bluuebunny/crossref_metadata_2025_split huggingface dataset:
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris
Authors: Pechter Kieran B. , Gallagher Larry , Pyles Harley , Manoil Colin S. , Harwood Caroline S. 
Published: December 2015

ABSTRACTRhodopseudomonas palustrisis an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility ofR. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacteriumCaulobacter crescentus, and 187 have essential gene homologs inEscherichia coli. There were 24R. palustrisgenes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essentialE. coligenes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism.R. palustriscells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in bothC. crescentusandR. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria likeE. coli.IMPORTANCEEssential genes in bacteria and other organisms are those absolutely required for viability.Rhodopseudomonas palustrishas served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes ofR. palustrisgrown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identifyR. palustrisgenes essential for viability under specialized growth conditions and also for survival under conditions of stress.
Permuting the PGF Signature Motif Blocks both Archaeosortase-Dependent C-Terminal Cleavage and Prenyl Lipid Attachment for the Haloferax volcanii S-Layer Glycoprotein
Authors: Abdul Halim Mohd Farid , Karch Kelly R. , Zhou Yitian , Haft Daniel H. , Garcia Benjamin A. , Pohlschroder Mechthild 
Published: December 2015

ABSTRACT

For years, the S-layer glycoprotein (SLG), the sole component of many archaeal cell walls, was thought to be anchored to the cell surface by a C-terminal transmembrane segment. Recently, however, we demonstrated that the
Haloferax volcanii
SLG C terminus is removed by an archaeosortase (ArtA), a novel peptidase. SLG, which was previously shown to be lipid modified, contains a C-terminal tripartite structure, including a highly conserved proline-glycine-phenylalanine (PGF) motif. Here, we demonstrate that ArtA does not process an SLG variant where the PGF motif is replaced with a PFG motif (
slg

G796F
,
F797G

). Furthermore, using radiolabeling, we show that SLG lipid modification requires the PGF motif and is ArtA dependent, lending confirmation to the use of a novel C-terminal lipid-mediated protein-anchoring mechanism by prokaryotes. Similar to the case for the Δ
artA
strain, the growth, cellular morphology, and cell wall of the
slg

G796F
,
F797G

strain, in which modifications of additional
H. volcanii
ArtA substrates should not be altered, are adversely affected, demonstrating the importance of these posttranslational SLG modifications. Our data suggest that ArtA is either directly or indirectly involved in a novel proteolysis-coupled, covalent lipid-mediated anchoring mechanism. Given that archaeosortase homologs are encoded by a broad range of prokaryotes, it is likely that this anchoring mechanism is widely conserved.

IMPORTANCE
Prokaryotic proteins bound to cell surfaces through intercalation, covalent attachment, or protein-protein interactions play critical roles in essential cellular processes. Unfortunately, the molecular mechanisms that anchor proteins to archaeal cell surfaces remain poorly characterized. Here, using the archaeon
H. volcanii
as a model system, we report the first
in vivo
studies of a novel protein-anchoring pathway involving lipid modification of a peptidase-processed C terminus. Our findings not only yield important insights into poorly understood aspects of archaeal biology but also have important implications for key bacterial species, including those of the human microbiome. Additionally, insights may facilitate industrial applications, given that photosynthetic cyanobacteria encode uncharacterized homologs of this evolutionarily conserved enzyme, or may spur development of unique drug delivery systems.
Surface modification and electrochemical properties of activated carbons for supercapacitor electrodes
Authors: Yang Dan , Qiu Wenmei , Xu Jingcai , Han Yanbing , Jin Hongxiao , Jin Dingfeng , Peng Xiaoling , Hong Bo , Li Ji , Ge Hongliang , Wang Xinqing 
Published: December 2015

