bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glucose, Nitrogen, and Phosphate Repletion in Saccharomyces cerevisiae: Common Transcriptional Responses to Different Nutrient Signals
Authors: Conway Michael K , Grunwald Douglas , Heideman Warren 
Published: November 2013

Abstract
Saccharomyces cerevisiae are able to control growth in response to changes in nutrient availability. The limitation for single macronutrients, including nitrogen (N) and phosphate (P), produces stable arrest in G1/G0. Restoration of the limiting nutrient quickly restores growth. It has been shown that glucose (G) depletion/repletion very rapidly alters the levels of more than 2000 transcripts by at least 2-fold, a large portion of which are involved with either protein production in growth or stress responses in starvation. Although the signals generated by G, N, and P are thought to be quite distinct, we tested the hypothesis that depletion and repletion of any of these three nutrients would affect a common core set of genes as part of a generalized response to conditions that promote growth and quiescence. We found that the response to depletion of G, N, or P produced similar quiescent states with largely similar transcriptomes. As we predicted, repletion of each of the nutrients G, N, or P induced a large (501) common core set of genes and repressed a large (616) common gene set. Each nutrient also produced nutrient-specific transcript changes. The transcriptional responses to each of the three nutrients depended on cAMP and, to a lesser extent, the TOR pathway. All three nutrients stimulated cAMP production within minutes of repletion, and artificially increasing cAMP levels was sufficient to replicate much of the core transcriptional response. The recently identified transceptors Gap1, Mep1, Mep2, and Mep3, as well as Pho84, all played some role in the core transcriptional responses to N or P. As expected, we found some evidence of cross talk between nutrient signals, yet each nutrient sends distinct signals.
Using Near-Infrared Spectroscopy to Resolve the Species, Gender, Age, and the Presence of Wolbachia Infection in Laboratory-Reared Drosophila
Authors: Aw Wen C , Dowell Floyd E , Ballard J William O 
Published: November 2013

AbstractThe aim of the study was to determine the accuracy of near-infrared spectroscopy (NIRS) in determining species, gender, age, and the presence of the common endosymbiont Wolbachia in laboratory-reared Drosophila. NIRS measures the absorption of light by organic molecules. Initially, a calibration model was developed for each study. An independent set with flies not involved in initial cross-validation was then used to validate the accuracy of each calibration model. Flies from the independent sets were correctly classified into Drosophila melanogaster and Drosophila simulans with 94% and 82% accuracy, respectively, whereas flies were successfully classified by gender with accuracy greater than 90%. In the age grading test, correlation plots of the actual and predicted age for males and females of D. melanogaster and D. simulans were shown to be overlapping between the adjacent age groups. It is, however, possible to predict the age of flies as less than 9 days of age with 62–88% accuracy and flies that are equal to or older than 9 days of age with 91–98% accuracy. Finally, we used NIRS to detect the presence of Wolbachia in flies. Flies from the independent sets were successfully identified as infected or not infected with Wolbachia with approximately 90% accuracy. These results suggest that NIRS has the potential to quantify the species, gender, and presence of Wolbachia in fly populations. However, additional optimization of the protocol may be necessary before the technique can reliably estimate fly age.
Mitochondrial Genome Evolution in a Single Protoploid Yeast Species
Authors: Jung Paul P , Friedrich Anne , Reisser Cyrielle , Hou Jing , Schacherer Joseph 
Published: November 2013

