bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial production host selection for converting second-generation feedstocks into bioproducts
Authors: Rumbold Karl , van Buijsen Hugo JJ , Overkamp Karin M , van Groenestijn Johan W , Punt Peter J , Werf Mariët J van der 
Published: December 2009

Abstract

Background
Increasingly lignocellulosic biomass hydrolysates are used as the feedstock for industrial fermentations. These biomass hydrolysates are complex mixtures of different fermentable sugars, but also inhibitors and salts that affect the performance of the microbial production host. The performance of six industrially relevant microorganisms, i.e. two bacteria (Escherichia coli and Corynebacterium glutamicum), two yeasts (Saccharomyces cerevisiae and Pichia stipitis) and two fungi (Aspergillus niger and Trichoderma reesei) were compared for their (i) ability to utilize monosaccharides present in lignocellulosic hydrolysates, (ii) resistance against inhibitors present in lignocellulosic hydrolysates, (iii) their ability to utilize and grow on different feedstock hydrolysates (corn stover, wheat straw, sugar cane bagasse and willow wood). The feedstock hydrolysates were generated in two manners: (i) thermal pretreatment under mild acid conditions followed by enzymatic hydrolysis and (ii) a non-enzymatic method in which the lignocellulosic biomass is pretreated and hydrolyzed by concentrated sulfuric acid. Moreover, the ability of the selected hosts to utilize waste glycerol from the biodiesel industry was evaluated.

Results
Large differences in the performance of the six tested microbial production hosts were observed. Carbon source versatility and inhibitor resistance were the major discriminators between the performances of these microorganisms. Surprisingly all 6 organisms performed relatively well on pretreated crude feedstocks. P. stipitis and A. niger were found to give the overall best performance C. glutamicum and S. cerevisiae were shown to be the least adapted to renewable feedstocks.

Conclusion
Based on the results obtained we conclude that a substrate oriented instead of the more commonly used product oriented approach towards the selection of a microbial production host will avoid the requirement for extensive metabolic engineering. Instead of introducing multiple substrate utilization and detoxification routes to efficiently utilize lignocellulosic hydrolysates only one biosynthesis route forming the product of interest has to be engineered.
Determination of the Plasmodium vivax relapse pattern in Camopi, French Guiana
Authors: Hanf Matthieu , Stéphani Aurélia , Basurko Célia , Nacher Mathieu , Carme Bernard 
Published: December 2009

Abstract

Background
Malaria is a major public health problem in French Guiana, where Plasmodium vivax has become the dominant malaria species since 2000. As in others endemic areas, it is important to specify the pattern of vivax malaria relapses and to try to discriminate efficiently re-infections from relapses.

Methods
This study was conducted in children born between January 1, 2001 and December 31, 2008 in Camopi, an Amerindian village located in the Amazon forest (n = 325), using an open cohort design. Primary and secondary attack rates of P. vivax were calculated using survival analysis. With the difference between the primary and secondary rates, this study aimed to estimate indirectly P. vivax relapse rate and evaluate its time evolution.

Results
Of the 1042 malaria attacks recorded, 689 (66%) were due to P. vivax (without mixed infection). One hundred and fifty one children had their primary attack with P. vivax and 106 had their two first attacks with P. vivax. In the absence of primaquine treatment, it was shown that P. vivax relapses mainly occurred during the first three months after the first attack. Thirty percent of children never had a relapse, 42% had a relapse before the first month after primary attack, 59% before the second month and 63% before the third month.

Conclusion
This study confirmed that the relapse pattern in Camopi was compatible with the pattern described for the P. vivax Chesson (tropical) strain. In addition, due to the relapse rate time evolution, a simple arbitrary classification rule could be constructed: before 90 days after the primary attack, the secondary attack is a relapse; after 90 days, it is a re-infection. Adapted management of malaria cases based on these results could be devised.
Haemoglobin interference and increased sensitivity of fluorimetric assays for quantification of low-parasitaemia Plasmodium infected erythrocytes
Authors: Moneriz Carlos , Marín-García Patricia , Bautista José M , Diez Amalia , Puyet Antonio 
Published: December 2009

Abstract

Background
Improvements on malarial diagnostic methods are currently needed for the correct detection in low-density Plasmodium falciparum infections. Microfluorimetric DNA-based assays have been previously used for evaluation of anti-malarial drug efficacy on Plasmodium infected erythrocytes. Several factors affecting the sensitivity of these methods have been evaluated, and tested for the detection and quantification of the parasite in low parasitaemia conditions.

