bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the Dynamic Regulation of Nitrogen Fixation in the Cyanobacterium
Trichodesmium
sp
Authors: Rabouille Sophie , Staal Marc , Stal Lucas J. , Soetaert Karline 
Published: May 2006

ABSTRACT

A physiological, unbalanced model is presented that explicitly describes growth of the marine cyanobacterium
Trichodesmium
sp. at the expense of N
2
(diazotrophy). The model involves the dynamics of intracellular reserves of carbon and nitrogen and allows the uncoupling of the metabolism of these elements. The results show the transient dynamics of N
2
fixation when combined nitrogen (NO
3
−
, NH
4
+
) is available and the increased rate of N
2
fixation when combined nitrogen is insufficient to cover the demand. The daily N
2
fixation pattern that emerges from the model agrees with measurements of rates of nitrogenase activity in laboratory cultures of
Trichodesmium
sp. Model simulations explored the influence of irradiance levels and the length of the light period on fixation activity and cellular carbon and nitrogen stoichiometry. Changes in the cellular C/N ratio resulted from allocations of carbon to different cell compartments as demanded by the growth of the organism. The model shows that carbon availability is a simple and efficient mechanism to regulate the balance of carbon and nitrogen fixed (C/N ratio) in filaments of cells. The lowest C/N ratios were obtained when the light regime closely matched nitrogenase dynamics.
Identifying Functionally Important Mutations from Phenotypically Diverse Sequence Data
Authors: Jensen Kyle , Alper Hal , Fischer Curt , Stephanopoulos Gregory 
Published: May 2006

ABSTRACT

Here we present a simple statistical method to determine the phenotypic
contribution of a single mutation from libraries of mutants with
diverse phenotypes in which each mutant contains a multitude of
mutations. The central premise of this method is that,
given
M
phenotypic classes, mutations that do not affect the
phenotype should partition among the
M
classes according to a
multinomial distribution. Deviations from this distribution are
indicative of a link between specific mutations and phenotypes. We
suggest that this method will aid the engineering of functional nucleic
acids, proteins, and other biomolecules by uncovering target sites for
rational mutagenesis. As a proof of the principle, we show how the
method can be used to deduce the individual effects of mutations in a
set of 69 P
L
-λ promoter variants. Each of these
promoters was generated by error-prone PCR and incorporated numerous
mutations. The activity of the promoters was assayed using flow
cytometry to measure the fluorescence of a green fluorescent protein
reporter gene. Our analysis of the sequences of these mutants revealed
seven positions having a statistically significant correlation with
promoter activity. Using site-directed mutagenesis, we constructed
point mutations for several sites, both statistically significant and
insignificant, and combinations of these sites. Our results show that
the statistical method correctly elucidated the phenotypic
manifestations of these mutations. We suggest that this method may be
useful for expediting directed evolution experiments by allowing both
desired and undesired mutations to be identified and incorporated
between rounds of
mutagenesis.
arsRBOCT
Arsenic Resistance System Encoded by Linear Plasmid pHZ227 in
Streptomyces
sp. Strain FR-008
Authors: Wang Lianrong , Chen Shi , Xiao Xiang , Huang Xi , You Delin , Zhou Xiufen , Deng Zixin 
Published: May 2006

ABSTRACT

In the arsenic resistance gene cluster from the large linear plasmid pHZ227, two novel genes,
arsO
(for a putative flavin-binding monooxygenase) and
arsT
(for a putative thioredoxin reductase), were coactivated and cotranscribed with
arsR1-arsB
and
arsC
, respectively. Deletion of the
ars
gene cluster on pHZ227 in
Streptomyces
sp. strain FR-008 resulted in sensitivity to arsenic, and heterologous expression of the
ars
gene cluster in the arsenic-sensitive
Streptomyces
strains conferred resistance on the new hosts. The pHZ227 ArsB protein showed homology to the yeast arsenite transporter Acr3p. The pHZ227 ArsC appears to be a bacterial thioredoxin-dependent ArsC-type arsenate reductase with four conserved cysteine thioredoxin-requiring motifs.
Campylobacter curvus
-Associated Hepatic Abscesses: a Case Report
Authors: Wetsch Nicole M. , Somani Karim , Tyrrell Gregory J. , Gebhart Carol , Bailey R. J. , Taylor Diane E. 
Published: May 2006