AbstractMitochondria are organelles, which play a key role in some essential functions, including respiration, metabolite biosynthesis, ion homeostasis, and apoptosis. The vast numbers of mitochondrial DNA (mtDNA) sequences of various yeast species, which have recently been published, have also helped to elucidate the structural diversity of these genomes. Although a large corpus of data are now available on the diversity of yeast species, little is known so far about the mtDNA diversity in single yeast species. To study the genetic variations occurring in the mtDNA of wild yeast isolates, we performed a genome-wide polymorphism survey on the mtDNA of 18 Lachancea kluyveri (formerly Saccharomyces kluyveri) strains. We determined the complete mt genome sequences of strains isolated from various geographical locations (in North America, Asia, and Europe) and ecological niches (Drosophila, tree exudates, soil). The mt genome of the NCYC 543 reference strain is 51,525 bp long. It contains the same core of genes as Lachancea thermotolerans, the nearest relative to L. kluyveri. To explore the mt genome variations in a single yeast species, we compared the mtDNAs of the 18 isolates. The phylogeny and population structure of L. kluyveri provide clear-cut evidence for the existence of well-defined geographically isolated lineages. Although these genomes are completely syntenic, their size and the intron content were found to vary among the isolates studied. These genomes are highly polymorphic, showing an average diversity of 28.5 SNPs/kb and 6.6 indels/kb. Analysis of the SNP and indel patterns showed the existence of a particularly high overall level of polymorphism in the intergenic regions. The dN/dS ratios obtained are consistent with purifying selection in all these genes, with the noteworthy exception of the VAR1 gene, which gave a very high ratio. These data suggest that the intergenic regions have evolved very fast in yeast mitochondrial genomes.
Metronomic Capecitabine in Advanced Hepatocellular Carcinoma Patients: A Phase II Study
Authors: Brandi Giovanni , Rosa Francesco , Agostini Valentina , Girolamo Stefania , Andreone Pietro , Bolondi Luigi , Serra Carla , Sama Claudia , Golfieri Rita , Gramenzi Annagiulia , Cucchetti Alessandro , Pinna Antonio Daniele , Trevisani Franco , Biasco Guido ,   ITALIAN LIVER CANCER (ITA.LI.CA) GROUP
Published: November 2013

Abstract

Background.
Anti-angiogenic treatment with targeted agents is effective in advanced hepatocellular carcinoma (HCC). This trial evaluated the safety and efficacy of metronomic capecitabine in patients with HCC.

Methods.
This single-institution phase II trial included 59 previously untreated patients with advanced HCC and 31 patients resistant to or intolerant of sorafenib. The treatment schedule was capecitabine 500 mg twice daily until progression of disease, unacceptable toxicity level, or withdrawal of informed consent. Progression-free survival (PFS) was chosen as the primary endpoint.

Results.
A total of 59 previously untreated and 31 previously treated patients with HCC were enrolled. The first cohort achieved a median PFS of 6.03 months and an overall survival (OS) of 14.47 months. Two patients achieved a complete response, 1 patient achieved partial response, and in 30 patients, stable disease was the best outcome. The second cohort achieved a median PFS of 3.27 months and a median OS of 9.77 months. No complete or partial responses were observed, but 10 patients had stable disease. An unscheduled comparison of the first cohort of patients with 3,027 untreated patients with HCC from the Italian Liver Cancer (ITA.LI.CA) database was performed. One-to-one matching according to demographic/etiologic/oncologic features was possible for 50 patients. The median OS for these 50 capecitabine-treated patients was 15.6 months, compared with a median OS of 8.0 months for the matched untreated patients (p = .043).

Conclusion.
Metronomic capecitabine is well tolerated by patients with advanced HCC and appears to have activity both in treatment-naive patients and in those previously treated with sorafenib.
Assessing the demographic, behavioural and environmental characteristics and the potential effectiveness of a household water filter in the Republic of Kiribati
Authors: Psutka Rebecca , Priest Patricia , Davies Tieren , Rakunuea Teretia , Iddings Steven , Reiffer Andre 
Published: November 2013

Aim: To measure diarrhoea burden, environmental hygiene and water quality in Kiribati, in order to assess whether a domestic water filter would be likely to improve child and community health.
Methods: Cross-sectional survey of randomly selected households using a questionnaire and analysis of drinking and source water samples.
Results: Female heads of 97 randomly selected households answered the questionnaire. One in four children younger than five years had experienced diarrhoea in the past month and 7% in the past week. Thirty-four percent of respondents and 57% of their children practised open defecation. Handwashing at important times was uncommon, as was safe water storage. Almost all households usually boil water. Overall, drinking water was less contaminated than source water (p = 0.05). Where paired samples of source and drinking water were available, drinking water that had been boiled was significantly less contaminated than source water (1 tailed t-test; p = 0.014).
Conclusion: Both ‘waterwashed’ and waterborne transmission are likely responsible for diarrhoea. In this setting where nearly all households boil water, in the absence of hygiene and storage improvements, the substitution of a filter is unlikely to improve water quality.
Acetaminophen Toxicity and 5-Oxoproline (Pyroglutamic Acid)
Authors: Emmett Michael 
Published: November 2013

