was decreased in SED (to 5.7 ± 0.4%; P = 0.019). Dilation to nitroglycerin was similar among groups. These data suggest that endothelial responses are maintained after exposure to a single bout of weight lifting in resistance and aerobic athletes. Resistance and aerobic exercise may confer similar protection against acute vascular insults such as exertional hypertension.