Modifications with different acids (HNO3, H2SO4, HCl and HF, respectively) were introduced to treat the activated carbons (ACs) surface. The microstructures and surface chemical properties were discussed by X-ray diffraction (XRD), thermogravimetric analysis (TGA), ASAP, Raman spectra and Fourier transform infrared (FTIR) spectra. The ACs electrode-based supercapacitors were assembled with 6 mol ⋅ L[Formula: see text] KOH electrolyte. The electrochemical properties were studied by galvanostatic charge–discharge and cyclic voltammetry. The results indicated that although the BET surface area of modified ACs decreased, the functional groups were introduced and the ash contents were reduced on the surface of ACs, receiving larger specific capacitance to initial AC. The specific capacitance of ACs modified with HCl, H2SO4, HF and HNO3 increased by 31.4%, 23%, 21% and 11.6%, respectively.
Physical mechanism of beam splitting based on reflective embedded double-layer grating
Authors: Wang Bo , Li Hongtao , Shu Wenhao , Li Wenhua , Chen Li , Lei Liang , Zhou Jinyun 
Published: December 2015

It is not easy to achieve high performance for conventional beam splitters, such as high efficiency, good uniformity, polarization-independence, and wide bandwidth. A reflective embedded double-layer grating is described for beam splitting. With optimized grating profiles, the novel beam splitter can diffract both TE and TM polarizations into two orders with high performance. For the easy production, the fabrication tolerance is investigated and given. Most importantly, efficiencies more than 45% can be split into two orders within the wide bandwidth of 1412–1647 nm for TE polarization. The beam splitter based on multilayer coatings is sensitive to the incident angle and wavelength. And the bandwidth needs to be improved for the beam splitter based on simple grating. The design is of benefit for the performance improvement of the beam splitter by new grating configuration compared with the conventional simple grating.
Silencing of CD24 Enhances the PRIMA-1–Induced Restoration of Mutant p53 in Prostate Cancer Cells
Authors: Zhang Wei , Yi Bin , Wang Chao , Chen Dongquan , Bae Sejong , Wei Shi , Guo Rong-Jun , Lu Changming , Nguyen Lisa L.H. , Yang Wei-Hsiung , Lillard James W. , Zhang Xingyi , Wang Lizhong , Liu Runhua 
Published: December 2015

Abstract
Purpose: In prostate cancer cells, there is CD24-dependent inactivation of mutant p53, but the mechanism and its significance remain largely unknown. Here, we validated this observation and explored the therapeutic potential of targeting CD24 in TP53 mutant prostate cancer cells.
Experimental Design: Overall, 553 prostate cancers (522 formalin-fixed paraffin-embedded and 31 frozen tissues) were assessed for protein or mRNA expression of CD24 and TP53. The effects of CD24 on p53-dependent transcriptional regulation, cancer cell growth, the cell cycle, apoptosis, and mutant p53 restoration were also determined.
Results: As determined with three sample cohorts, CD24 and p53 were not expressed in prostate epithelial cells but in prostate cancer cells in 48% of cases for CD24 and 16% of cases for p53 (mutant form). Expressions of CD24 and mutant p53 were more frequently observed in late-stage and metastatic prostate tumors. Mutant p53 accompanied with CD24 was expressed in most cases (91.6%, 76/83). Silencing of CD24 increased the transcriptional activity of p53 target genes, such as CDKNA1, VDR, and TP53INP1, leading to suppression of p53-dependent cell growth, cell-cycle arrest, and apoptosis in most TP53-mutant prostate cancer cells. Silencing of CD24 enhanced restoration of PRIMA-1–induced mutant p53 in endogenous TP53P223L/V274F DU145 cells and in PC3 cells transfected with TP53R273H.
Conclusions: In human prostate cancers, there is CD24-dependent inactivation of mutant p53. The coexpression of CD24 and p53 may help identify aggressive cancers. Targeting CD24 provides a strategy to enhance mutant p53-restoring therapies, especially in patients with TP53R273H prostate cancer. Clin Cancer Res; 22(10); 2545–54. ©2015 AACR.
Comparison of Echocardiographic Measures in a Hispanic/Latino Population With the 2005 and 2015 American Society of Echocardiography Reference Limits (The Echocardiographic Study of Latinos)
Authors: Qureshi Waqas T. , Leigh J. Adam , Swett Katrina , Dharod Ajay , Allison Matthew A. , Cai Jianwen , Gonzalez Franklyn , Hurwitz Barry E. , Shah Sanjiv J. , Desai Ankit A. , Spevack Daniel M. , Rodriguez Carlos J. 
Published: December 2015

Background—
Reference limits for echocardiographic quantification of cardiac chambers in Hispanics are not well studied.

