bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying essential genes in bacterial metabolic networks with machine learning methods
Authors: Plaimas Kitiporn , Eils Roland , König Rainer 
Published: May 2010

Abstract

Background
Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.

Results
We developed a machine learning technique to identify essential genes using the experimental data of genome-wide knock-out screens from one bacterial organism to infer essential genes of another related bacterial organism. We used a broad variety of topological features, sequence characteristics and co-expression properties potentially associated with essentiality, such as flux deviations, centrality, codon frequencies of the sequences, co-regulation and phyletic retention. An organism-wise cross-validation on bacterial species yielded reliable results with good accuracies (area under the receiver-operator-curve of 75% - 81%). Finally, it was applied to drug target predictions for Salmonella typhimurium. We compared our predictions to the viability of experimental knock-outs of S. typhimurium and identified 35 enzymes, which are highly relevant to be considered as potential drug targets. Specifically, we detected promising drug targets in the non-mevalonate pathway.

Conclusions
Using elaborated features characterizing network topology, sequence information and microarray data enables to predict essential genes from a bacterial reference organism to a related query organism without any knowledge about the essentiality of genes of the query organism. In general, such a method is beneficial for inferring drug targets when experimental data about genome-wide knockout screens is not available for the investigated organism.
The role of renin angiotensin system inhibition in kidney repair
Authors: van der Meer Irene M , Cravedi Paolo , Remuzzi Giuseppe 
Published: May 2010

Abstract
Chronic kidney diseases share common pathogenic mechanisms that, independently from the initial injury, lead to glomerular hyperfiltration, proteinuria, and progressive renal scarring and function loss. Inhibition of the renin angiotensin system (RAS) has been consistently found to reduce or halt the progressive deterioration of renal function through reduction of blood pressure and proteinuria, the two main determinants of renal function decline. In few instances, RAS inhibition may even promote amelioration of the glomerular filtration rate. Animal data suggest that chronic therapy with angiotensin-converting enzyme inhibitors or angiotensin II receptor type I blockers promotes regression of glomerulosclerosis, even in later phases of the disease. In humans, studies investigating the effect of angiotensin II inhibition on renal structural changes have shown inconsistent results, possibly due to small numbers and/or short duration of follow-up. Whether regression of glomerulosclerosis relies on a direct regenerative effect of RAS inhibition or on spontaneous kidney self-repair after the injury has been removed is still unknown. Improved understanding of mechanisms that promote renal regeneration may help in designing specific therapies to prevent the development of end-stage renal disease. This is a desirable goal, considering the economic burden of chronic kidney diseases and their effect on morbidity and mortality.
Inhibiting miRNA in Caenorhabditis elegans using a potent and selective antisense reagent
Authors: Zheng Genhua , Ambros Victor , Li Wen-hong 
Published: May 2010

Abstract

Background
Antisense reagents can serve as efficient and versatile tools for studying gene function by inhibiting nucleic acids in vivo. Antisense reagents have particular utility for the experimental manipulation of the activity of microRNAs (miRNAs), which are involved in the regulation of diverse developmental and physiological pathways in animals. Even in traditional genetic systems, such as the nematode Caenorhabditis elegans, antisense reagents can provide experimental strategies complementary to mutational approaches. Presently no antisense reagents are available for inhibiting miRNAs in the nematode C. elegans.

Results
We have developed a new class of fluorescently labelled antisense reagents to inhibit miRNAs in developing worms. These reagents were synthesized by conjugating dextran with 2'-O-methyl oligoribonucleotide. The dextran-conjugated antisense reagents can be conveniently introduced into the germline of adult hermaphrodites and are transmitted to their progeny, where they efficiently and specifically inhibit a targeted miRNA in different tissues, including the hypodermis, the vulva and the nervous system. We show that these reagents can be used combinatorially to inhibit more than one miRNA in the same animal.

