Sc Regions Research Articles

245 Linking Cervical Spinal Cord White Matter Magnetization Transfer Ratio to NIH Toolbox Based Analyses of Motor Function in Degenerative Cervical Myelopathy

INTRODUCTION: Traditional spine imaging technique present disparity between degenerative cervical myelopathy (DCM) disease severity and prognosis. Advancement in spine neuroimaging has unveiled key changes that enhance our understanding of DCM pathogenesis. We investigated region- and tract-specific SC white matter (WM) damage and their relationship to motor deficit in DCM. METHODS: A cohort of 20 DCM and 23 age-matched HC participants were recruited in a cross-sectional study. We utilized a consensus MT-imaging protocol, Spinal cord Toolbox, and objective motor assessment tool battery to assess the extent of WM injury and functional deficits in DCM. The SC WM region- and tract-based MTR were calculated in three different ROIs: maximum compressed level (MCL), caudal uncompressed level (C7), and central region of compression. RESULTS: DCM patients demonstrated significant functional deficits compared to HC in motor assessments. DCM exhibited reduced MTR measures denoting WM injury in the anterior region of the SC and within selected motor tracts in the ROIs. MTR values in reticulospinal, vestibulospinal, and lateral corticospinal tracts were significantly associated with dexterity and grip strength measures. CONCLUSIONS: Our methodology enables precise mapping of ROIs within the SC allowing us to demonstrate an association between tract-specific WM damage and functional motor deficits in DCM patients. Additionally, the observation of decreased MTR measures in seemingly uncompressed SC regions indicates the pathophysiology of DCM that may provide insight into the varying presentations of DCM. Identification of specific WM injury may help better understand DCM deficits that can be targeted for effective interventions to improve patient outcomes

Plastid genome and its phylogenetic implications of Asiatic Spiraea (Rosaceae).

Spiraea L. is a genus comprising approximately 90 species that are distributed throughout the northern temperate regions. China is recognized as the center of species diversity for this genus, hosting more than 70 species, including 47 endemic species. While Spiraea is well-known for its ornamental value, its taxonomic and phylogenetic studies have been insufficient. In this study, we conducted sequencing and assembly of the plastid genomes (plastomes) of 34 Asiatic Spiraea accessions (representing 27 Asiatic Spiraea species) from China and neighboring regions. The Spiraea plastid genome exhibits typical quadripartite structures and encodes 113-114 genes, including 78-79 protein-coding genes (PCGs), 30 tRNA genes, and 4 rRNA genes. Linear regression analysis revealed a significant correlation between genome size and the length of the SC region. By the sliding windows method, we identified several hypervariable hotspots within the Spiraea plastome, all of which were localized in the SC regions. Our phylogenomic analysis successfully established a robust phylogenetic framework for Spiraea, but it did not support the current defined section boundaries. Additionally, we discovered that the genus underwent diversification after the Early Oligocene (~ 30Ma), followed by a rapid speciation process during the Pliocene and Pleistocene periods. The plastomes of Spiraea provided us invaluable insights into its phylogenetic relationships and evolutionary history. In conjunction with plastome data, further investigations utilizing other genomes, such as the nuclear genome, are urgently needed to enhance our understanding of the evolutionary history of this genus.

Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes.

Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum. Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed. The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production. This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.

Complete chloroplast genome structural characterization of two Phalaenopsis (Orchidaceae) species and comparative analysis with their alliance