Methods and Results—

We examined the reference values of left atrium and left ventricle (LV) structure in a large ethnically diverse Hispanic cohort. Two-dimensional transthoracic echocardiography was performed in 1818 participants of the Echocardiographic Study of Latinos (ECHO-SOL). Individuals with body mass index ≥30 kg/m
2
, hypertension, diabetes mellitus, coronary artery disease, and atrial fibrillation were excluded leaving 525 participants defined as healthy reference cohort. We estimated 95th weighted percentiles of LV end systolic volume, LV end diastolic volume, relative wall and septal thickness, LV mass, and left atrial volume. We then used upper reference limits of the 2005 and 2015 American Society of Echocardiography (ASE) and 95th percentile of reference cohort to classify the Hispanic Community Health Study/Study of Latinos (HCHS/SOL) target population into abnormal and normal. Reference limits were also calculated for each of 6 Hispanic origins. Using ASE 2015 defined reference values, we categorized 7%, 21%, 57%, and 17% of men and 18%, 29%, 60%, and 26% of women as having abnormal LV mass index, relative, septal, and posterior wall thickness, respectively. Conversely, 10% and 11% of men and 4% and 2% of women were classified as having abnormal end-diastolic volume and internal diameter by ASE 2015 cutoffs, respectively. Similar differences were found when we used 2005 ASE cutoffs. Several differences were noted in distribution of cardiac structure and volumes among various Hispanic/Latino origins. Cubans had highest values of echocardiographic measures, and Central Americans had the lowest.

Conclusions—
This is the first large study that provides normal reference values for cardiac structure. It further demonstrates that a considerable segment of Hispanic/Latinos residing in the United States may be classified as having abnormal measures of cardiac chambers when 2015 and 2005 ASE reference cutoffs are used.
Reperfusion Beyond 6 Hours Reduces Infarct Probability in Moderately Ischemic Brain Tissue
Authors: An Hongyu , Ford Andria L. , Eldeniz Cihat , Chen Yasheng , Vo Katie D. , Zhu Hongtu , Powers William J. , Lin Weili , Lee Jin-Moo 
Published: December 2015

Background and Purpose—
We aimed to examine perfusion changes between 3 and 6 and 6 and 24 hours after stroke onset and their impact on tissue outcome.

Methods—

Acute ischemic stroke patients underwent perfusion magnetic resonance imaging at 3, 6, and 24 hours after stroke onset and follow-up fluid-attenuated inversion recovery at 1 month to assess tissue fate. Mean transit time prolongation maps (MTTp=MTT–[median MTT of contralateral hemisphere]) were obtained at 3 (MTTp
3 h
), 6 (MTTp
6 h
), and 24 hours (MTTp
24 h
). Perfusion changes between 3 and 6 hours (ΔMTTp
3_6
) and 6 and 24 hours (ΔMTTp
6_24
) were calculated. A 2-step analysis was performed to evaluate the impact of ΔMTTp
3_6
and ΔMTTp
6_24
on tissue fate. First, a voxel-based multivariable logistic regression was performed for each individual patient with MTTp
3 h
, ΔMTTp
3_6
, and ΔMTT
6_24
as independent variables and tissue fate as outcome. Second, Wilcoxon signed-rank tests on logistic regression coefficients were performed across patients to evaluate whether ΔMTTp
3_6
and ΔMTT
6_24
had significant impact on tissue fate for varying severities of baseline perfusion.