Conclusion
This class of antisense reagents represents a new addition to the toolkit for studying miRNA in C. elegans. Combined with numerous mutants or reporter stains available, these reagents should provide a convenient approach to examine genetic interactions that involve miRNA, and may facilitate studying functions of miRNAs, especially ones whose deletion strains are difficult to generate.
See related research article: http://jbiol.com/content/9/3/20
Prostate-Specific Antigen Kinetics During Follow-Up Are an Unreliable Trigger for Intervention in a Prostate Cancer Surveillance Program
Authors: Ross Ashley E. , Loeb Stacy , Landis Patricia , Partin Alan W. , Epstein Jonathan I. , Kettermann Anna , Feng Zhaoyong , Carter H. Ballentine , Walsh Patrick C. 
Published: May 2010

PurposeTo assess the predictive ability of prostate-specific antigen (PSA) velocity (PSAV) and doubling time (PSADT) for biopsy progression and adverse pathology at prostatectomy among men with low-risk prostate cancer enrolled on an active-surveillance program.MethodsWe evaluated 290 men who met criteria for active surveillance (ie, PSA density < 0.15 ng/mL/cm3and Gleason score ≤ 6 with no pattern ≥ 4, involving ≤ 2 cores with cancer, and ≤ 50% involvement of any core by cancer) with two or more serial PSA measurements after diagnosis from 1994 to 2008. Follow-up included twice-yearly digital rectal exam and PSA measurements and yearly surveillance biopsy. Treatment was recommended for biopsy progression (ie, Gleason score ≥ 7, or > 2 positive cores, or > 50% core involvement). Sensitivity and specificity of postdiagnostic PSAV and PSADT were explored by using receiver operating characteristic (ROC) analysis.ResultsOverall, 188 (65%) men remained on active surveillance, and 102 (35%) developed biopsy progression at a median follow-up of 2.9 years. PSADT was not significantly associated with subsequent adverse biopsy findings (P = .83), and PSAV was marginally significant (P = .06). No PSAV or PSADT cut point had both high sensitivity and specificity (area under the curve, 0.61 and 0.59, respectively) for biopsy progression. In those who eventually underwent radical prostatectomy, PSAV (P = .79) and PSADT (P = .87) were not associated with the presence of unfavorable surgical pathology.ConclusionPostdiagnostic PSA kinetics do not reliably predict adverse pathology and should not be used to replace annual surveillance biopsy for monitoring men on active surveillance.
Example‐based learning: Effects of model expertise in relation to student expertise
Authors: Boekhout Paul , van Gog Tamara , van de Wiel Margje W. J. , Gerards‐Last Dorien , Geraets Jacques 
Published: May 2010

Background. Worked examples are very effective for novice learners. They typically present a written‐out ideal (didactical) solution for learners to study.Aims. This study used worked examples of patient history taking in physiotherapy that presented a non‐didactical solution (i.e., based on actual performance). The effects of model expertise (i.e., worked example based on advanced, third‐year student model or expert physiotherapist model) in relation to students' expertise (i.e., first‐ or second‐year) were investigated.Sample. One hundred and thirty‐four physiotherapy students (61 first‐year and 73 second‐year).Methods. Design was 2×2 factorial with factors ‘Student Expertise’ (first‐year vs. second‐year) and ‘Model Expertise’ (expert vs. advanced student). Within expertise levels, students were randomly assigned to the Expert Example or the Advanced Student Example condition. All students studied two examples (content depending on their assigned condition) and then completed a retention and test task. They rated their invested mental effort after each example and test task.Results. Second‐year students invested less mental effort in studying the examples, and in performing the retention and transfer tasks than first‐year students. They also performed better on the retention test, but not on the transfer test. In contrast to our hypothesis, there was no interaction between student expertise and model expertise: all students who had studied the Expert examples performed better on the transfer test than students who had studied Advanced Student Examples.Conclusions. This study suggests that when worked examples are based on actual performance, rather than an ideal procedure, expert models are to be preferred over advanced student models.
The physical and emotional threads of the archetypal hero's journey: proposing common terminology and re-examining the narrative model
Authors: Batty Craig 
Published: May 2010