BackgroundThe taxonomy and infrageneric delimitation of Phalaenopsis Blume has been significantly disputed due to some overlapping morphological features between species related, which needed further evidence for clarification. The structural characterization of complete chloroplast genomes of P. storbatiana and P. wilsonii were analyzed and compared with those of related taxa to provide a better understanding of their genomic information on taxonomy and phylogeny.ResultsIt was shown that chloroplast genomes of Phalaenopsis storbatiana and P. wilsonii had a typical quadripartite structure with conserved genome arrangements and moderate divergence. The chloroplast genomes of P. storbatiana and P. wilsonii were 145,885 bp and 145,445 bp in length, respectively, and shared a similar GC content of 36.8%. Gene annotations of two species revealed 109 single-copy genes consistently. In addition, 20 genes duplicated in the inverted regions, 16 genes each possessed one or more introns, and five ndh (NA (D)H dehydrogenase) genes were observed in both. Comparative analysis of the total cp genomes of P. storbatiana and P. wilsonii with those of other six related Phalaenopsis species confirmed the stable sequence identity for coding and non-coding regions and higher sequence variation in SC regions than IR regions. Most of their protein-coding genes had a high degree of codon preference. Moreover, 45 genes were discovered with significantly positive selection. However, different amplifications in IR regions were observed in these eight species. Phylogenetic analysis based on CDS from 60 species representing main clades in Orchidaceae indicated that Phalaenopsis species including P. stobartiana and P. wilsonii formed a monophyletic clade with high bootstrap nested in tribe Vandeae of Epidendroideae, which was consistent with those from previous studies.ConclusionsThe results could provide insight into understanding the plastome evolution and phylogenetic relationships of Phalaenopsis.

Influence of horizontal resolution and complexity of aerosol–cloud interactions on marine stratocumulus and stratocumulus‐to‐cumulus transition in HadGEM3‐GC3.1

AbstractStratocumulus (Sc) clouds and stratocumulus‐to‐cumulus transitions (SCTs) are challenging to represent in global models and they contribute to a large spread in modeled subtropical cloud feedbacks. We evaluate the impact of increasing the horizontal model resolution (∼135, 60 and 25 km, respectively) and increasing the complexity of the aerosol–cloud interaction parameterization (interactive versus non‐interactive at medium resolution) on springtime subtropical marine Sc properties and SCTs in the atmosphere‐only version of HadGEM3‐GC3.1. No significant impact on the spatial location of the SCT could be found between the different model versions. Increasing horizontal resolution led to small but significant increases in liquid water content and a stronger (more negative) shortwave (SW) cloud radiative effect (CRE), in particular over the southern‐hemisphere Sc regions. However, for two out of the four studied regions, the stronger SW CRE also brought the model outside the range of satellite‐derived values of the SW CRE. Applying non‐interactive aerosols instead of interactive aerosols also led to significantly higher liquid water content and a stronger SW CRE over the southern‐hemisphere Sc regions, while over the northern‐hemisphere Sc regions, a competition between a substantial increase in the cloud droplet number concentration and small changes in the liquid water content resulted in a weaker SW CRE or non‐significant changes. In general, using interactive instead of non‐interactive aerosol–cloud interactions brought the model closer to satellite‐retrieved mean values of the SW CRE. Our results suggest that increasing the horizontal resolution or the complexity of the aerosol–cloud parameterization has a small but statistically significant effect on the SW CRE of marine Sc, in particular over regions with high liquid water content. For these regions, the effect of introducing non‐interactive versus interactive aerosol–cloud interactions is about as large as increasing the horizontal resolution from medium to high.

Molecular Structure and Variation Characteristics of the Plastomes from Six Malus baccata (L.) Borkh. Individuals and Comparative Genomic Analysis with Other Malus Species.