Methods
Parasitaemia was assessed by measuring SYBRGreen I® (SGI) and PicoGreen® (PG) fluorescence of P. falciparum Dd2 cultures on human red blood cells. Different modifications of standard methods were tested to improve the detection sensitivity. Calculation of IC50 for chloroquine was used to validate the method.

Results
Removal of haemoglobin from infected red-blood cells culture (IRBC) increased considerably the fluorescent signal obtained from both SGI and PG. Detergents used for cell lysis also showed to have an effect on the fluorescent signal. Upon depletion of haemoglobin and detergents the fluorescence emission of SGI and PG increased, respectively, 10- and 60-fold, extending notably the dynamic range of the assay. Under these conditions, a 20-fold higher PG vs. SGI fluorescent signal was observed. The estimated limits of detection and quantification for the PG haemoglobin/detergent-depleted method were 0.2% and 0.7% parasitaemia, respectively, which allow the detection of ~10 parasites per microliter. The method was validated on whole blood-infected samples, displaying similar results as those obtained using IRBC. Removal of white-blood cells prior to the assay allowed to increase the accuracy of the measurement, by reducing the relative uncertainty at the limit of detection from 0.5 to 0.1.

Conclusion
The use of PG microassays on detergent-free, haemoglobin-depleted samples appears as the best choice both for the detection of Plasmodium in low-density infections and anti-malarial drugs tests.
Involvement of cyclin B1 in progesterone-mediated cell growth inhibition, G2/M cell cycle arrest, and apoptosis in human endometrial cell
Authors: Tang Li , Zhang Yu , Pan Hong , Luo Qiong , Zhu Xiao-Ming , Dong Min-Yue , Leung Peter CK , Sheng Jian-Zhong , Huang He-Feng 
Published: December 2009

Abstract

Background
Progesterone plays an important role in the proliferation and differentiation of human endometrial cells (hECs). Large-dose treatment with progesterone has been used for treatment of endometrial proliferative disorders. However, the mechanisms behind remain unknown.

Methods
To investigate the role of cyclin B1 in proliferation and differentiation of hECs in menstrual cycle, the expression of cyclin B1 throughout the menstrual cycle was evaluated in hECs. To determine the effects of progesterone on the proliferation, cell cycle progression and apoptosis of hECs and to test if cyclin B1 is involved in these effects, progesterone and/or Alsterpaullone (Alp, a specific inhibitor of Cyclin B1/Cdc2) were added to primary hECs. Cellular proliferation was evaluated with MTT test, cell cycle with propidium iodide (PI) staining and flow cytometry, apoptosis with FITC-Annexin V and the expression of cyclin B1 with Western blotting.

Results
The expression level of cyclin B1 in secretory endometria was significantly lower than in proliferative endometria (p < 0.01). Progesterone significantly inhibited the growth of hECs in a concentration-dependent manner (P < 0.01). The treatment with progesterone significantly decreased the expression of cyclin B1, increased the proportions of cell in G2/M phase, and apoptotic cells (P < 0.05 for all). The presence of Alp significantly enhanced the effects of progesterone on cyclin B1 down-regulation, G2/M cell cycle arrest and induction of apoptosis (P < 0.01 for all).

Conclusion
Our findings suggest that cyclin B1 is a critical factor in proliferation and differentiation of hECs. Progesterone may inhibit cell proliferation, mediate G2/M cell cycle arrest and induce apoptosis in hECs via down-regulating Cyclin B1.
Initiation of the expression of peroxisome proliferator - activated receptor gamma (PPAR gamma) in the rat ovary and the role of FSH
Authors: Long Mary J , Sairam M Ram , Komar Carolyn M 
Published: December 2009