This article will discuss how, in mainstream film screenplays, the protagonist undergoes both an actual, physical journey and an internal, emotional journey, pulled together by the invisible hand of the screenwriter in order to create the complete narrative experience. Central to the
article is an evaluation of how character transformation (arc) is positioned against physical action (plot), arguing that the two can be mapped out as individual yet symbiotic threads of a narrative: the physical and the emotional journeys.
After mapping the territory of what is already
written on this subject, the works of Joseph Campbell and his protg Christopher Vogler (Clayton 2007: 210) will be drawn together to offer a re-examination of the model of the Hero's Journey. Assessing these two narrative threads (physical and emotional) as both distinct and symbiotic, it
will be clear that a special relationship exists between plot and character, where character transformation is encouraged to take place within the frame of the physical action of the plot. The substance of such a transformation, the emotional core of the narrative experience, is what lives
on in the audience, post-text; the physical action of a film story may frame emotion, but emotion has the power to break the frame and take on a life of its own.
Laboratory testing in pharmacies
Authors: Lippi Giuseppe , Plebani Mario , Favaloro Emmanuel J. , Trenti Tommaso 
Published: May 2010

Abstract
Point-of-care testing (POCT) is traditionally defined as laboratory diagnostics performed at or near the site where clinical care is delivered. POCT thereby combines sample collection, analysis, and reporting of results into a robust integrated testing structure, with a simple user interface. The availability of reliable devices and consolidated tests for patient screening, diagnosis and monitoring has allowed broad diffusion of POCT to the patient's bedside, physician offices, pharmacies, other healthcare facilities, supermarkets, and even into the patient's home. However, current evidence clearly shows that POCT can be subjective, and might even amplify the traditional problems encountered in the preanalytical, analytical and postanalytical phases of the total testing process. This may especially be seen in inappropriateness of the test request, collection of unsuitable biological materials, inaccurate test performances, larger analytical imprecision, unsuitable report formatting, delayed reporting of critical value, and report recording/retrieval. POCT patient care service in the pharmacy can be regarded as a valuable option for the present and future since it might be beneficial for all parties. However, several economic, clinical and regulatory issues should also be addressed before this opportunity can turn into a real advantage for patients and the entire healthcare system. The most appropriate allocation of POCT within the diagnostic pathway, as well as its adjuvant role in screening, diagnosis and monitoring of diseases should also be clearly established in order to prevent widespread and deregulated implementation.
Clin Chem Lab Med 2010;48:943–53.
Point-of-care testing in critical care: the clinician's point of view
Authors: Casagranda Ivo 
Published: May 2010

Abstract
Point-of-care testing (POCT) is increasingly used in the Emergency Department (ED) by emergency physicians. They often need to have test results readily available in order to make prompt diagnosis, define risk stratification and establish early therapy or make changes to therapy. The use of POCT is important in patients who present to the ED with symptoms, such as chest pain, dyspnea or other critical medical conditions, as well as in trauma patients. The essential tests should have a turn-around time that allows state-of-the-art management of critical patients. The quality of POCT analyses can only be assured through an optimal relationship with the clinical laboratory, and all POCT activities should be discussed and agreed upon between the Clinical Laboratory and the ED.
Clin Chem Lab Med 2010;48:931–4.
Pre-extraction of hemicelluloses and subsequent ASA and ASAM pulping: Comparison of autohydrolysis and alkaline extraction
Authors: Al-Dajani Waleed Wafa , Tschirner Ulrike W. 
Published: May 2010

AbstractCommercial aspen wood chips were treated with hot water (autohydrolysis) and with alkali to extract part of the hemicelluloses. The extracted residues and an unextracted wood (control) were subjected to pulping based on the alkaline sulfite anthraquinone (ASA) and alkaline sulfite anthraquinone methanol (ASAM) methods to afford pulps useful for paper production with the same degree of delignification. Unlike the autohydrolysis residue, the alkali extracted residue was shown to favor subsequent pulping in terms of pulping yield, charges of chemicals, cooking times and properties of pulps. The experimental conditions and results are discussed.
Energy reduction of refining by cellulases
Authors: Lecourt Michael , Meyer Valérie , Sigoillot Jean-Claude , Petit-Conil Michel 
Published: May 2010