Malus baccata (L.) Borkh. is an important wild species of Malus. Its rich variation types and population history are not well understood. Chloroplast genome mining plays an active role in germplasm identification and genetic evolution. In this study, by assembly and annotation, six complete cp genome sequences, ranging in size from 160,083 to 160,295 bp, were obtained. The GC content of stable IR regions (42.7%) was significantly higher than that of full length (36.5%) and SC regions (LSC-34.2%, SSC-30.4%). Compared with other Malus species, it was found that there were more sites of polymorphisms and hotspots of variation in LSC and SSC regions, with high variation sites including trnR/UCU-atpA, trnT/UGU-trnL/UAA, ndhF-rpl32 and ccsA-ndhD. The intraspecific and interspecific collinearity was good, and no structural rearrangement was observed. A large number of repeating elements and different boundary expansions may be involved in shaping the cp genome size. Up to 77 or 78 coding genes were annotated in the cp genomes of M. baccata, and high frequency codons such as UUA (Leu), GCU (Ala) and AGA (Arg) were identified by relative synonymous codon usage analysis. Phylogeographic analysis showed that 12 individuals of M. baccata clustered into three different groups with complex structure, whereas variant xiaojinensis (M.H. Cheng & N.G. Jiang) was not closely related to M. baccata evolutionarily. The phylogenetic analysis suggested that two main clades of different M. baccata in the genus Malus were formed and that I and II diverged about 9.7 MYA. In conclusion, through cp genome assembly and comparison, the interspecific relationships and molecular variations of M. baccata were further elucidated, and the results of this study provide valuable information for the phylogenetic evolution and germplasm conservation of M. baccata and Malus.

Comparative genomic analysis of esophageal squamous cell carcinoma among different geographic regions.

Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence, survival, and risk factors. Although the genomic characteristics of ESCC have been extensively characterized, the genomic differences between different geographic regions remain unclear. In this study, we sequenced 111 patients with ESCC from northern (NC) and southern (SC) China, combined their data with those of 1081 cases from previous reports, and performed a comparative analysis among different regions. In total, 644 ESCC cases were collected from six geographic regions (NC, SC, Xinjiang, China [XJC], Japan [JP], Vietnam [VN], and Europe & America [EA]) as the discovery cohort. Validation cohort 1 included 437 patients with ESCC from the NC region. Validation cohort 2 included 54 and 57 patients from the NC and SC regions, respectively. Patients with ESCC in different regions had different genomic characteristics, including DNA signatures, tumor mutation burdens, significantly mutated genes (SMGs), altered signaling pathways, and genes associated with clinical features. Based on both the DNA mutation signature and the mutation profile of the most common genes, the NC and SC groups were clustered close together, followed by the JP, XJC, EA, and VN groups. Compared to patients with ESCC from SC, SMGs, including KMT2D, FAT1, and NOTCH1 were more frequently identified in patients with ESCC from NC. Furthermore, some genes (TDG and DNAH8) correlated with overall survival in completely opposite ways in patients with ESCC from different geographical regions. Our study provides insights into genomic differences in ESCC among different regions. These differences may be related to differences in environmental carcinogens, incidence, and survival.

Mapping of PET/CT-based regional nodes distribution of recurrent/advanced breast cancer and comparison with current delineation atlas.

To localize the distribution of regional nodes in recurrent/advanced breast cancer patients based on 18-fludeoxyglucose (FDG) positron emission tomography/CT (PET/CT) images and validate the coverage of clinical target volumes (CTVs) for regional nodes with current contouring guidelines. We enrolled 154 recurrent/advanced breast cancer patients with FDG-avid regional nodes who underwent PET/CT between January 2018 and June 2020. Involvement of lymph node regions including axillary lymph node level I-III (ALN-I, ALN-II, ALN-III), Rotter's nodes (RN), medial supraclavicular (SC-M), lateral supraclavicular (SC-L) and internal mammary nodes (IMN) was recorded respectively. Coverage of the CTVs in different atlases and the locations of out-of-field were evaluated. A total of 348 lymph node regions containing disease were identified, including ALN-I 109, ALN-II 46, ALN-III 36, RN 17, SC-M 68, SC-L 36 and IMN 36. Recurrent ALNs mainly located cranially and ventrally to the axillary vein (AV). Ipsilateral cervical nodes were simultaneously affected in 33/76 SC positive patients. RADCOMP (306/348) and RUIJIN (291/348) guidelines had higher coverage compared with RTOG (205/348) and ESTRO (202/348) guidelines (p < 0.001, respectively). In primary non-metastastic and recurrent patients, major missings located in SC-L (7/7, 17/17) and IMN (7/10, 15/19) for RTOG guideline while SC-L (7/7, 17/17) for ESTRO guideline (p < 0.001, respectively). Among recurrent patients, SC-M (22/31) was another major missing area for ESTRO guideline (p < 0.001). The current guidelines effectively cover most regional nodes in postoperative breast cancer patients. SC-L and IMN were the major missing regions. Recurrent ALNs were most often seen in cranial and ventral to the AV. The CTV of patients with clinically positive SC was recommended to extend up to the hyoid level. The CTVs should be adjusted based on risks of recurrence individually. The difference of regional nodes delineation between current guidelines mainly located in SC and IMN regions. High axilla including subclavicular nodes and the RN above AV for recurrent patients and the region between cricoid and hyoid for positive SC patients should be meticulously contoured.