ABSTRACT

Campylobacter curvus
was isolated from blood cultures of a patient with liver abscesses. Bacterial identification involved Gram staining, biochemical analysis, gas-liquid chromatography, and 16S rRNA sequencing. The difficulty in isolation, identification, and growth of the species confirms previous work that these organisms may be overlooked by conventional detection methods.
Evidence for the Postconquest Demographic Collapse of the Americas in Historical CO2 Levels
Authors: Faust Franz X. , Gnecco Cristóbal , Mannstein Hermann , Stamm Jörg 
Published: May 2006

AbstractThis article promotes the hypothesis that the massive demographic collapse of the native populations of the Americas triggered by the European colonization brought about the abandonment of large expanses of agricultural fields soon recovered by forests, which in due turn fixed atmospheric CO2 in significant quantities. This hypothesis is supported by measurements of atmospheric CO2 levels in ice cores from Law Dome, Antarctica. Changing the focus from paleoclimate to global population dynamics and using the same causal chain, the measured drop in historic atmospheric CO2 levels can also be looked upon as further, strong evidence for the postconquest demographic collapse of the Americas.
Back to the wild: will reintroduction and rehabilitation help the long-term conservation of orang-utans in Indonesia?
Authors: Grundmann Emmanuelle 
Published: May 2006

English The orang-utans (Pongo pygmaeus and Pongo abelii) living on the islands of Borneo and Sumatra are among the first victims of the large-scale deforestation and exploitation of the south-east tropical rainforest. Rehabilitation and reintroduction of confiscated orang-utans back into their original habitat were initiated in the 1960s. The orang-utan community that has been reintroduced in the Meratus forest since 1997 presents an ideal opportunity to study the successes and failures of the re-adaptation of individuals whose maternal bond has been broken at various ages, interrupting their learning phase. This study enables us to evaluate to what extent learning from others, including humans, is crucial to this process and in what ways ethology and ethnology might merge to achieve a better understanding of the rehabilitation process. French Les orangs-outans (Pongo pygmaeus et Pongo abelii) vivant sur les îles de Bornéo et Sumatra comptent parmi les premières victimes de la déforestation galopante pour l'exploitation du bois et les monocultures qui, aujourd'hui, mettent à mal les forêts tropicales du sud-est asiatique. La réhabilitation et la réintroduction dans leur habitat d'orangs-outans orphelins ayant été confisqués aux braconniers a débuté dans les années 1960. La communauté d'orangs-outans ayant été réintroduite dans la forêt de Meratus depuis 1997 offre une opportunité de choix pour étudier les succès et échecs du processus de réadaptation d'individus dont le lien maternel a été brisé à des âges variés, cassant, de fait, le processus d'apprentissage. Enfin, à travers cette étude, nous souhaitions évaluer dans quelle mesure l'apprentissage auprès d'autres individus, orangs-outans mais aussi humains, peut s'avérer crucial lors du processus d'apprentissage, mais aussi de quelle manière l'éthologie et l'ethnologie peuvent, de concert, permettre une meilleure compréhension du processus de réhabilitation.
Effect of poly(ethylene oxide) molecular mass on miscibility and hydrogen bonding with lignin
Authors: Kubo Satoshi , Kadla John F. 
Published: May 2006

AbstractThe effect of the molecular mass of poly(ethylene oxide) (PEO) on lignin-PEO blends was studied using thermal analysis and FT-IR. Differential scanning calorimetry (DSC) analysis revealed miscible blends over the entire blend ratio. A negative deviation inTgfrom a simple weighted average was observed, indicating the existence of relatively weak favorable interactions between blend components. Analysis of the data revealed no difference in the magnitude or propensity of intermolecular interactions with increasing PEO molecular mass in the kraft lignin-PEO blends. By contrast, the fitting parameters obtained for organosolv lignin were substantially different; the higher molecular mass PEO had a higher propensity to form slightly stronger intermolecular inter-actions than the lower molecular mass PEO. Low molecular mass poly(ethylene glycol) dimethylether (M-PEG)-lignin blends had a much higher degree of crystallinity than the PEO blends, resulting in an increase inTgat high PEG content. FT-IR analysis revealed the presence of strong intermolecular hydrogen bonding between lignin and PEO. However, the band shape of the νOHregion of the M-PEG blends was slightly different from the PEO blends; some of the original lignin inter- and intramolecular hydrogen bonding was still present in the M-PEG-lignin blends.
Formic and acetic acids in archaeological wood. A comparison between the Vasa Warship, the Bremen Cog, the Oberländer Boat and the Danish Viking Ships
Authors: Glastrup Jens , Shashoua Yvonne , Egsgaard Helge , Nordvig Mortensen Martin 
Published: May 2006