SummaryThe acquired form of 5-oxoproline (pyroglutamic acid) metabolic acidosis was first described in 1989 and its relationship to chronic acetaminophen ingestion was proposed the next year. Since then, this cause of chronic anion gap metabolic acidosis has been increasingly recognized. Many cases go unrecognized because an assay for 5-oxoproline is not widely available. Most cases occur in malnourished, chronically ill women with a history of chronic acetaminophen ingestion. Acetaminophen levels are very rarely in the toxic range; rather, they are usually therapeutic or low. The disorder generally resolves with cessation of acetaminophen and administration of intravenous fluids. Methionine orN-acetyl cysteine may accelerate resolution and methionine is protective in a rodent model. The disorder has been attributed to glutathione depletion and activation of a key enzyme in theγ-glutamyl cycle. However, the specific metabolic derangements that cause the 5-oxoproline accumulation remain unclear. An ATP-depleting futile 5-oxoproline cycle can explain the accumulation of 5-oxoproline after chronic acetaminophen ingestion. This cycle is activated by the depletion of both glutathione and cysteine. This explanation contributes to our understanding of acetaminophen-induced 5-oxoproline metabolic acidosis and the beneficial role ofN-acetyl cysteine therapy. The ATP-depleting futile 5-oxoproline cycle may also play a role in the energy depletions that occur in other acetaminophen-related toxic syndromes.
Diabetes Clinic at a Distance: Telemedicine Bridges the Gap
Authors: Malasanos Toree , Ramnitz Mary Scott 
Published: November 2013

In Brief
Clinic-to-clinic telemedicine has been shown to be an efficient and effective means of providing diabetes care to remote, underserved regions. Improved access to care has the potential to improve the health of and reduce health care costs for individuals in underserved regions. This article reviews the evidence related to, benefits of, and barriers to this mode of care.
Improvement of Manufacturing Process Quality According to Final Inspection Results
Authors: Andrássyová Zuzana , Hrubec Jozef , Del Carmen Bas Cerdá Maria 
Published: November 2013

Abstract
Final inspection represents the last inspection operation of production line before the product reaches a customer. If nonconformities are not detected within the production process, final inspection has to ensure their detection. This contribution focuses on the final inspection results of the manufacturing process of automobile’s front seats. The outputs of final inspection are prepared by means of quality management tools (Pareto analysis). Inspection items, their changes, remedies and precautions leading to seat quality improvement are defined. The evaluation of final inspection for the following period confirms the improvement of the manufacturing process or control quality for selected inspection items.
Design and Verification of Tractor Wheels Equipped with Automatically Extensible Blades
Authors: Abrahám Rudolf , Majdan Radoslav , Mojžiš Miroslav 
Published: November 2013

Abstract
This paper focuses on the possibility of increasing the drawbar pull of an agricultural tractor on the soil and grass-covered surface. We have compared the tractor tyre traction properties with a newly developed system of automatically extensible blades next to the tractor drive wheel tyres. The tractor with wheels equipped with auto-extensible blades reached a higher drawbar pull at an average of 70 % on the soil and 80 % on grass compared to tyres.
Patient Global Ratings of Change Did Not Adequately Reflect Change Over Time: A Clinical Cohort Study
Authors: Schmitt John S. , Abbott J. Haxby 
Published: November 2013