Complete chloroplast genome of Lilium ledebourii (Baker) Boiss and its comparative analysis: lights into selective pressure and adaptive evolution

Lilium ledebourii (Baker) Boiss is a rare species, which exhibits valuable traits. However, before its genetic diversity and evolutionary were uncovered, its wild resources were jeopardized. Moreover, some ambiguities in phylogenetic relationships of this genus remain unresolved. Therefore, obtaining the whole chloroplast sequences of L. ledebourii and its comparative analysis along with other Lilium species is crucial and pivotal to understanding the evolution of this genus as well as the genetic populations. A multi-scale genome-level analysis, especially selection pressure, was conducted. Detailed third‑generation sequencing and analysis revealed a whole chloroplast genome of 151,884 bp, with an ordinary quadripartite and protected structure comprising 37.0% GC. Overall, 113 different genes were recognized in the chloroplast genome, consisting of 30 distinct tRNA genes, four distinct ribosomal RNAs genes, and 79 unique protein-encoding genes. Here, 3234 SSRs and 2053 complex repeats were identified, and a comprehensive analysis was performed for IR expansion and contraction, and codon usage bias. Moreover, genome-wide sliding window analysis revealed the variability of rpl32-trnL-ccsA, petD-rpoA, ycf1, psbI-trnS-trnG, rps15-ycf1, trnR, trnT-trnL, and trnP-psaJ-rpl33 were higher among the 48 Lilium cp genomes, displaying higher variability of nucleotide in SC regions. Following 1128 pairwise comparisons, ndhB, psbJ, psbZ, and ycf2 exhibit zero synonymous substitution, revealing divergence or genetic restriction. Furthermore, out of 78 protein-coding genes, we found that accD and rpl36 under positive selection: however, at the entire-chloroplast protein scale, the Lilium species have gone through a purifying selection. Also, a new phylogenetic tree for Lilium was rebuilt, and we believe that the Lilium classification is clearer than before. The genetic resources provided here will aid future studies in species identification, population genetics, and Lilium conservation.

Putting small and big pieces together: a genome assembly approach reveals the largest Lamiid plastome in a woody vine.

The plastid genome of flowering plants generally shows conserved structural organization, gene arrangement, and gene content. While structural reorganizations are uncommon, examples have been documented in the literature during the past years. Here we assembled the entire plastome of Bignonia magnifica and compared its structure and gene content with nine other Lamiid plastomes. The plastome of B. magnifica is composed of 183,052 bp and follows the canonical quadripartite structure, synteny, and gene composition of other angiosperms. Exceptionally large inverted repeat (IR) regions are responsible for the uncommon length of the genome. At least four events of IR expansion were observed among the seven Bignoniaceae species compared, suggesting multiple expansions of the IRs over the SC regions in the family. A comparison with 6,231 other complete plastomes of flowering plants available on GenBank revealed that the plastome of B. magnifica is the longest Lamiid plastome described to date. The newly generated plastid genome was used as a source of selected genes. These genes were combined with orthologous regions sampled from other species of Bignoniaceae and all gene alignments concatenated to infer a phylogeny of the family. The tree recovered is consistent with known relationships within the Bignoniaceae.