Results—

Perfusion change was common during both time periods: 85% and 81% of patients had perfusion improvement during 3- to 6- and 6- and 24-hour time intervals, respectively. ΔMTT
3_6
significantly influenced 1-month infarct probability across a wide range of baseline perfusion (MTTp 0–15 s). ΔMTT
6_24
also impacted 1-month infarct probability, but its influence was restricted to tissue with milder baseline ischemia (MTTp 0–10 s).

Conclusions—
Brain tissue with mild to moderate ischemia can be salvaged by reperfusion even after 6 hours. Such tissue could be targeted for intervention beyond current treatment windows.
On the Role of Temperature and Salinity Data Assimilation to Constrain a Coupled Physical–Biogeochemical Model in the Baltic Sea
Authors: Fu Weiwei 
Published: December 2015

AbstractA three-dimensional variational data assimilation (3DVAR) method is implemented in a coupled physical–biogeochemical (CPB) model in the Baltic Sea. This study carries out a 10-yr assimilation experiment with satellite sea surface temperature (SST) and observed in situ temperature (T) and salinity (S) profiles. The impact of the assimilation is assessed with the focus on how the biogeochemical model responds to the improved hydrodynamics. The assimilation of temperature and salinity data yields considerable improvements in the physical model. On a basin scale, the mean bias of SST, T, S, and mixed layer depth (MLD) is decreased by 0.18°C (57%), 0.31°C (49%), 0.34 psu (43%), and 1.8 m (43%), respectively. More importantly, the biogeochemical simulation is improved in response to the physical data assimilation. Compared with in situ observations, the mean biases of chlorophyll a (Chl), dissolved inorganic nitrogen (DIN) and phosphorus (DIP) are decreased by 0.09 mg m−3 (15.5%), 0.19 mmol m−3 (9%), and 0.15 mmol m−3 (23%). Physical data assimilation also improves the simulated variability of Chl, DIN, and DIP and their correlations with observation. Compared with satellite observations, the mean bias of surface chlorophyll is reduced by 0.10–0.32 mg m−3 especially in the Skagerrak–Kattegat area and Bornholm basin. The decrease of total Chl change is caused by different mechanisms for winter and summer. While the deepened mixed layer acts as a dilution factor in winter, strengthened stratification agrees well with the decrease of chlorophyll in summer. In the vertical, relatively large changes of DIN and DIP occur below 60 m, which corresponds to the mean permanent halocline depth (~60–80 m) of the Baltic Sea.
On the Mediterranean Water Composition
Authors: Carracedo L. I. , Pardo P. C. , Flecha S. , Pérez F. F. 
Published: December 2015

AbstractThe Mediterranean Outflow Water (MOW) spills from the Mediterranean Sea (east North Atlantic basin) west off the Strait of Gibraltar. As MOW outflows, it entrains eastern North Atlantic Central Waters (ENACW) and Intermediate Waters to form the neutrally buoyant Mediterranean Water (MW) that can be traced over the entire North Atlantic basin. Its high salinity content influences the thermohaline properties of the intermediate–deep water column in the North Atlantic and its dynamics. Here, the composition of MW in its source region (the Gulf of Cádiz, west off Strait of Gibraltar) is investigated on the basis of an optimum multiparameter analysis. The results obtained indicate that mixing of MOW (34.1% ± 0.3%) occurs mainly with overlying ENACW (57.1% ± 0.8%) in a process broadly known as central water entrainment. A diluted form (80% of dilution) of the Antarctic Intermediate Water (AAIW) reaches the region and also takes part in MW formation (8.3% ± 0.5%). Finally, the underlying Labrador Sea Water (LSW) also contributes (0.4% ± 0.1%) to the characteristics of MW. From these results and considering 0.74 Sverdrups (Sv; 1 Sv ≡ 106 m3 s−1) as the mean outflow of MOW, the MW exportation rate was inferred (2.2 Sv), which, decomposing MW, means that the MOW outflow is accompanied by 1.24 Sv of entrained ENACW, 0.18 Sv of AAIW, and <0.01 Sv of LSW.
Interannual Variability of Equatorial Eastern Indian Ocean Upwelling: Local versus Remote Forcing
Authors: Chen Gengxin , Han Weiqing , Li Yuanlong , Wang Dongxiao 
Published: December 2015