BackgroundGlobal ratings of change (GROCs) are commonly used in research and clinical practice to determine which patients respond to therapy, but their validity as a criterion for change has not been firmly established. One factor related to their validity is the length of the recall period.ObjectiveThe study objective was to examine the influence of the length of the recall period on the validity of a GROC for determining true change over time in the clinical setting.DesignThis was a longitudinal, single-cohort observational study.MethodsData from the Focus on Therapeutic Outcomes clinical database were collected for 8,955 patients reporting for physical therapy treatment of a knee disorder. Computerized adaptive testing was used to assess knee functional status (FS) at the initial and final (discharge) physical therapy visits. Each patient's GROC was obtained at discharge. Correlation and linear regression analyses of knee FS and GROC, stratified by length of time between intake and discharge, were conducted.ResultsCorrelations of GROC with knee FS change scores were modest even for the shortest period of recall (0–30 days) and were slightly lower for longer recall periods. Regression analyses using knee FS to predict GROC scores revealed similar findings. Correlations of GROC with intake and discharge scores indicated a strong bias toward discharge status, with little or no influence of baseline status. Standardized regression coefficients fitted the pattern expected for a valid measure of change but confirmed the strong bias toward discharge status.LimitationsOne version of the GROC administered serially in a cohort of patients seen in clinical practice was examined.ConclusionsThese results call into question the validity of GROCs for measuring change over time in routine clinical practice.
Self-reported Causes of Weight Gain: Among Prebariatric Surgery Patients
Authors: Ferguson Sarah , Al-Rehany Layla , Tang Cathy , Gougeon Lorraine , Warwick Katie , Madill Janet 
Published: November 2013

Purpose: Bariatric surgery is accepted by the medical community as the most effective treatment for obesity; however, weight regain after surgery remains common. Long-term weight loss and weight maintenance may be aided when dietitians who provide perioperative care understand the causes of weight gain leading to bariatric surgery. In this study, the most common causes for weight gain were examined among prebariatric surgery patients. Methods: A retrospective chart review was conducted for 160 patients enrolled in a bariatric surgery program. Data were collected for 20 variables : puberty, pregnancy, menopause, change in living environment, change in job/career, financial problems, quitting smoking, drug or alcohol use, medical condition, surgery, injury affecting mobility, chronic pain, dieting, others’ influence over diet, abuse, mental health condition, stress, death of a loved one, divorce/end of a relationship, and other causes. Frequency distribution and chi-square tests were performed using SPSS. Results: Sixty-three percent of participants selected stress as a cause of weight gain, while 56% selected dieting. Significant differences existed between women and men in the selection of dieting and change in living environment. Conclusions: This information may allow dietitians to better identify causes for weight gain leading to bariatric surgery, and to address these causes appropriately before and after surgery.
Cerebral vascular malformations in hereditary hemorrhagic telangiectasia
Authors: Woodall M. Neil , McGettigan Melissa , Figueroa Ramon , Gossage James R. , Alleyne Cargill H. 
Published: November 2013

Object
Hereditary hemorrhagic telangiectasia (HHT) is a hereditary disorder characterized by mucocutaneous telangiectasias, frequent nosebleeds, and visceral arteriovenous malformations (AVMs). Few reports have outlined the prevalence of the various cerebral vascular malformations found in patients with HHT. The authors set out to define the prevalence of cerebral vascular malformations in a population of HHT patients who underwent imaging with 3-T imaging (MRI/MR angiography [MRA]) of the brain.

Methods
A retrospective review of prospectively collected data was carried out using a database of 372 HHT patients who were seen and examined at the Georgia Regents University HHT Center and screened with 3-T MRI/MRA. Data were tabulated for numbers and types of vascular malformations in this population.

Results
Arteriovenous malformations were identified in 7.7%, developmental venous anomalies in 4.3%, and cerebral aneurysms in 2.4% of HHT patients. The HHT AVMs tended to be supratentorial, small, and cortical in this series, findings consistent with other recent studies in the literature. An arteriovenous fistula, cavernous malformation, and capillary telangiectasia were identified in 0.5%, 1%, and 1.9% of HHT patients, respectively.

Conclusions
Few studies have investigated the prevalence of the various vascular malformations found in HHT patients screened with 3-T MRI/MRA of the brain. Hereditary hemorrhagic telangiectasia AVMs are more likely to be multiple and have a tendency toward small size and cortical location. As such, they are often treated using a single-modality therapy.
Magma fracture and hybrid earthquakes in the conduit of Augustine Volcano
Authors: Buurman Helena , West Michael E. 
Published: November 2013