Comparative and phylogenetic analyses of six Kenya Polystachya (Orchidaceae) species based on the complete chloroplast genome sequences

BackgroundPolystachya Hook. is a large pantropical orchid genus (c. 240 species) distributed in Africa, southern Asia and the Americas, with the center of diversity in Africa. Previous studies on species of this genus have not obtained the complete chloroplast genomes, structures and variations. Additionally, the phylogenetic position of the genus in the Orchidaceae is still controversial and uncertain. Therefore, in this study, we sequenced the complete plastomes of six Kenya Polystachya species based on genome skimming, subjected them to comparative genomic analysis, and reconstructed the phylogenetic relationships with other Orchidaceae species.ResultsThe results exhibited that the chloroplast genomes had a typical quadripartite structure with conserved genome arrangement and moderate divergence. The plastomes of the six Polystachya species ranged from 145,484 bp to 149,274 bp in length and had an almost similar GC content of 36.9–37.0%. Gene annotation revealed 106–109 single-copy genes. In addition, 19 genes are duplicated in the inverted regions, and 16 genes each possessd one or more introns. Although no large structural variations were observed among the Polystachya plastomes, about 1 kb inversion was found in Polystachya modesta and all 11 ndh genes in the Polystachya plastomes were lost or pseudogenized. Comparative analysis of the overall sequence identity among six complete chloroplast genomes confirmed that for both coding and non-coding regions in Polystachya, SC regions exhibit higher sequence variation than IRs. Furthermore, there were various amplifications in the IR regions among the six Polystachya species. Most of the protein-coding genes of these species had a high degree of codon preference. We screened out SSRs and found seven relatively highly variable loci. Moreover, 13 genes were discovered with significant positive selection. Phylogenetic analysis showed that the six Polystachya species formed a monophyletic clade and were more closely related to the tribe Vandeae. Phylogenetic relationships of the family Orchidaceae inferred from the 85 chloroplast genome sequences were generally consistent with previous studies and robust.ConclusionsOur study is the initial report of the complete chloroplast genomes of the six Polystachya species, elucidates the structural characteristics of the chloroplast genome of Polystachya, and filters out highly variable sequences that can contribute to the development of DNA markers for use in the study of genetic variability and evolutionary studies in Polystachya. In addition, the phylogenetic results strongly support that the genus of Polystachya is a part of the tribe Vandeae.

Impact of nematicity on the relationship between antiferromagnetic fluctuations and superconductivity in FeSe0.91S0.09 under pressure

The sulfur substituted FeSe system, FeSe$_{1-x}$S$_{x}$, provides a versatile platform for studying the relationship between nematicity, antiferromagnetism, and superconductivity. Here, by nuclear magnetic resonance (NMR) and resistivity measurements up to 4.73 GPa on FeSe$_{0.91}$S$_{0.09}$, we established the pressure($p$)-temperature($T$) phase diagram in which the nematic state is suppressed with pressure showing a nematic quantum phase transition (QPT) around $p$ = 0.5 GPa, two SC regions, separated by the QPT, appear and antiferromagnetic (AFM) phase emerges above $\sim$3.3 GPa. From the NMR results up to 2.1 GPa, AFM fluctuations are revealed to be characterized by the stripe-type wavevector which remains the same for the two SC regions. Furthermore, the electronic state is found to change in character from non-Fermi liquid to Fermi liquid around the nematic QPT and persists up to $\sim$ 2.1 GPa. In addition, although the AFM fluctuations correlate with $T_{\rm c}$ in both SC states, demonstrating the importance of the AFM fluctuations for the appearance of SC in the system, we found that, when nematic order is absent, $T_{\rm c}$ is strongly correlated with the AFM fluctuations, whereas $T_{\rm c}$ weakly depends on the AFM fluctuations when nematic order is present. Our findings on FeSe$_{0.91}$S$_{0.09}$ were shown to be applied to the whole FeSe$_{1-x}$S$_{x}$ system and also provide a new insight into the relationship between AFM fluctuations and SC in Fe-based superconductors.