Abstract
A method has been developed to analyse and quantify formic and acetic acids in archaeological and fresh wood. The method takes advantage of the fact that, in equilibrium, the gas-phase concentrations of formic and acetic acids over pulverised archaeological wood in a sulfuric acid solution are proportional to their absolute concentrations in wood. The method is based on automated solid-phase micro extraction (SPME) combined with gas chromatography-mass spectrometry (GC-MS). Good linearity of the calibration curves was observed. The content of formic and acetic acids in archaeological wood from ships conserved with polyethylene glycol (PEG) was determined. The content of formic acid is related to the intensity of conservation and, hence, the PEG content in wood. Accordingly, formic acid found in the hull of the ships may partly be a result of PEG degradation. The formic acid content in the Vasa warship is, on average, not higher than in the other ships analysed. In contrast, the acetic acid content in PEG-preserved archaeological wood is lower than in fresh wood. The acetic acid content is age-dependent and is lowest in 1000-year-old wood. The acetic acid probably originates from the wood.
Longitudinal Evaluation of Loss of Attachment in HIV‐Infected Women Compared to HIV‐Uninfected Women
Authors: Alves Mario , Mulligan Roseann , Passaro Douglas , Gawell Susan , Navazesh Mahvash , Phelan Joan , Greenspan Deborah , Greenspan John S. 
Published: May 2006

Background: The Women's Interagency HIV Study (WIHS) is the largest, most detailed, controlled longitudinal collection of data to evaluate the influence of human immunodeficiency virus (HIV) disease and its therapies on the periodontium.Methods: This report evaluates periodontal probing depth (PD), attachment loss (AL), and tooth loss from 584 HIV‐seropositive and 151 HIV‐seronegative women, recorded at 6‐month intervals from 1995 to 2002. Using the random split‐mouth method, PD and AL were recorded from four sites per tooth: mesial‐buccal, buccal, distal‐buccal, and lingual. Influence of viral load, CD4 count, race, smoking, drug use, low income, and level of education were evaluated.Results: At baseline, AL was 1.6 versus 1.1 mm (P = 0.003) and PD was marginally deeper (2.1 versus 2.0 mm; P = 0.02) in HIV‐seropositive versus HIV‐seronegative women. Adjusted longitudinal analysis showed that HIV infection did not increase the mean PD (rate ratio [RR], 1.00; 95% confidence interval [CI], 0.96 to 1.04), worst PD (RR, 1.03; 95% CI, 0.98 to 1.09), mean AL (RR, 0.97; 95% CI, 0.96 to 1.02), worst AL (RR, 1.01; 95% CI, 0.94 to 1.07), or tooth loss (RR, 1.02; 95% CI, 1.0 to 1.05).Conclusions: CD4 count and viral load had no consistent effects on PD or AL. Among HIV‐infected women, a 10‐fold increase in viral load was associated with a marginal increase in tooth loss. The progression of periodontal disease measured by PD and AL did not significantly differ between HIV‐infected and HIV‐uninfected women. The HIV‐seropositive women lost more teeth. Race, smoking, drug use, income, and education level did not influence the results for either group.
Differences in Home Health Services and Outcomes Between Traditional Medicare and Medicare Advantage
Authors: Prusynski Rachel A. , D’Alonzo Anthony , Johnson Michael P. , Mroz Tracy M. , Leland Natalie E. 
Published: March 2024