Abstract
PPARgamma is highly expressed in granulosa cells by 23 days post-partum (pp) and is down-regulated in response to the LH surge. We tested the hypothesis that high levels of FSH during the neonatal period trigger the expression of PPARgamma. To determine when PPARgamma expression is initiated, ovaries were collected from neonatal rats. Messenger RNA for PPARgamma was undetectable on day 1, low from days 5-14, and increased by day 19 pp (p < 0.05). PPARgamma was detected in select granulosa cells in primary/early secondary follicles. Messenger RNA for the FSH receptor was detected as early as day 1 and remained steady throughout day 19 pp. The FSH receptor was detected by immunoblot analysis in ovaries collected 1, 2, and 5-9 days pp. In a subsequent experiment, neonatal rats were treated with acyline (GnRH antagonist) which significantly reduced FSH (p < 0.05) but not levels of mRNA for PPARgamma. The role of FSH in the induction of PPARgamma expression was further assessed in ovarian tissue from FORKO mice. Both mRNA and protein for PPARgamma were identified in ovarian tissue from FORKO mice. In summary, the FSH/FSH receptor system is present in granulosa cells prior to the onset of expression of PPARgamma. Reducing FSH during the neonatal period, or the ability to respond to FSH, did not decrease expression of mRNA for PPARgamma. These data indicate that FSH is not a primary factor initiating the expression of PPARgamma and that other agents play a role in activating its expression in the ovary.
Multiple non-cell-autonomous defects underlie neocortical callosal dysgenesis in Nfib-deficient mice
Authors: Piper Michael , Moldrich Randal X , Lindwall Charlotta , Little Erica , Barry Guy , Mason Sharon , Sunn Nana , Kurniawan Nyoman Dana , Gronostajski Richard M , Richards Linda J 
Published: December 2009

Abstract
Background
Agenesis of the corpus callosum is associated with many human developmental syndromes. Key mechanisms regulating callosal formation include the guidance of axons arising from pioneering neurons in the cingulate cortex and the development of cortical midline glial populations, but their molecular regulation remains poorly characterised. Recent data have shown that mice lacking the transcription factor Nfib exhibit callosal agenesis, yet neocortical callosal neurons express only low levels of Nfib. Therefore, we investigate here how Nfib functions to regulate non-cell-autonomous mechanisms of callosal formation.

Results
Our investigations confirmed a reduction in glial cells at the midline in Nfib-/- mice. To determine how this occurs, we examined radial progenitors at the cortical midline and found that they were specified correctly in Nfib mutant mice, but did not differentiate into mature glia. Cellular proliferation and apoptosis occurred normally at the midline of Nfib mutant mice, indicating that the decrease in midline glia observed was due to deficits in differentiation rather than proliferation or apoptosis. Next we investigated the development of callosal pioneering axons in Nfib-/- mice. Using retrograde tracer labelling, we found that Nfib is expressed in cingulate neurons and hence may regulate their development. In Nfib-/- mice, neuropilin 1-positive axons fail to cross the midline and expression of neuropilin 1 is diminished. Tract tracing and immunohistochemistry further revealed that, in late gestation, a minor population of neocortical axons does cross the midline in Nfib mutants on a C57Bl/6J background, forming a rudimentary corpus callosum. Finally, the development of other forebrain commissures in Nfib-deficient mice is also aberrant.

Conclusion
The formation of the corpus callosum is severely delayed in the absence of Nfib, despite Nfib not being highly expressed in neocortical callosal neurons. Our results indicate that in addition to regulating the development of midline glial populations, Nfib also regulates the expression of neuropilin 1 within the cingulate cortex. Collectively, these data indicate that defects in midline glia and cingulate cortex neurons are associated with the callosal dysgenesis seen in Nfib-deficient mice, and provide insight into how the development of these cellular populations is controlled at a molecular level.
Altemeier operation associated with dynamic graciloplasty: a case report
Authors: Mongardini Massimo , Iachetta Roberto Paolo , Cola Alessandra , Effetti Eleonora Degli , Custureri Filippo 
Published: December 2009

Abstract

Introduction
More than 80% of patients with full-thickness rectal prolapse have co-existing fecal incontinence. Choosing the ideal surgical strategy is always a difficult task. We combined an Altemeier rectosigmoid resection with anal dynamic graciloplasty to provide a functional neosphincter. We found no published reports describing this surgical association.

Case presentation
We report the case of a 72-year-old Caucasian woman with full-thickness rectal prolapse associated with fecal incontinence from severe neuromuscular damage.