The Complete Chloroplast Genome of Trichopus zeylanicus, And Phylogenetic Analysis with Dioscoreales.

We presents the first chloroplast genome from the genus Trichopus. Comparative analysis revealed that the IR regions are more conserved than the SC regions. Highly divergent sequence hot spots were identified, which could be used as molecular markers. Phylogenetic analysis gave insight into the evolutionary history of Trichopus zeylanicus. In this study, we determined the complete sequence of the chloroplast genome of an important, rare, and endangered medicinal plant, Trichopus zeylanicus. The analysis of the genome showed that the complete chloroplast genome of Trichopus zeylanicus is 153,497 bp in size, and has a quadripartite structure with a large single copy of 81,091 bp and a small single copy of 17,512 bp separated by inverted repeats of 27,447 bp. Sequence analysis revealed that the chloroplast genome encodes 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. We also identified 95 simple sequence repeats and 54 long repeats including 34 forward repeats, seven inverted repeats, nine palindromes, three reverse repeats, and one complementary repeat within the chloroplast genome of Trichopus zeylanicus. Whole chloroplast genome comparison with those of other Dioscoreales indicated that the inverted regions are more conserved than large single copy and small single copy regions. In the phylogenetic trees based on complete chloroplast genome and 78 shared chloroplast protein-coding genes in 15 monocot species, including 14 Dioscoreales, Trichopus zeylanicus formed a distinct clade. In summary, the first chloroplast genome from the genus Trichopus reported in this study gave a better insight into the phylogenetic relationships of different genera within the order Dioscoreales. Moreover, the present data will be a valuable chloroplast genomic resource for population genetics.

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Quercus bawanglingensis Huang, Li et Xing, a Vulnerable Oak Tree in China

Quercus bawanglingensis Huang, Li et Xing, an endemic evergreen oak of the genus Quercus (Fagaceae) in China, is currently listed in the Red List of Chinese Plants as a vulnerable (VU) plant. No chloroplast (cp) genome information is currently available for Q. bawanglingensis, which would be essential for the establishment of guidelines for its conservation and breeding. In the present study, the cp genome of Q. bawanglingensis was sequenced and assembled into double-stranded circular DNA with a length of 161,394 bp. Two inverted repeats (IRs) with a total of 51,730 bp were identified, and the rest of the sequence was separated into two single-copy regions, namely, a large single-copy (LSC) region (90,628 bp) and a small single-copy (SSC) region (19,036 bp). The genome of Q. bawanglingensis contains 134 genes (86 protein-coding genes, 40 tRNAs and eight rRNAs). More forward (29) than inverted long repeats (21) are distributed in the cp genome. A simple sequence repeat (SSR) analysis showed that the genome contains 82 SSR loci, involving 84.15% A/T mononucleotides. Sequence comparisons among the nine complete cp genomes, including the genomes of Q. bawanglingensis, Q. tarokoensis Hayata (NC036370), Q. aliena var. acutiserrata Maxim. ex Wenz. (KU240009), Q. baronii Skan (KT963087), Q. aquifolioides Rehd. et Wils. (KX911971), Q. variabilis Bl. (KU240009), Fagus engleriana Seem. (KX852398), Lithocarpus balansae (Drake) A. Camus (KP299291) and Castanea mollissima Bl. (HQ336406), demonstrated that the diversity of SC regions was higher than that of IR regions, which might facilitate identification of the relationships within this extremely complex family. A phylogenetic analysis showed that Fagus engleriana and Trigonobalanus doichangensis form the basis of the produced evolutionary tree. Q. bawanglingensis and Q. tarokoensis, which belong to the group Ilex, share the closest relationship. The analysis of the cp genome of Q. bawanglingensis provides crucial genetic information for further studies of this vulnerable species and the taxonomy, phylogenetics and evolution of Quercus.