AbstractWe exploit subtle but systematic shifts in seismic waveforms to examine a 2 h cluster of repeating hybrid volcanic earthquakes preceding the first magmatic explosions at Augustine Volcano in January 2006. We extract differential P wave traveltimes of <0.01 s to determine that the source locations migrated downward by approximately 35 m. Waveform characteristics, GPS observations, and visual reports of lava effusion at the summit suggest that the earthquakes were sourced by fracturing magma in the upper conduit. As the lava cooled and degassed at the surface, the conditions in the upper conduit changed causing the zone in which magma fracture could occur to move downward through the magma column. These changes may also have been the first indicators that the conduit was becoming choked, causing a buildup in pressure that resulted in the large magmatic explosions that followed 36 h later.
Spliceosome
Authors: Anthony Kelsey C , Pomeranz Krummel Daniel 
Published: November 2013

Abstract

The removal of noncoding regions or introns and the splicing together of the protein‐coding regions or exons from
precursor messenger ribonucleic acid (pre‐mRNA)
transcripts is fundamental to metzoan cell development, as well as its maintenance. The nuclear process of pre‐mRNA splicing is a complex phenomenon catalysed by the ‘spliceosome’. The spliceosome consists of greater than a hundred protein and RNA molecules. Integral to the spliceosome are five RNA–protein complexes, the U1, U2, U4, U5 and U6 small nuclear ribonucleoproteins (snRNPs). The numerous proteins and the U snRNPs that make up the spliceosome come on and off during the spliceosome's reaction cycle. This article places an emphasis on our current understanding of the dynamics, composition and structure of the spliceosome.

Key Concepts:

Specific sequences defining the boundaries between a protein‐coding gene's noncoding regions or introns and its protein‐coding regions or exons are recognised by components of the pre‐mRNA splicing ‘machinery’ – the spliceosome.

The spliceosome is composed of a large number of RNA and protein molecules. The protein subunits have diverse domain structures, whereas the RNA subunits form hydrogen bonding or base‐pairing interactions with critical sequences in a pre‐mRNA as well as with each other.

The spliceosome reaction cycle involves an ordered assembly onto a pre‐mRNA transcript to ultimately catalyse two
trans
‐esterification reactions that result in the removal or excision of an intron and the splicing together of two exons.

Integral to the function of the spliceosome are five U snRNPs, each of which has a single RNA and 3–12 protein constituents including a homologous set of proteins (Sm or LSm) that forms a structural unit critical to the biogensis and integrity of each U snRNP.

The U1, U2, U4 and U5 snRNPs all have a common core structure that consists of seven Sm proteins which assemble around a short U‐rich single‐stranded RNA sequence (the Sm site) present in the U1, U2, U4 and U5 snRNAs to form a heptameric ring with the single‐stranded RNA Sm site leafing through the central hole.

Metazoan U1 snRNP functions to initiate the assembly of the spliceosome onto a pre‐mRNA transcript; its single RNA subunit (U1 snRNA) forms a cruciform‐like structure onto which the Sm proteins assemble to form the Sm core, while its three additional U‐specific proteins (U1‐A, U1‐70K, and U1‐C) participate in particle specific functions – including recognition of a pre‐mRNA transcripts 5' splice site sequence.
Manihot esculenta
(Cassava)
Authors: Beeching John R 
Published: November 2013

Abstract

Cassava (

Manihot esculenta

) is the world's seventh most important crop in terms of production and provides the staple food for more than 500 million people in the humid tropics. Owing to its ability to survive adverse environmental conditions and its high efficiency at fixing CO
2
into carbohydrate compared with other crops, cassava has a vital role to play in a planet faced with the interrelated challenges of population growth, food scarcity, fuel shortage and climate change. Despite these advantages, cassava storage roots are nutritionally deficient, cyanogenic, deteriorate rapidly on harvest and the crop is prone to pests and diseases. However, through exploiting germplasm diversity, breeding and biotechnology many of these challenges can be addressed for the benefit of producers, processers and consumers.

Key Concepts:

Cassava storage roots are the staple food of hundreds of millions in the humid tropics.

Owing to its drought tolerance and ability to grow on impoverished soils cassava is a vitally important famine reserve crop in sub‐Saharan Africa.

Breeding and biotechnology can address the current limitations of cassava in order to make it a more productive, versatile and nutritious crop.

Enhanced germplasm combined with improved agronomic practice can enable cassava to make a significant contribution to global food security.

In addition to food, cassava is processed into industrial products and is of increasing interest for biofuel production.