ImportancePrivate Medicare Advantage (MA) plans recently surpassed traditional Medicare (TM) in enrollment. However, MA plans are facing scrutiny for burdensome prior authorization and potential rationing of care, including home health. MA beneficiaries are less likely to receive home health, but recent evidence on differences in service intensity and outcomes among home health patients is lacking.ObjectiveTo examine differences in home health service intensity and patient outcomes between MA and TM.Design, Setting, and ParticipantsThis cross-sectional study was conducted from January 2019 to December 2022 in 102 home health locations in 19 states and included 178 195 TM and 107 102 MA patients 65 years or older with 2 or fewer 60-day home health episodes. It included a secondary analysis of standardized assessment and visit data. Inverse probability of treatment weighting regression compared service intensity and patient outcomes between MA and TM episodes, accounting for differences in demographic characteristics, medical complexity, functional and cognitive impairments, social environment, caregiver support, and local community factors. Models included office location, year, and reimbursement policy fixed effects. Data were analyzed between September 2023 and July 2024ExposureTM vs MA plan.Main Outcomes and MeasuresHome health length of stay and number of visits from nursing, physical, occupational, and speech therapy, social work, and home health aides. Patient outcomes included improvement in self-care and mobility function, discharge to the community, and transfer to an inpatient facility during home health.ResultsOf 285 297 total patients, 180 283 (63.2%) were female; 586 (0.2%) were American Indian/Alaska Native, 8957 (3.1%) Asian, 28 694 (10.1%) Black, 7406 (2.6%) Hispanic, 1959 (0.7%) Native Hawaiian/Pacific Islander, 237 017 (83.1%) non-Hispanic White, and 678 (0.2%) multiracial individuals. MA patients had shorter home health length of stay by 1.62 days (95% CI, −1.82 to 1.42) and received fewer visits from all disciplines except social work. There were no differences in inpatient transfers. MA patients had 3% and 4% lower adjusted odds of improving in mobility and self-care, respectively (mobility odds ratio [OR], 0.97; 95% CI, 0.94-0.99; self-care OR, 0.96; 95% CI, 0.92-0.99). MA patients were 5% more likely to discharge to the community compared with TM (OR, 1.05; 95% CI, 1.01-1.08).Conclusions and RelevanceThe results of this cross-sectional study suggest that MA patients receive shorter and less intensive home health care vs TM patients with similar needs. Differences may be due to the administrative burden and cost-limiting incentives of MA plans. MA patients experienced slightly worse functional outcomes but were more likely to discharge to the community, which may have negative implications for MA patients, including reduced functional independence or increased caregiver burden.
JAZ
Genes in Cotton: Prospects for Improvements to Vegetative and Fibre Growth by Addressing Lepidopteran Herbivory Resistance Mechanisms
Authors: Rock Christopher D. , Adhikari Indra P. , Parajulee Megha N. 
Published: March 2024

Abstract

Evolution of insect resistance is the primary threat to the long‐term efficacy of
Bacillus thuringiensis
(Bt) transgene technologies. Plants have a deeply conserved defence response to pests: Jasmonic acid (JA) hormone signalling mediated by transcriptional repressors called JASMONATE‐ZIM‐DOMAIN/JAZ. JAZs normally limit expression of plant defence pathways, promoting assimilate partitioning towards growth and reproduction, by their carboxyl terminal Jas motif that antagonises MYeloCytomatosis (MYC) master transcription factor activities. Deletion, alternative splicing/intron retention, or disruption of the Jas motif results in JA insensitivity and increased resistance to pathogens including arthropod herbivores, for example by production of secondary metabolites and new leaves with higher trichome density. JA‐mediated trichome initiation and elongation also impact cotton fibre production. Since its release in 2017, the third‐generation stacked commercial Bt insecticidal Vip3A protein traits are increasingly under severe pressure for evolution of
Helicoverpa zea
(bollworm) resistance. Regional differences in efficacy of Bollgard
®
3 and WideStrike
®
3 against lepidopteran pests and increasing pesticide use are emerging issues. Future transgenic field control failures from bollworm infestations and incursions of
Helicoverpa armigera
from Central America are likely in the U.S. Cotton Belt. In this systematic primer on the problem, we take a conceptual approach to consider
JAZ
genes as means to leverage ‘internal’ host‐derived herbivore resistance in cotton. We consider the genetic redundancy and pleiotropic nature of JAZ master regulators on tissue‐specific growth, development, crosstalk with hormonal and small RNA pathways as nodes in networks, and limitations of JAZ efficacy due to fitness costs/growth trade‐offs versus prospects for enhancing resistance networks to orchestrate transgressive segregation (generation of extreme phenotypes in breeding progeny not seen in parental lines).
The use of dose surface maps as a tool to investigate spatial dose delivery accuracy for the rectum during prostate radiotherapy
Authors: Patrick Haley M. , Kildea John 
Published: March 2024