On the role of the stratiform cloud scheme in the inter‐model spread of cloud feedback

AbstractThis study explores the role of the stratiform cloud scheme in the inter‐model spread of cloud feedback. Six diagnostic cloud schemes used in various CMIP (Coupled Model Intercomparison Experiment] climate models are implemented (at low and midlevels) into two testbed climate models, and the impacts on cloud feedback are investigated. Results suggest that the choice of stratiform cloud scheme may contribute up to roughly half of the intermodel spread of cloud radiative responses in stratocumulus (Sc) regions, and may determine or favor a given sign of the feedback there. Cloud schemes assuming a probability density function for total water content consistently predict a positive feedback in Sc regions in our experiments. A large negative feedback in Sc regions is obtained only with schemes that consider variables other than relative humidity (e.g., stability). The stratiform cloud scheme also significantly affects cloud feedback at the scale of the tropics and at global scale. Results are slightly less consistent for tropical means, likely indicating coupling with other boundary layer processes such as convective mixing.

Chemokine-ligands/receptors: multiplayers in traumatic spinal cord injury.

Spinal cord injury (SCI) results in complex posttraumatic sequelae affecting the whole neuraxis. Due to its involvement in varied neuromodulatory processes, the chemokine-ligand/receptor-network is a key element of secondary lesion cascades induced by SCI. This review will provide a synopsis of chemokine-ligand/receptor-expression along the whole neuraxis after traumatic spinal cord (sc) insults on basis of recent in vivo and in vitro findings in a SCI paradigm of thoracic force-defined impact lesions (Infinite Horizon Impactor) in adult rats. Analyses of chemokine-ligand/receptor-expression at defined time points after sc lesion of different severity grades or sham operation revealed that these inflammatory mediators are induced in distinct anatomical sc regions and in thalamic nuclei, periaqueductal grey, and hippocampal structures in the brain. Cellular and anatomical expression profiles together with colocalization/expression of neural stem/progenitor cell markers in adult sc stem cells niches or with pain-related receptors and mediators in dorsal horns, dorsal columns, and pain-processing brain areas support the notion that chemokines are involved in distinct cascades underlying clinical posttraumatic impairments and syndromes. These aspects and their implication in concepts of tailored SCI treatment are reviewed in the context of the recent literature on chemokine-ligand/receptor involvement in complex secondary lesion cascades.

Impact of chemokines on the properties of spinal cord-derived neural progenitor cells in a rat spinal cord lesion model.

The existence of endogenous neural progenitor cells (NPCs) in the adult spinal cord (sc) provides the potential for tailored repair therapies after spinal cord injury (SCI). This study investigates the impact of inflammatory mediators on properties of NPC cultures derived from adult rats after SCI. The Infinite Horizon impactor was used to apply 200-kdyn thoracic sc lesions in adult rats. Control groups received laminectomies to equivalent sc regions. Thoracic sc segments were taken for neurosphere cell cultures. Cell proliferation was found to be significantly higher in lesion groups. Neurosphere-derived cells differentiated into neurons, oligodendroglia, and astroglia. Lesion cultures exhibited significantly higher amounts of glial fibrillary acidic protein (GFAP) mRNA (P < 0.0005) and β-III-tubulin mRNA (P < 0.05) compared with sham animals. Neurospheres from different treatment groups exhibited the same amounts of tumor necrosis factor-α, interleukin (IL)-1β, and IL-6 mRNA. C-C chemokine receptor (CCR) expression on neurospheres was examined by real-time RT-PCR. CCR1 was expressed most consistently in mRNA levels in neurospheres from both treatment groups. After cell differentiation, CCR1 mRNA amounts decreased. CCR1 was detectable by immunohistochemistry in neurospheres and differentiated cells of both groups. Application of CCL3 during differentiation cycles led to significantly higher GFAP mRNA amounts in sham animals compared with CCL3-free cultures; in contrast, CCL3 had no impact on cell differentiation in the lesion group. In conclusion, impact SCI alters differentiation tendencies and proliferation rates of adult-derived sc NPCs. Thereby, CCR1/CCL3 promotes specifically astroglial differentiation of NPCs, which provides a potential target for future neurorestorative approaches.