AbstractThe equatorial eastern Indian Ocean (EIO) upwelling occurs in the Indian Ocean warm pool, differing from the equatorial Pacific and Atlantic upwelling that occurs in the cold tongue. By analyzing observations and performing ocean model experiments, this paper quantifies the remote versus local forcing in causing interannual variability of the equatorial EIO upwelling from 2001 to 2011 and elucidates the associated processes. For all seasons, interannual variability of thermocline depth in the EIO, as an indicator of upwelling, is dominated by remote forcing from equatorial Indian Ocean winds, which drive Kelvin waves that propagate along the equator and subsequently along the Sumatra–Java coasts. Upwelling has prominent signatures in sea surface temperature (SST) and chlorophyll-a concentration but only in boreal summer–fall (May–October). Local forcing plays a larger role than remote forcing in producing interannual SST anomaly (SSTA). During boreal summer–fall, when the mean thermocline is relatively shallow, SSTA is primarily driven by the upwelling process, with comparable contributions from remote and local forcing effects. In contrast, during boreal winter–spring (November–April), when the mean thermocline is relatively deep, SSTA is controlled by surface heat flux and decoupled from thermocline variability. Advection affects interannual SSTA in all cases. The remote and local winds that drive the interannual variability of the equatorial EIO upwelling are closely associated with Indian Ocean dipole events and to a lesser degree with El Niño–Southern Oscillation.
A Numerical Study of the 6 May 2012 Tsukuba City Supercell Tornado. Part I: Vorticity Sources of Low-Level and Midlevel Mesocyclones
Authors: Mashiko Wataru 
Published: December 2015

Abstract
On 6 May 2012, an F3 supercell tornado, one of the most destructive tornadoes ever recorded in Japan, hit Tsukuba City in eastern Japan and caused severe damage. To clarify the generation mechanisms of the tornadic storm and tornado, high-resolution numerical simulations were conducted under realistic environmental conditions using triply nested grids. The innermost simulation with a 50-m mesh successfully reproduced the Tsukuba City tornadic supercell storm.
In this study (the first of a two-part study), the vorticity sources responsible for mesocyclogenesis prior to tornadogenesis were investigated by analyzing vortex lines and the evolution of circulation of the mesocyclones. Vortex lines that passed through the midlevel mesocyclone (4-km height) originated from the environmental streamwise vorticity, whereas the low-level mesocyclone and low-level mesoanticyclone were connected by several arching vortex lines over the rear-flank downdraft associated with the hook-shaped distribution of hydrometeors (hereafter hook echo). Most of the circulation for the circuit surrounding the midlevel mesocyclone was conserved, although the baroclinity associated with positive buoyancy within the storm led to an up-and-down trend. The circulation of the material circuit encircling the low-level mesocyclone showed a gradual increase caused by baroclinity along the forward-flank gust front. Friction also had a positive net effect on the circulation. In contrast, most of the negative circulation of the low-level mesoanticyclone was rapidly acquired owing to baroclinity around the tip of the hook echo. Just after tornadogenesis, the low-level mesocyclone intensified significantly and developed upward, which caused retrograde motion of the midlevel mesocyclone.
Using Routinely Available Information to Estimate Tropical Cyclone Wind Structure
Authors: Knaff John A. , Slocum Christopher J. , Musgrave Kate D. , Sampson Charles R. , Strahl Brian R. 
Published: December 2015

AbstractA relatively simple method to estimate tropical cyclone (TC) wind radii from routinely available information including storm data (location, motion, and intensity) and TC size is introduced. The method is based on a combination of techniques presented in previous works and makes an assumption that TCs are largely symmetric and that asymmetries are based solely on storm motion and location. The method was applied to TC size estimates from two sources: infrared satellite imagery and global model analyses. The validation shows that the methodology is comparable with other objective methods based on the error statistics. The technique has a variety of practical research and operational applications, some of which are also discussed.