Conclusion
Combined dynamic graciloplasty and an Altemeier operation could be a valid therapeutic option in patients with severe rectal prolapse with fecal incontinence from severe neurogenic damage.
Antimicrobial effect of silver-impregnated cellulose: potential for antimicrobial therapy
Authors: Kim Juyoung , Kwon Soonjo , Ostler Erik 
Published: December 2009

Abstract

Background
Silver has long been known to have antimicrobial activity. To incorporate this property into multiple applications, a silver-impregnated cellulose (SIC) with low cytotoxicity to human cells was developed. SIC differs from other silver treatment methods in that the leaching of silver particles is non-existent and the release of ionic silver is highly controlled.

Results

Candida albicans, Micrococcus luteu, Pseudomonas putida, and Escherichia coli were used for antimicrobial testing. No microbial cells were able to grow in the presence of SIC at concentrations above 0.0035 Ag w/v %. Even at a concentration of 0.00035 Ag w/v %, P. putida and M. luteu failed to grow, and C. albicans and E. coli exhibited diminished growth. To determine the cytotoxic effect of silver on human cells, five different concentrations of SIC were tested on human fibroblasts. In SIC concentrations of 0.035 Ag w/v % and below, no cytotoxicity was observed.

Conclusion
The optimal concentration of SIC for a broad range of anti-microbial activity and low or negligible cytotoxicity was 0.0035 Ag w/v %. Although the highly controlled releasing characteristics of SIC would prove a substantial improvement over current technologies, further investigation for genotoxicity and other biocompatibility test will be required.
The impacts of pretreatment on the fermentability of pretreated lignocellulosic biomass: a comparative evaluation between ammonia fiber expansion and dilute acid pretreatment
Authors: Lau Ming W , Gunawan Christa , Dale Bruce E 
Published: December 2009

Abstract

Background
Pretreatment chemistry is of central importance due to its impacts on cellulosic biomass processing and biofuels conversion. Ammonia fiber expansion (AFEX) and dilute acid are two promising pretreatments using alkaline and acidic pH that have distinctive differences in pretreatment chemistries.

Results
Comparative evaluation on these two pretreatments reveal that (i) AFEX-pretreated corn stover is significantly more fermentable with respect to cell growth and sugar consumption, (ii) both pretreatments can achieve more than 80% of total sugar yield in the enzymatic hydrolysis of washed pretreated solids, and (iii) while AFEX completely preserves plant carbohydrates, dilute acid pretreatment at 5% solids loading degrades 13% of xylose to byproducts.

Conclusion
The selection of pretreatment will determine the biomass-processing configuration, requirements for hydrolysate conditioning (if any) and fermentation strategy. Through dilute acid pretreatment, the need for hemicellulase in biomass processing is negligible. AFEX-centered cellulosic technology can alleviate fermentation costs through reducing inoculum size and practically eliminating nutrient costs during bioconversion. However, AFEX requires supplemental xylanases as well as cellulase activity. As for long-term sustainability, AFEX has greater potential to diversify products from a cellulosic biorefinery due to lower levels of inhibitor generation and lignin loss.
3PFDB - A database of Best Representative PSSM Profiles (BRPs) of Protein Families generated using a novel data mining approach
Authors: Shameer Khader , Nagarajan Paramasivam , Gaurav Kumar , Sowdhamini Ramanathan 
Published: December 2009