Intermodel variances of subtropical stratocumulus environments simulated in CMIP5 models

AbstractThis paper investigates simulation biases associated with the large‐scale environments of subtropical marine stratocumulus (Sc) in present climate simulations from the Coupled Model Intercomparison Project Phase 5 models. Comparison of eight major variables that strongly control the Sc clouds, including jumps of temperature and vapor across the inversion layer, indicates that these models all have similar shortcomings, such as overestimation of sensible and latent surface fluxes. The differences among the biases of these major variables between the Sc regions were also evaluated. Of all Sc regions, the Namibian Sc region showed the largest biases. The modeled simulation skill of the annual variation of low cloud cover (LCC) increases when the correlation coefficient between LCC and lower atmospheric stability is higher. This paper reemphasizes the importance, suggested in previous studies, of an improved relationship between lower tropospheric stability and LCC if we are to better predict annual variations in subtropical LCC.

Glioblastoma Multiforme: Relationship to Subventricular Zone and Recurrence

Neurogenesis in the adult mammalian brain is active in two areas: the subgranular zone in the dentate gyrus of the hippocampus and the subventricular zone. Cancer stem cells have been isolated from malignant brain tumors and it is widely believed they arise from transformed endogenous stem cells. We sought to determine if the initial location of glioblastoma (GB) as seen on conventional MRI and its relationship to the subventricular zone (SVZ) predicts the pattern of recurrence. We analyzed the initial (prior to any treatment) and last follow-up MR studies in 49 patients with GB. On post contrast images all non-treated GB were divided into three groups according to the relationship of their enhancing margins to the SVZ: Group I (directly in contact with the SVZ), Group II (in the subcortical [SC] region) and Group III (in both the SVZ and SC regions). Recurrences or continuous growth seen as enhancing areas on follow-up studies were characterized as local, spread, or distant according to their contact with the surgical bed and correlated with the locations of the initial tumors. Local and spread patterns of recurrence occurred with nearly equal frequency (45 and 43% each, respectively) and distant in 12%. In Group I, 80% showed a spread pattern, 20% a local pattern, and none a distant pattern. In Group II, 45% showed a spread pattern, 35% a local pattern, and a 20% distant one. In Group III, 58% showed a local pattern, 33% a spread pattern, and 8% distant one. Unlike other reports, the location of GB in relation to the SVZ in our patients did not predict the pattern of tumor recurrence and/or extension in our patients.

Segregation of alloying atoms on the Fe(1 0 0) surface and their effects on oxygen adsorption

The segregation of 3d transition metals and their effects on oxygen adsorption on the Fe(100) surface are systematically studied using the first-principles calculations. On the one hand, Sc, Ti, Mn, Ni, Cu, and Zn have a tendency to segregate towards the surface, while V, Cr, and Co prefer to remain in the interior of Fe bulk. Furthermore, the segregation energies varies monotonically from layers 1–5 for all 3d transition metals except Ti, Cr, Mn, whose subsurface layer provides a large barrier for surface segregation. On the other hand, attractive/repulsive interaction has been observed between oxygen and alloying atom with lower/higher atomic number than that of Fe. Based on the above results, the oxidation should be expected to occur preferentially at the Sc, Ti, and Mn segregation regions on the Fe(100) surface.