AbstractThe effect of three different commercial cellulase treatments applied on softwood bleached kraft pulp before the refining step was studied. Disc refining was applied under similar conditions as usual in paper mills. Two cellulase treatments allowed an energy saving of 20% to reach a given drainage index or breaking length. Water retention value (WRV), which characterizes the water absorption inside the fibre wall, was increased by the cellulase treatment. However, tear index losses were observed upon enzyme treatment. The third cellulase did not have an impact either on any parameters of the refining or on the pulp properties, except WRV. Viscosity measurements showed that the two first cellulases have strong endoglucanase activities but are lacking exoglucanase activities. Probably, endoglucanase activity weakens the fibre structure by generation of weak points or kinks. This hypothesis would explain the important cutting and fibrillation phenomena observed in the case of these two cellulases. It can be concluded that cellulase treatment could save 20% of electrical energy needed for refining, i.e., 50 kWh t-1, if a paper quality with a high tensile resistance but lowered tear strength is acceptable.
Fine Mapping of ui6.1, a Gametophytic Factor Controlling Pollen-Side Unilateral Incompatibility in Interspecific Solanum Hybrids
Authors: Li Wentao , Royer Suzanne , Chetelat Roger T 
Published: May 2010

Abstract
Unilateral incompatibility (UI) is a prezygotic reproductive barrier in plants that prevents fertilization by foreign (interspecific) pollen through the inhibition of pollen tube growth. Incompatibility occurs in one direction only, most often when the female is a self-incompatible species and the male is self-compatible (the “SI × SC rule”). Pistils of the wild tomato relative Solanum lycopersicoides (SI) reject pollen of cultivated tomato (S. lycopersicum, SC), but accept pollen of S. pennellii (SC accession). Expression of pistil-side UI is weakened in S. lycopersicum × S. lycopersicoides hybrids, as pollen tube rejection occurs lower in the style. Two gametophytic factors are sufficient for pollen compatibility on allotriploid hybrids: ui1.1 on chromosome 1 (near the S locus), and ui6.1 on chromosome 6. We report herein a fine-scale map of the ui6.1 region. Recombination around ui6.1 was suppressed in lines containing a short S. pennellii introgression, but less so in lines containing a longer introgression. More recombinants were obtained from female than male meioses. A high-resolution genetic map of this region delineated the location of ui6.1 to ∼0.128 MU, or 160 kb. Identification of the underlying gene should elucidate the mechanism of interspecific pollen rejection and its relationship to self-incompatibility.
Autophosphorylation Within the Atg1 Activation Loop Is Required for Both Kinase Activity and the Induction of Autophagy in Saccharomyces cerevisiae
Authors: Yeh Yuh-Ying , Wrasman Kristie , Herman Paul K 
Published: May 2010

Abstract
Autophagy is an evolutionarily conserved degradative pathway that has been implicated in a number of physiological events important for human health. This process was originally identified as a response to nutrient deprivation and is thought to serve in a recycling capacity during periods of nutritional stress. Autophagy activity appears to be highly regulated and multiple signaling pathways are known to target a complex of proteins that contains the Atg1 protein kinase. The data here extend these observations and identify a particular phosphorylation event on Atg1 as a potential control point within the autophagy pathway in Saccharomyces cerevisiae. This phosphorylation occurs at a threonine residue, T226, within the Atg1 activation loop that is conserved in all Atg1 orthologs. Replacing this threonine with a nonphosphorylatable residue resulted in a loss of Atg1 protein kinase activity and a failure to induce autophagy. This phosphorylation required the presence of a functional Atg1 kinase domain and two known regulators of Atg1 activity, Atg13 and Atg17. Interestingly, the levels of this modification were found to increase dramatically upon exposure to conditions that induce autophagy. In addition, T226 phosphorylation was associated with an autophosphorylated form of Atg1 that was found specifically in cells undergoing the autophagy process. In all, these data suggest that autophosphorylation within the Atg1 activation loop may represent a point of regulatory control for this degradative process.
Patient-, Provider-, and Clinic-Level Predictors of Unrecognized Elevated Blood Pressure in Children
Authors: Brady Tammy M. , Solomon Barry S. , Neu Alicia M. , Siberry George K. , Parekh Rulan S. 
Published: May 2010

OBJECTIVE:
The goal was to determine patient-, provider-, and clinic-level predictors of unrecognized elevated blood pressure (BP) in children. We hypothesized that being of healthy weight, having a BP of &lt;120/80 mmHg, and being seen by a less experienced provider would result in decreased recognition.