AbstractPurposeThis study aims to address the lack of spatial dose comparisons of planned and delivered rectal doses during prostate radiotherapy by using dose‐surface maps (DSMs) to analyze dose delivery accuracy and comparing these results to those derived using DVHs.MethodsTwo independent cohorts were used in this study: twenty patients treated with 36.25 Gy in five fractions (SBRT) and 20 treated with 60 Gy in 20 fractions (IMRT). Daily delivered rectum doses for each patient were retrospectively calculated using daily CBCT images. For each cohort, planned and average‐delivered DVHs were generated and compared, as were planned and accumulated DSMs. Permutation testing was used to identify DVH metrics and DSM regions where significant dose differences occurred. Changes in rectal volume and position between planning and delivery were also evaluated to determine possible correlation to dosimetric changes.ResultsFor both cohorts, DVHs and DSMs reported conflicting findings on how planned and delivered rectum doses differed from each other. DVH analysis determined average‐delivered DVHs were on average 7.1% ± 7.6% (p ≤ 0.002) and 5.0 ± 7.4% (p ≤ 0.021) higher than planned for the IMRT and SBRT cohorts, respectively. Meanwhile, DSM analysis found average delivered posterior rectal wall dose was 3.8 ± 0.6 Gy (p = 0.014) lower than planned in the IMRT cohort and no significant dose differences in the SBRT cohort. Observed dose differences were moderately correlated with anterior‐posterior rectal wall motion, as well as PTV superior‐inferior motion in the IMRT cohort. Evidence of both these relationships were discernable in DSMs.ConclusionDSMs enabled spatial investigations of planned and delivered doses can uncover associations with interfraction motion that are otherwise masked in DVHs. Investigations of dose delivery accuracy in radiotherapy may benefit from using DSMs over DVHs for certain organs such as the rectum.
Argument‐based intervention as a way to reduce covid‐19 unfounded beliefs and vaccination hesitancy
Authors: Teličák Peter , Šrol Jakub , Halama Peter 
Published: March 2024

AbstractThe aim of the experimental study was to verify the reduction of Covid‐19 unfounded beliefs through arguments in favor of vaccination. The sample includes 720 participants recruited by Qualtrics (50% women, age: M = 38.8, SD = 10.90). The participants were equally and randomly divided into three groups. The control group was given the task of reading a neutral text about Norway. The first experimental group was provided with a debunking text that corrected popular misinformation and unfounded beliefs about vaccination against polio and vaccination against Covid‐19. The second experimental group read the same text as the first, with two additional paragraphs addressing the motives and errors in the thinking of unfounded belief spreaders. The results confirmed that exposing the participants to arguments for vaccination reduces the endorsement of Covid‐19 unfounded beliefs and increases the willingness to be vaccinated against Covid‐19 disease.
Oxygen‐Vacancy‐Rich Monolayer BiO2−X Nanosheets for Bacterial Sepsis Management via Dual Physically Antibacterial and Chemically Anti‐inflammatory Functions
Authors: Liu Fang , Zhang Kun , Lu Bin , Wang Xiaochun , Dong Qingrong , Xue Tingyu , Tan Yan , Wang Xing , Du Jiangfeng 
Published: March 2024

AbstractSepsis is defined as a life‐threatening organ dysfunction caused by a dysregulated host response to infection. Effective treatment of bacterial sepsis remains challenging due to the rapid progression of infection and the systemic inflammatory response. In this study, monolayer BiO2−X nanosheets (BiO2−X NSs) with oxygen‐rich vacancies through sonication‐assisted liquid‐phase exfoliation are successfully synthesized. Herein, the BiO2−X NSs exhibit a novel nanozyme‐enabled intervention strategy for the management of bacterial sepsis, based on its pH dependent dual antibacterial and anti‐inflammatory functions. BiO2−X NSs exhibit effective antibacterial by utilizing oxidase (OXD)‐like activity. Additionally, BiO2−X NSs can scavenge multiple reactive oxygen species (ROS) and mitigate systemic hyperinflammation by mimicking superoxide dismutase (SOD) and catalase (CAT). These dual capabilities of BiO2−X NSs allow them to address bacterial infection, proinflammatory cytokines secretion and ROS burst collaboratively, effectively reversing the progression of bacterial sepsis. In vivo experiments have demonstrated that BiO2−X NSs significantly reduce bacterial burden, attenuate systemic hyperinflammation, and rapidly rescued organ damage. Importantly, no obvious adverse effects are observed at the administered dose of BiO2−X NSs. This study presents a novel defect engineering strategy for the rational design of high‐performance nanozymes and development of new nanomedicines for managing bacterial sepsis.