AbstractBackgroundProtein families could be related to each other at broad levels that group them as superfamilies. These relationships are harder to detect at the sequence level due to high evolutionary divergence. Sequence searches are strongly directed and influenced by the best representatives of families that are viewed as starting points. PSSMs are useful approximations and mathematical representations of protein alignments, with wide array of applications in bioinformatics approaches like remote homology detection, protein family analysis, detection of new members and evolutionary modelling. Computational intensive searches have been performed using the neural network based sensitive sequence search method called FASSM to identify the Best Representative PSSMs for families reported in Pfam database version 22.ResultsWe designed a novel data mining approach for the assessment of individual sequences from a protein family to identify a single Best Representative PSSM profile (BRP) per protein family. Using the approach, a database of protein family-specific best representative PSSM profiles called 3PFDB has been developed. PSSM profiles in 3PFDB are curated using performance of individual sequence as a reference in a rigorous scoring and coverage analysis approach using FASSM. We have assessed the suitability of 10, 85,588 sequences derived from seed or full alignments reported in Pfam database (Version 22). Coverage analysis using FASSM method is used as the filtering step to identify the best representative sequence, starting from full length or domain sequences to generate the final profile for a given family. 3PFDB is a collection of best representative PSSM profiles of 8,524 protein families from Pfam database.ConclusionAvailability of an approach to identify BRPs and a curated database of best representative PSI-BLAST derived PSSMs for 91.4% of current Pfam family will be a useful resource for the community to perform detailed and specific analysis using family-specific, best-representative PSSM profiles. 3PFDB can be accessed using the URL:http://caps.ncbs.res.in/3pfdb
Ectopic thymoma of the lung; a rare case report and review of the literature
Authors: Skoutelis Kostas , Nikolopoulos Dimitrios D , Markopoulos Kostas , Chabipi Katerina , Stoungioti Sofia , Papastamatiou Miltiadis 
Published: December 2009

Abstract

Introduction
Ectopic thymoma is a rare neoplasm, which can be developed in various sites, with the lung being amongst the rarest.

Case presentation
In this paper, we present the case of a woman with a slow-growing ectopic thymoma, stemming from the visceral pleura of the upper lobe of the left lung anteriorly, extending into the left lung and the cardiac wall, invading the fatty tissue near the pericardium, notably without infiltrating the lung or cardiac parenchyma. The thymoma was successfully removed via thoracotomy.

Conclusion
Ectopic thymoma is an uncommon neoplasm. To our knowledge, a case of an ectopic thymoma stemming from the visceral pleura of the lung is extremely rare.
Changes in stroke volume induced by passive leg raising in spontaneously breathing patients: comparison between echocardiography and Vigileo™/FloTrac™ device
Authors: Biais Matthieu , Vidil Lionel , Sarrabay Philippe , Cottenceau Vincent , Revel Philippe , Sztark François 
Published: December 2009

Abstract
Introduction
Passive leg raising (PLR) is a simple reversible maneuver that mimics rapid fluid loading and increases cardiac preload. The effects of this endogenous volume expansion on stroke volume enable the testing of fluid responsiveness with accuracy in spontaneously breathing patients. However, this maneuver requires the determination of stroke volume with a fast-response device, because the hemodynamic changes may be transient. The Vigileo™ monitor (Vigileo™; Flotrac™; Edwards Lifesciences, Irvine, CA, USA) analyzes systemic arterial pressure wave and allows continuous stroke volume monitoring. The aims of this study were (i) to compare changes in stroke volume induced by passive leg raising measured with the Vigileo™ device and with transthoracic echocardiography and (ii) to compare their ability to predict fluid responsiveness.

Methods
Thirty-four patients with spontaneous breathing activity and considered for volume expansion were included. Measurements of stroke volume were obtained with transthoracic echocardiography (SV-TTE) and with the Vigileo™ (SV-Flotrac) in a semi-recumbent position, during PLR and after volume expansion (500 ml saline). Patients were responders to volume expansion if SV-TTE increased ≥ 15%.

Results
Four patients were excluded. No patients received vasoactive drugs. Seven patients presented septic hypovolemia. PLR-induced changes in SV-TTE and in SV-Flotrac were correlated (r2 = 0.56, P < 0.0001). An increase in SV-TTE ≥ 13% during PLR was predictive of response to volume expansion with a sensitivity of 100% and a specificity of 80%. An increase in SV-Flotrac ≥16% during PLR was predictive of response to volume expansion with a sensitivity of 85% and a specificity of 90%. There was no difference between the area under the ROC curve for PLR-induced changes in SV-TTE (AUC = 0.96 ± 0.03) or SV-Flotrac (AUC = 0.92 ± 0.05). Volume expansion-induced changes in SV-TTE correlated with volume expansion-induced changes in SV-Flotrac (r2 = 0.77, P < 0.0001). In all patients, the highest plateau value of SV-TTE recorded during PLR was obtained within the first 90 s following leg elevation, whereas it was 120 s for SV-Flotrac.

Conclusions
PLR-induced changes in SV-Flotrac are able to predict the response to volume expansion in spontaneously breathing patients without vasoactive support.