METHODS:
A cross-sectional study of clinic visits for children 3 to 20 years of age at an urban, pediatric primary care practice between January 1, 2006, and June 30, 2006, was performed. Children with elevated systolic or diastolic BP (≥90th percentile or ≥120/80 mmHg) were included. Recognition was defined as having any of the following documented: repeat BP measurement, elevated-BP/hypertension diagnosis, plan to recheck BP, or initiation of hypertension evaluation. Multivariate logistic regression analysis was used to identify characteristics associated with underrecognition.

RESULTS:
Elevated BP occurred in 779 (39%) of 2000 visits. Of 726 cases included in the analysis, 87% were not recognized by providers. Patient-level predictors of underrecognition included systolic BP of &lt;120 mmHg (odds ratio: 7.7 [95% confidence interval: 3.2–18.6]), diastolic BP of &lt;80 mmHg (odds ratio: 2.4 [95% confidence interval: 1.1–5.0]), decreasing BMI z score, male gender, older age, lack of family history of cardiovascular disease, and negative medical history findings. Being seen by a nurse practitioner and being seen by a less-experienced provider also were significant predictors.

CONCLUSIONS:
Most BP elevations were not recognized by providers. Poor recognition was most influenced by the absence of obviously elevated BP, obesity, and family history of cardiovascular disease.
Tritrophic Effects of Host Plants on an Herbivore-Pathogen Interaction
Authors: Gassmann Aaron J , Stock S Patricia , Tabashnik Bruce E , Singer Michael S 
Published: May 2010

Abstract
Tritrophic interactions may include directly harmful effects of host plants on herbivores, and directly or indirectly harmful effects of host plants on the natural enemies of herbivores. Tritrophic interactions involving parasitoids and predators have received considerable attention but less is known about how host plants affect entomopathogens. We compared growth and resistance to entomopathogenic nematodes for “woolly bear” caterpillars, Grammia incorrupta (=geneura) (Hy. Edwards) (Lepidoptera: Arctiidae) fed lettuce, Lactuca sativa L. (Asteraceae), versus threadleaf groundsel, Senecio longilobus Benth. (Asteraceae). Both plants are members of the Asteraceae, but only S.longilobus contains pyrrolizidine alkaloids. Caterpillars gained more mass when fed L.sativa compared with S.longilobus; yet, in one of four cases studied, resistance to nematodes was higher when caterpillars ate S.longilobus. Caterpillar resistance to nematodes did not differ between host plants in the other cases. In addition, nematode reproduction was higher in cadavers of G. incorrupta that had been fed L.sativa instead of S.longilobus, suggesting that S.longilobus had indirectly detrimental effects on entomopathogenic nematodes. Our results illustrate how trade-offs may arise in tritrophic interactions involving entomopathogens, as the cost of decreased growth imposed by S.longilobus was accompanied by the benefit of greater resistance to entomopathogenic nematodes.
Guest Column: Queer Ecology
Authors: Morton Timothy 
Published: May 2010

nearer than breathing, closer than hands and feet—George Morrison, “The Reawakening of Mysticism”Ecological criticism and queer theory seem incompatible, but if they met, there would be a fantastic explosion. How shall we accomplish this perverse, Frankensteinian meme splice? I'll propose some hypothetical methods and frameworks for a field that doesn't quite exist—queer ecology. (The pathbreaking work of Catriona Sandilands, Greta Gaard, and the journalUndercurrentsmust be acknowledged here.) This exercise in hubris is bound to rattle nerves and raise hackles, but please bear with me on this test flight. Start with the basics. Let's not create this field by comparing literary-critical apples and oranges. Let's do it the hard way, up from foundations (or unfoundations). Let's do it in the name of ecology itself, which demands intimacies with other beings that queer theory also demands, in another key. Let's do it because our era requires it—we are losing touch with a fantasy Nature that never really existed (I capitalizeNatureto make it look less natural), while we actively and passively destroy life-forms inhabiting and constituting the biosphere, in Earth's sixth mass extinction event. Giving up a fantasy is even harder than giving up a reality.